diff --git a/src/envo/Makefile b/src/envo/Makefile index 15b896e2..78d66880 100644 --- a/src/envo/Makefile +++ b/src/envo/Makefile @@ -338,8 +338,8 @@ imports/%_combined_seed.tsv: imports/%_terms.txt imports/seed.txt # We use the standard catalog, but rewrite the import to X to be a local mirror of ALL of X. # After extraction, we further reduce the ontology by creating a "mingraph" (removes all annotations except label) and by imports/%_import.owl: mirror/%.owl envo-edit.owl imports/%_combined_seed.tsv - echo "Skipping" - #$(ROBOT) extract -i $< -T imports/$*_combined_seed.tsv -m BOT -O $(ENVO_IMPORTS_BASE_URI)/$@ -o $@.tmp.owl && mv $@.tmp.owl $@ + $(ROBOT) extract -i $< -T imports/$*_combined_seed.tsv -m BOT -O $(ENVO_IMPORTS_BASE_URI)/$@ \ + remove --select "" remove --select "" -o $@.tmp.owl && mv $@.tmp.owl $@ imports/%_import.obo: imports/%_import.owl $(OWLTOOLS) $(USECAT) $< -o -f obo --no-check $@ diff --git a/src/envo/envo-edit.owl b/src/envo/envo-edit.owl index b92e4d36..91a67700 100644 --- a/src/envo/envo-edit.owl +++ b/src/envo/envo-edit.owl @@ -4228,6 +4228,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) diff --git a/src/envo/imports/chebi_import.obo b/src/envo/imports/chebi_import.obo index 230bc858..e0c23f41 100644 --- a/src/envo/imports/chebi_import.obo +++ b/src/envo/imports/chebi_import.obo @@ -11,16 +11,6 @@ id: CHEBI:131621 name: C19-steroid is_a: CHEBI:35341 ! steroid -[Term] -id: CHEBI:131927 -name: dicarboxylic acids and O-substituted derivatives -is_a: CHEBI:36586 ! carbonyl compound - -[Term] -id: CHEBI:133331 -name: metal oxide -is_a: CHEBI:24836 ! inorganic oxide - [Term] id: CHEBI:13389 name: NAD @@ -53,12 +43,6 @@ id: CHEBI:13643 name: glycol is_a: CHEBI:23824 ! diol -[Term] -id: CHEBI:136861 -name: pyrrolopurine -is_a: CHEBI:26979 ! organic heterotricyclic compound -is_a: CHEBI:38101 ! organonitrogen heterocyclic compound - [Term] id: CHEBI:137980 name: metalloid atom @@ -74,43 +58,12 @@ id: CHEBI:139120 name: carotenoid beta-end derivative is_a: CHEBI:23044 ! carotenoid -[Term] -id: CHEBI:139291 -name: chlorophyll(1-) -is_a: CHEBI:58941 ! cyclic tetrapyrrole anion - -[Term] -id: CHEBI:139292 -name: chlorophyllide(2-) -is_a: CHEBI:35757 ! monocarboxylic acid anion -is_a: CHEBI:58941 ! cyclic tetrapyrrole anion - [Term] id: CHEBI:140503 name: kaolin is_a: CHEBI:48730 ! aluminosilicate mineral is_a: CHEBI:60004 ! mixture -[Term] -id: CHEBI:143004 -name: ultra-long-chain fatty acid -is_a: CHEBI:27283 ! very long-chain fatty acid - -[Term] -id: CHEBI:143005 -name: ultra-long-chain fatty acid anion -is_a: CHEBI:58950 ! very long-chain fatty acid anion - -[Term] -id: CHEBI:143901 -name: manganese dihydroxide -is_a: CHEBI:143907 ! manganese hydroxide - -[Term] -id: CHEBI:143907 -name: manganese hydroxide -is_a: CHEBI:25154 ! manganese molecular entity - [Term] id: CHEBI:15022 name: electron donor @@ -121,11 +74,6 @@ id: CHEBI:15339 name: acceptor is_a: CHEBI:51086 ! chemical role -[Term] -id: CHEBI:15368 -name: acrolein -is_a: CHEBI:51688 ! enal - [Term] id: CHEBI:15377 name: water @@ -133,14 +81,6 @@ is_a: CHEBI:33693 ! oxygen hydride is_a: CHEBI:37176 ! mononuclear parent hydride is_a: CHEBI:52625 ! inorganic hydroxy compound -[Term] -id: CHEBI:15378 -name: hydron -is_a: CHEBI:25414 ! monoatomic monocation -is_a: CHEBI:33251 ! monoatomic hydrogen -is_a: CHEBI:33252 ! atomic nucleus -is_a: CHEBI:60242 ! monovalent inorganic cation - [Term] id: CHEBI:15379 name: dioxygen @@ -154,23 +94,6 @@ name: ATP is_a: CHEBI:37045 ! purine ribonucleoside 5'-triphosphate is_a: CHEBI:37096 ! adenosine 5'-phosphate -[Term] -id: CHEBI:155827 -name: argon-39 atom -is_a: CHEBI:49475 ! argon atom - -[Term] -id: CHEBI:155903 -name: copper(II) phthalocyanine -is_a: CHEBI:155908 ! copper tetrapyrrole -is_a: CHEBI:51585 ! metallophthalocyanine - -[Term] -id: CHEBI:155908 -name: copper tetrapyrrole -is_a: CHEBI:33909 ! metallotetrapyrrole -is_a: CHEBI:37403 ! copper coordination entity - [Term] id: CHEBI:15611 name: sarcosine @@ -251,12 +174,6 @@ name: hydrogen peroxide is_a: CHEBI:24837 ! inorganic peroxide is_a: CHEBI:26523 ! reactive oxygen species -[Term] -id: CHEBI:16261 -name: chitosan -is_a: CHEBI:22506 ! aminoglycan -is_a: CHEBI:72813 ! exopolysaccharide - [Term] id: CHEBI:16301 name: nitrite @@ -305,11 +222,6 @@ name: peptide is_a: CHEBI:37622 ! carboxamide is_a: CHEBI:50047 ! organic amino compound -[Term] -id: CHEBI:166975 -name: soybean oil -is_a: CHEBI:60004 ! mixture - [Term] id: CHEBI:16701 name: nucleoside 5'-phosphate @@ -332,38 +244,18 @@ id: CHEBI:167559 name: glycan is_a: CHEBI:78616 ! carbohydrates and carbohydrate derivatives -[Term] -id: CHEBI:167564 -name: paralytic shellfish toxin -is_a: CHEBI:136861 ! pyrrolopurine -is_a: CHEBI:22315 ! alkaloid -is_a: CHEBI:24436 ! guanidines -is_a: CHEBI:63734 ! ketone hydrate - [Term] id: CHEBI:16842 name: formaldehyde is_a: CHEBI:17478 ! aldehyde is_a: CHEBI:64708 ! one-carbon compound -[Term] -id: CHEBI:16900 -name: chlorophyllide a -is_a: CHEBI:25248 ! methyl ester -is_a: CHEBI:36244 ! dicarboxylic acid monoester -is_a: CHEBI:38206 ! chlorophyllide - [Term] id: CHEBI:16908 name: NADH is_a: CHEBI:13389 ! NAD is_a: CHEBI:13392 ! NAD(P)H -[Term] -id: CHEBI:16966 -name: heteroglycan -is_a: CHEBI:18154 ! polysaccharide - [Term] id: CHEBI:16997 name: propane-1,2-diol @@ -376,12 +268,6 @@ name: chitin is_a: CHEBI:21638 ! N-acylglucosamine is_a: CHEBI:22506 ! aminoglycan -[Term] -id: CHEBI:17045 -name: dinitrogen oxide -is_a: CHEBI:138675 ! gas molecular entity -is_a: CHEBI:35196 ! nitrogen oxide - [Term] id: CHEBI:17051 name: fluoride @@ -423,13 +309,6 @@ id: CHEBI:17544 name: hydrogencarbonate is_a: CHEBI:35604 ! carbon oxoanion -[Term] -id: CHEBI:17548 -name: alginic acid -is_a: CHEBI:16966 ! heteroglycan -is_a: CHEBI:53310 ! copolymer macromolecule -is_a: CHEBI:72813 ! exopolysaccharide - [Term] id: CHEBI:17578 name: toluene @@ -528,29 +407,11 @@ is_a: CHEBI:16646 ! carbohydrate is_a: CHEBI:167559 ! glycan is_a: CHEBI:33694 ! biomacromolecule -[Term] -id: CHEBI:18230 -name: chlorophyll a -is_a: CHEBI:25248 ! methyl ester -is_a: CHEBI:28966 ! chlorophyll - -[Term] -id: CHEBI:18246 -name: (1->4)-beta-D-glucan -is_a: CHEBI:28793 ! beta-D-glucan - [Term] id: CHEBI:18248 name: iron atom is_a: CHEBI:33356 ! iron group element atom -[Term] -id: CHEBI:18276 -name: dihydrogen -is_a: CHEBI:138675 ! gas molecular entity -is_a: CHEBI:25362 ! elemental molecule -is_a: CHEBI:33260 ! elemental hydrogen - [Term] id: CHEBI:18291 name: manganese atom @@ -574,11 +435,6 @@ name: hydrogen cyanide is_a: CHEBI:33405 ! hydracid is_a: CHEBI:64708 ! one-carbon compound -[Term] -id: CHEBI:18422 -name: sulfur dioxide -is_a: CHEBI:48154 ! sulfur oxide - [Term] id: CHEBI:190295 name: inorganic calcium salt @@ -631,11 +487,6 @@ is_a: CHEBI:33318 ! main group element atom is_a: CHEBI:33521 ! metal atom is_a: CHEBI:33559 ! s-block element atom -[Term] -id: CHEBI:22315 -name: alkaloid -is_a: CHEBI:35352 ! organonitrogen compound - [Term] id: CHEBI:22323 name: alkyl group @@ -715,11 +566,6 @@ id: CHEBI:22985 name: calcium molecular entity is_a: CHEBI:33299 ! alkaline earth molecular entity -[Term] -id: CHEBI:23003 -name: carbamate ester -is_a: CHEBI:33308 ! carboxylic ester - [Term] id: CHEBI:23014 name: carbon oxide @@ -736,12 +582,6 @@ id: CHEBI:23042 name: carotene is_a: CHEBI:35193 ! tetraterpene -[Term] -id: CHEBI:23043 -name: epoxycarotenoid -is_a: CHEBI:27325 ! xanthophyll -is_a: CHEBI:32955 ! epoxide - [Term] id: CHEBI:23044 name: carotenoid @@ -855,11 +695,6 @@ id: CHEBI:24433 name: group is_a: CHEBI:24431 ! chemical entity -[Term] -id: CHEBI:24436 -name: guanidines -is_a: CHEBI:35352 ! organonitrogen compound - [Term] id: CHEBI:24455 name: guanosine phosphate @@ -899,12 +734,6 @@ id: CHEBI:24632 name: hydrocarbon is_a: CHEBI:33245 ! organic fundamental parent -[Term] -id: CHEBI:24636 -name: proton -is_a: CHEBI:15378 ! hydron -is_a: CHEBI:33253 ! nucleon - [Term] id: CHEBI:24651 name: hydroxides @@ -1012,12 +841,6 @@ id: CHEBI:25108 name: magnesium molecular entity is_a: CHEBI:33299 ! alkaline earth molecular entity -[Term] -id: CHEBI:25111 -name: magnesium porphyrin -is_a: CHEBI:25216 ! metalloporphyrin -is_a: CHEBI:38251 ! magnesium tetrapyrrole - [Term] id: CHEBI:25154 name: manganese molecular entity @@ -1034,18 +857,6 @@ name: metal cation is_a: CHEBI:23906 ! monoatomic cation is_a: CHEBI:36915 ! inorganic cation -[Term] -id: CHEBI:25216 -name: metalloporphyrin -is_a: CHEBI:26214 ! porphyrins -is_a: CHEBI:33240 ! coordination entity -is_a: CHEBI:33909 ! metallotetrapyrrole - -[Term] -id: CHEBI:25248 -name: methyl ester -is_a: CHEBI:33308 ! carboxylic ester - [Term] id: CHEBI:25274 name: methylamines @@ -1077,11 +888,6 @@ id: CHEBI:25388 name: monohydroxybenzoate is_a: CHEBI:24675 ! hydroxybenzoate -[Term] -id: CHEBI:25414 -name: monoatomic monocation -is_a: CHEBI:23906 ! monoatomic cation - [Term] id: CHEBI:25430 name: monoatomic polycation @@ -1104,12 +910,6 @@ name: naphthalenes is_a: CHEBI:33836 ! benzenoid aromatic compound is_a: CHEBI:36785 ! carbobicyclic compound -[Term] -id: CHEBI:25501 -name: neoxanthin -is_a: CHEBI:35307 ! epoxycarotenol -is_a: CHEBI:37602 ! allenes - [Term] id: CHEBI:25512 name: neurotransmitter @@ -1172,11 +972,6 @@ name: organic cation is_a: CHEBI:25699 ! organic ion is_a: CHEBI:36916 ! cation -[Term] -id: CHEBI:25698 -name: ether -is_a: CHEBI:36963 ! organooxygen compound - [Term] id: CHEBI:25699 name: organic ion @@ -1224,14 +1019,6 @@ id: CHEBI:25806 name: oxygen molecular entity is_a: CHEBI:33304 ! chalcogen molecular entity -[Term] -id: CHEBI:25812 -name: ozone -is_a: CHEBI:138675 ! gas molecular entity -is_a: CHEBI:25362 ! elemental molecule -is_a: CHEBI:26523 ! reactive oxygen species -is_a: CHEBI:33265 ! triatomic oxygen - [Term] id: CHEBI:25900 name: aldopentose phosphate @@ -1273,22 +1060,11 @@ id: CHEBI:26167 name: polar amino acid is_a: CHEBI:33709 ! amino acid -[Term] -id: CHEBI:26178 -name: polyester macromolecule -is_a: CHEBI:33839 ! macromolecule -is_a: CHEBI:35701 ! ester - [Term] id: CHEBI:26191 name: polyol is_a: CHEBI:33822 ! organic hydroxy compound -[Term] -id: CHEBI:26214 -name: porphyrins -is_a: CHEBI:36309 ! cyclic tetrapyrrole - [Term] id: CHEBI:26216 name: potassium atom @@ -1343,16 +1119,6 @@ name: pyridines is_a: CHEBI:25693 ! organic heteromonocyclic compound is_a: CHEBI:38101 ! organonitrogen heterocyclic compound -[Term] -id: CHEBI:26490 -name: quinate -is_a: CHEBI:36125 ! cyclitol carboxylic acid anion - -[Term] -id: CHEBI:26519 -name: radical -is_a: CHEBI:23367 ! molecular entity - [Term] id: CHEBI:26523 name: reactive oxygen species @@ -1369,16 +1135,6 @@ id: CHEBI:26562 name: ribose phosphate is_a: CHEBI:25900 ! aldopentose phosphate -[Term] -id: CHEBI:26607 -name: saturated fatty acid -is_a: CHEBI:35366 ! fatty acid - -[Term] -id: CHEBI:26675 -name: silicic acid -is_a: CHEBI:33328 ! silicon oxoacid - [Term] id: CHEBI:26677 name: silicon molecular entity @@ -1444,29 +1200,11 @@ id: CHEBI:26873 name: terpenoid is_a: CHEBI:24913 ! isoprenoid -[Term] -id: CHEBI:26878 -name: tertiary alcohol -is_a: CHEBI:30879 ! alcohol - -[Term] -id: CHEBI:26932 -name: tetrapyrrole -is_a: CHEBI:33833 ! heteroarene -is_a: CHEBI:38077 ! polypyrrole - [Term] id: CHEBI:26935 name: tetraterpenoid is_a: CHEBI:26873 ! terpenoid -[Term] -id: CHEBI:26979 -name: organic heterotricyclic compound -is_a: CHEBI:36688 ! heterotricyclic compound -is_a: CHEBI:38166 ! organic heteropolycyclic compound -is_a: CHEBI:51959 ! organic tricyclic compound - [Term] id: CHEBI:26986 name: threonine @@ -1495,11 +1233,6 @@ id: CHEBI:27027 name: micronutrient is_a: CHEBI:33284 ! nutrient -[Term] -id: CHEBI:2706 -name: Anatoxin a -is_a: CHEBI:37332 ! tropane alkaloid - [Term] id: CHEBI:27081 name: transition element atom @@ -1522,16 +1255,6 @@ id: CHEBI:27275 name: vanadium molecular entity is_a: CHEBI:33746 ! vanadium group molecular entity -[Term] -id: CHEBI:27283 -name: very long-chain fatty acid -is_a: CHEBI:35366 ! fatty acid - -[Term] -id: CHEBI:27295 -name: violaxanthin -is_a: CHEBI:35307 ! epoxycarotenol - [Term] id: CHEBI:27325 name: xanthophyll @@ -1615,11 +1338,6 @@ is_a: CHEBI:22160 ! acetamides is_a: CHEBI:29347 ! monocarboxylic acid amide is_a: CHEBI:83628 ! N-acylammonia -[Term] -id: CHEBI:27888 -name: chlorophyll b -is_a: CHEBI:28966 ! chlorophyll - [Term] id: CHEBI:27889 name: lead(0) @@ -1637,11 +1355,6 @@ name: nickel atom is_a: CHEBI:33362 ! nickel group element atom is_a: CHEBI:88184 ! metal allergen -[Term] -id: CHEBI:28315 -name: alloxanthine -is_a: CHEBI:38669 ! pyrazolopyrimidine - [Term] id: CHEBI:28425 name: alpha-carotene @@ -1670,11 +1383,6 @@ id: CHEBI:28793 name: beta-D-glucan is_a: CHEBI:37163 ! glucan -[Term] -id: CHEBI:28798 -name: rubber particle -is_a: CHEBI:60027 ! polymer - [Term] id: CHEBI:28838 name: lutein @@ -1698,11 +1406,6 @@ id: CHEBI:28963 name: amino sugar is_a: CHEBI:63299 ! carbohydrate derivative -[Term] -id: CHEBI:28966 -name: chlorophyll -is_a: CHEBI:25111 ! magnesium porphyrin - [Term] id: CHEBI:28976 name: carbonic acid @@ -1731,26 +1434,11 @@ name: hydrogen fluoride is_a: CHEBI:18140 ! hydrogen halide is_a: CHEBI:37176 ! mononuclear parent hydride -[Term] -id: CHEBI:29233 -name: deuteron -is_a: CHEBI:15378 ! hydron - -[Term] -id: CHEBI:29237 -name: deuterium atom -is_a: CHEBI:49637 ! hydrogen atom - [Term] id: CHEBI:29238 name: tritium atom is_a: CHEBI:49637 ! hydrogen atom -[Term] -id: CHEBI:29241 -name: silicate(4-) -is_a: CHEBI:48123 ! silicate ion - [Term] id: CHEBI:29337 name: azanide @@ -1778,17 +1466,6 @@ id: CHEBI:29919 name: hydrosulfide is_a: CHEBI:33535 ! sulfur hydride -[Term] -id: CHEBI:30033 -name: bacteriochlorophyll a -is_a: CHEBI:25248 ! methyl ester -is_a: CHEBI:38201 ! bacteriochlorophyll - -[Term] -id: CHEBI:30050 -name: gold(0) -is_a: CHEBI:33970 ! elemental gold - [Term] id: CHEBI:30052 name: copper(0) @@ -1799,64 +1476,22 @@ id: CHEBI:30145 name: lithium atom is_a: CHEBI:22314 ! alkali metal atom -[Term] -id: CHEBI:30187 -name: aluminium oxide -is_a: CHEBI:33623 ! aluminium oxides - [Term] id: CHEBI:30212 name: photon is_a: CHEBI:36341 ! boson -[Term] -id: CHEBI:30216 -name: alpha-particle -is_a: CHEBI:33252 ! atomic nucleus -is_a: CHEBI:33316 ! helium(2+) - -[Term] -id: CHEBI:30217 -name: helium atom -is_a: CHEBI:33309 ! noble gas atom -is_a: CHEBI:33559 ! s-block element atom - -[Term] -id: CHEBI:30218 -name: helium-3 atom -is_a: CHEBI:30217 ! helium atom - -[Term] -id: CHEBI:30222 -name: neutron -is_a: CHEBI:33253 ! nucleon - -[Term] -id: CHEBI:30225 -name: positron -is_a: CHEBI:36338 ! lepton - [Term] id: CHEBI:30356 name: isobutyl group is_a: CHEBI:22323 ! alkyl group is_a: CHEBI:50325 ! proteinogenic amino-acid side-chain group -[Term] -id: CHEBI:30412 -name: monoatomic dication -is_a: CHEBI:23906 ! monoatomic cation - [Term] id: CHEBI:30440 name: thallium is_a: CHEBI:33317 ! boron group element atom -[Term] -id: CHEBI:30496 -name: sulfur hexafluoride -is_a: CHEBI:50094 ! sulfur coordination entity - [Term] id: CHEBI:30512 name: silver atom @@ -1893,19 +1528,6 @@ id: CHEBI:30879 name: alcohol is_a: CHEBI:33822 ! organic hydroxy compound -[Term] -id: CHEBI:31001 -name: octacosanoic acid -is_a: CHEBI:143004 ! ultra-long-chain fatty acid -is_a: CHEBI:39418 ! straight-chain saturated fatty acid - -[Term] -id: CHEBI:31002 -name: octacosanoate -is_a: CHEBI:143005 ! ultra-long-chain fatty acid anion -is_a: CHEBI:58954 ! straight-chain saturated fatty acid anion -is_a: CHEBI:78130 ! fatty acid anion 28:0 - [Term] id: CHEBI:32178 name: Talc @@ -1943,22 +1565,11 @@ id: CHEBI:32952 name: amine is_a: CHEBI:50047 ! organic amino compound -[Term] -id: CHEBI:32955 -name: epoxide -is_a: CHEBI:37407 ! cyclic ether - [Term] id: CHEBI:32988 name: amide is_a: CHEBI:51143 ! nitrogen molecular entity -[Term] -id: CHEBI:32999 -name: europium atom -is_a: CHEBI:33319 ! lanthanoid atom -is_a: CHEBI:33562 ! f-block element atom - [Term] id: CHEBI:3311 name: calcium carbonate @@ -2024,23 +1635,6 @@ id: CHEBI:33250 name: atom is_a: CHEBI:24431 ! chemical entity -[Term] -id: CHEBI:33251 -name: monoatomic hydrogen -is_a: CHEBI:33238 ! monoatomic entity -is_a: CHEBI:33260 ! elemental hydrogen - -[Term] -id: CHEBI:33252 -name: atomic nucleus -is_a: CHEBI:36347 ! nuclear particle - -[Term] -id: CHEBI:33253 -name: nucleon -is_a: CHEBI:36339 ! baryon -is_a: CHEBI:36347 ! nuclear particle - [Term] id: CHEBI:33256 name: primary amide @@ -2051,13 +1645,6 @@ id: CHEBI:33259 name: elemental molecular entity is_a: CHEBI:23367 ! molecular entity -[Term] -id: CHEBI:33260 -name: elemental hydrogen -is_a: CHEBI:24835 ! inorganic molecular entity -is_a: CHEBI:33259 ! elemental molecular entity -is_a: CHEBI:33608 ! hydrogen molecular entity - [Term] id: CHEBI:33261 name: organosulfur compound @@ -2076,11 +1663,6 @@ id: CHEBI:33263 name: diatomic oxygen is_a: CHEBI:33262 ! elemental oxygen -[Term] -id: CHEBI:33265 -name: triatomic oxygen -is_a: CHEBI:33262 ! elemental oxygen - [Term] id: CHEBI:33266 name: diatomic nitrogen @@ -2173,31 +1755,6 @@ id: CHEBI:33306 name: carbon group element atom is_a: CHEBI:33560 ! p-block element atom -[Term] -id: CHEBI:33308 -name: carboxylic ester -is_a: CHEBI:35701 ! ester -is_a: CHEBI:36586 ! carbonyl compound - -[Term] -id: CHEBI:33309 -name: noble gas atom -is_a: CHEBI:138675 ! gas molecular entity -is_a: CHEBI:25585 ! nonmetal atom -is_a: CHEBI:33318 ! main group element atom - -[Term] -id: CHEBI:33315 -name: monoatomic helium -is_a: CHEBI:33238 ! monoatomic entity -is_a: CHEBI:33680 ! elemental helium - -[Term] -id: CHEBI:33316 -name: helium(2+) -is_a: CHEBI:30412 ! monoatomic dication -is_a: CHEBI:33315 ! monoatomic helium - [Term] id: CHEBI:33317 name: boron group element atom @@ -2208,16 +1765,6 @@ id: CHEBI:33318 name: main group element atom is_a: CHEBI:33250 ! atom -[Term] -id: CHEBI:33319 -name: lanthanoid atom -is_a: CHEBI:33321 ! rare earth metal atom - -[Term] -id: CHEBI:33321 -name: rare earth metal atom -is_a: CHEBI:27081 ! transition element atom - [Term] id: CHEBI:33324 name: strontium atom @@ -2229,31 +1776,6 @@ name: silicon oxide is_a: CHEBI:24836 ! inorganic oxide is_a: CHEBI:26677 ! silicon molecular entity -[Term] -id: CHEBI:33328 -name: silicon oxoacid -is_a: CHEBI:24833 ! oxoacid -is_a: CHEBI:46890 ! silicon hydroxide - -[Term] -id: CHEBI:33331 -name: yttrium atom -is_a: CHEBI:33321 ! rare earth metal atom -is_a: CHEBI:33335 ! scandium group element atom -is_a: CHEBI:33561 ! d-block element atom - -[Term] -id: CHEBI:33335 -name: scandium group element atom -is_a: CHEBI:27081 ! transition element atom - -[Term] -id: CHEBI:33336 -name: lanthanum atom -is_a: CHEBI:33319 ! lanthanoid atom -is_a: CHEBI:33335 ! scandium group element atom -is_a: CHEBI:33562 ! f-block element atom - [Term] id: CHEBI:33340 name: zinc group element atom @@ -2264,23 +1786,12 @@ id: CHEBI:33341 name: titanium atom is_a: CHEBI:33345 ! titanium group element atom -[Term] -id: CHEBI:33344 -name: niobium atom -is_a: CHEBI:33347 ! vanadium group element atom - [Term] id: CHEBI:33345 name: titanium group element atom is_a: CHEBI:27081 ! transition element atom is_a: CHEBI:33561 ! d-block element atom -[Term] -id: CHEBI:33347 -name: vanadium group element atom -is_a: CHEBI:27081 ! transition element atom -is_a: CHEBI:33561 ! d-block element atom - [Term] id: CHEBI:33350 name: chromium group element atom @@ -2317,41 +1828,6 @@ name: copper group element atom is_a: CHEBI:27081 ! transition element atom is_a: CHEBI:33561 ! d-block element atom -[Term] -id: CHEBI:33369 -name: cerium -is_a: CHEBI:33319 ! lanthanoid atom -is_a: CHEBI:33562 ! f-block element atom - -[Term] -id: CHEBI:33372 -name: neodymium atom -is_a: CHEBI:33319 ! lanthanoid atom -is_a: CHEBI:33562 ! f-block element atom - -[Term] -id: CHEBI:33374 -name: samarium atom -is_a: CHEBI:33319 ! lanthanoid atom -is_a: CHEBI:33562 ! f-block element atom - -[Term] -id: CHEBI:33375 -name: gadolinium atom -is_a: CHEBI:33319 ! lanthanoid atom -is_a: CHEBI:33562 ! f-block element atom - -[Term] -id: CHEBI:33377 -name: dysprosium atom -is_a: CHEBI:33319 ! lanthanoid atom -is_a: CHEBI:33562 ! f-block element atom - -[Term] -id: CHEBI:33400 -name: platinum(0) -is_a: CHEBI:49202 ! elemental platinum - [Term] id: CHEBI:33402 name: sulfur oxoacid @@ -2470,16 +1946,6 @@ id: CHEBI:33497 name: transition element molecular entity is_a: CHEBI:23367 ! molecular entity -[Term] -id: CHEBI:33498 -name: actinoid molecular entity -is_a: CHEBI:33677 ! f-block molecular entity - -[Term] -id: CHEBI:33499 -name: uranium molecular entity -is_a: CHEBI:33498 ! actinoid molecular entity - [Term] id: CHEBI:33521 name: metal atom @@ -2524,11 +1990,6 @@ name: d-block element atom is_a: CHEBI:27081 ! transition element atom is_a: CHEBI:33521 ! metal atom -[Term] -id: CHEBI:33562 -name: f-block element atom -is_a: CHEBI:27081 ! transition element atom - [Term] id: CHEBI:33575 name: carboxylic acid @@ -2587,18 +2048,6 @@ id: CHEBI:33620 name: aluminium molecular entity is_a: CHEBI:33581 ! boron group molecular entity -[Term] -id: CHEBI:33623 -name: aluminium oxides -is_a: CHEBI:133331 ! metal oxide -is_a: CHEBI:33620 ! aluminium molecular entity - -[Term] -id: CHEBI:33627 -name: monoatomic aluminium -is_a: CHEBI:33238 ! monoatomic entity -is_a: CHEBI:33628 ! elemental aluminium - [Term] id: CHEBI:33628 name: elemental aluminium @@ -2724,27 +2173,12 @@ id: CHEBI:33676 name: d-block molecular entity is_a: CHEBI:33497 ! transition element molecular entity -[Term] -id: CHEBI:33677 -name: f-block molecular entity -is_a: CHEBI:33497 ! transition element molecular entity - [Term] id: CHEBI:33679 name: helium molecular entity is_a: CHEBI:33583 ! noble gas molecular entity is_a: CHEBI:33674 ! s-block molecular entity -[Term] -id: CHEBI:33680 -name: elemental helium -is_a: CHEBI:33679 ! helium molecular entity - -[Term] -id: CHEBI:33687 -name: diatomic helium -is_a: CHEBI:33680 ! elemental helium - [Term] id: CHEBI:33692 name: hydrides @@ -2771,6 +2205,7 @@ is_a: CHEBI:36916 ! cation [Term] id: CHEBI:33703 name: amino-acid cation +is_a: CHEBI:25697 ! organic cation is_a: CHEBI:33702 ! polyatomic cation [Term] @@ -2893,11 +2328,6 @@ id: CHEBI:33893 name: reagent is_a: CHEBI:33232 ! application -[Term] -id: CHEBI:33909 -name: metallotetrapyrrole -is_a: CHEBI:36309 ! cyclic tetrapyrrole - [Term] id: CHEBI:33937 name: macronutrient @@ -2914,27 +2344,6 @@ id: CHEBI:33969 name: gold molecular entity is_a: CHEBI:33745 ! copper group molecular entity -[Term] -id: CHEBI:33970 -name: elemental gold -is_a: CHEBI:33969 ! gold molecular entity - -[Term] -id: CHEBI:33976 -name: magnesium coordination entity -is_a: CHEBI:25108 ! magnesium molecular entity -is_a: CHEBI:35217 ! alkaline earth coordination entity - -[Term] -id: CHEBI:34970 -name: saxitoxin -is_a: CHEBI:136861 ! pyrrolopurine -is_a: CHEBI:167564 ! paralytic shellfish toxin -is_a: CHEBI:22315 ! alkaloid -is_a: CHEBI:23003 ! carbamate ester -is_a: CHEBI:24436 ! guanidines -is_a: CHEBI:63734 ! ketone hydrate - [Term] id: CHEBI:35106 name: nitrogen hydride @@ -2962,16 +2371,6 @@ id: CHEBI:35163 name: cyclic carotene is_a: CHEBI:23042 ! carotene -[Term] -id: CHEBI:35170 -name: vanadium(0) -is_a: CHEBI:35171 ! elemental vanadium - -[Term] -id: CHEBI:35171 -name: elemental vanadium -is_a: CHEBI:27275 ! vanadium molecular entity - [Term] id: CHEBI:35175 name: sulfate salt @@ -3010,12 +2409,6 @@ id: CHEBI:35209 name: label is_a: CHEBI:33232 ! application -[Term] -id: CHEBI:35217 -name: alkaline earth coordination entity -is_a: CHEBI:33299 ! alkaline earth molecular entity -is_a: CHEBI:36562 ! main-group coordination entity - [Term] id: CHEBI:35222 name: inhibitor @@ -3055,12 +2448,6 @@ name: ortho-fused polycyclic arene is_a: CHEBI:33848 ! polycyclic arene is_a: CHEBI:35427 ! ortho-fused polycyclic hydrocarbon -[Term] -id: CHEBI:35307 -name: epoxycarotenol -is_a: CHEBI:23043 ! epoxycarotenoid -is_a: CHEBI:23045 ! carotenol - [Term] id: CHEBI:35341 name: steroid @@ -3084,12 +2471,6 @@ name: organonitrogen compound is_a: CHEBI:33285 ! heteroorganic entity is_a: CHEBI:51143 ! nitrogen molecular entity -[Term] -id: CHEBI:35366 -name: fatty acid -is_a: CHEBI:18059 ! lipid -is_a: CHEBI:25384 ! monocarboxylic acid - [Term] id: CHEBI:35402 name: chromium oxoanion @@ -3155,11 +2536,6 @@ name: analgesic is_a: CHEBI:23888 ! drug is_a: CHEBI:52210 ! pharmacological role -[Term] -id: CHEBI:35552 -name: heterocyclic organic fundamental parent -is_a: CHEBI:33245 ! organic fundamental parent - [Term] id: CHEBI:35554 name: cardiovascular drug @@ -3183,11 +2559,6 @@ id: CHEBI:35620 name: vasodilator agent is_a: CHEBI:35554 ! cardiovascular drug -[Term] -id: CHEBI:35681 -name: secondary alcohol -is_a: CHEBI:30879 ! alcohol - [Term] id: CHEBI:35701 name: ester @@ -3250,36 +2621,12 @@ name: inorganic chloride is_a: CHEBI:23114 ! chloride salt is_a: CHEBI:24839 ! inorganic salt -[Term] -id: CHEBI:36125 -name: cyclitol carboxylic acid anion -is_a: CHEBI:35757 ! monocarboxylic acid anion - -[Term] -id: CHEBI:36244 -name: dicarboxylic acid monoester -is_a: CHEBI:131927 ! dicarboxylic acids and O-substituted derivatives -is_a: CHEBI:33308 ! carboxylic ester -is_a: CHEBI:33575 ! carboxylic acid - -[Term] -id: CHEBI:36309 -name: cyclic tetrapyrrole -is_a: CHEBI:26932 ! tetrapyrrole -is_a: CHEBI:47882 ! cyclic polypyrrole - [Term] id: CHEBI:36338 name: lepton is_a: CHEBI:33233 ! fundamental particle is_a: CHEBI:36340 ! fermion -[Term] -id: CHEBI:36339 -name: baryon -is_a: CHEBI:36340 ! fermion -is_a: CHEBI:36344 ! hadron - [Term] id: CHEBI:36340 name: fermion @@ -3294,26 +2641,6 @@ is_a: CHEBI:36342 ! subatomic particle id: CHEBI:36342 name: subatomic particle -[Term] -id: CHEBI:36343 -name: composite particle -is_a: CHEBI:36342 ! subatomic particle - -[Term] -id: CHEBI:36344 -name: hadron -is_a: CHEBI:36343 ! composite particle - -[Term] -id: CHEBI:36347 -name: nuclear particle -is_a: CHEBI:36342 ! subatomic particle - -[Term] -id: CHEBI:36352 -name: neutrino -is_a: CHEBI:36338 ! lepton - [Term] id: CHEBI:36357 name: polyatomic entity @@ -3342,29 +2669,6 @@ name: alkaline earth salt is_a: CHEBI:24866 ! salt is_a: CHEBI:33299 ! alkaline earth molecular entity -[Term] -id: CHEBI:36388 -name: saturated organic heterocyclic parent -is_a: CHEBI:35552 ! heterocyclic organic fundamental parent - -[Term] -id: CHEBI:36389 -name: saturated organic heteromonocyclic parent -is_a: CHEBI:25693 ! organic heteromonocyclic compound -is_a: CHEBI:36388 ! saturated organic heterocyclic parent - -[Term] -id: CHEBI:36468 -name: polycyclic ether -is_a: CHEBI:37407 ! cyclic ether -is_a: CHEBI:38166 ! organic heteropolycyclic compound - -[Term] -id: CHEBI:36562 -name: main-group coordination entity -is_a: CHEBI:33240 ! coordination entity -is_a: CHEBI:33579 ! main group molecular entity - [Term] id: CHEBI:36586 name: carbonyl compound @@ -3382,11 +2686,6 @@ name: organochlorine compound is_a: CHEBI:17792 ! organohalogen compound is_a: CHEBI:23117 ! chlorine molecular entity -[Term] -id: CHEBI:36688 -name: heterotricyclic compound -is_a: CHEBI:33671 ! heteropolycyclic compound - [Term] id: CHEBI:36785 name: carbobicyclic compound @@ -3403,36 +2702,6 @@ id: CHEBI:36838 name: 17-hydroxy steroid is_a: CHEBI:35350 ! hydroxy steroid -[Term] -id: CHEBI:36871 -name: inorganic radical -is_a: CHEBI:24835 ! inorganic molecular entity -is_a: CHEBI:26519 ! radical - -[Term] -id: CHEBI:36874 -name: radical cation -is_a: CHEBI:36875 ! radical ion -is_a: CHEBI:36916 ! cation - -[Term] -id: CHEBI:36875 -name: radical ion -is_a: CHEBI:24870 ! ion -is_a: CHEBI:26519 ! radical - -[Term] -id: CHEBI:36878 -name: inorganic radical ion -is_a: CHEBI:36871 ! inorganic radical -is_a: CHEBI:36875 ! radical ion - -[Term] -id: CHEBI:36879 -name: inorganic radical cation -is_a: CHEBI:36874 ! radical cation -is_a: CHEBI:36878 ! inorganic radical ion - [Term] id: CHEBI:36892 name: elemental fluorine @@ -3449,21 +2718,11 @@ name: chalcogen hydride is_a: CHEBI:33242 ! inorganic hydride is_a: CHEBI:33304 ! chalcogen molecular entity -[Term] -id: CHEBI:36907 -name: neon molecular entity -is_a: CHEBI:33583 ! noble gas molecular entity - [Term] id: CHEBI:36908 name: argon molecular entity is_a: CHEBI:33583 ! noble gas molecular entity -[Term] -id: CHEBI:36909 -name: krypton molecular entity -is_a: CHEBI:33583 ! noble gas molecular entity - [Term] id: CHEBI:36914 name: inorganic ion @@ -3481,21 +2740,6 @@ id: CHEBI:36916 name: cation is_a: CHEBI:24870 ! ion -[Term] -id: CHEBI:36927 -name: carbon-14 atom -is_a: CHEBI:27594 ! carbon atom - -[Term] -id: CHEBI:36928 -name: carbon-13 atom -is_a: CHEBI:27594 ! carbon atom - -[Term] -id: CHEBI:36934 -name: nitrogen-15 atom -is_a: CHEBI:25555 ! nitrogen atom - [Term] id: CHEBI:36961 name: chalcocarbonic acid @@ -3600,19 +2844,6 @@ id: CHEBI:37176 name: mononuclear parent hydride is_a: CHEBI:33692 ! hydrides -[Term] -id: CHEBI:37190 -name: silicon coordination entity -is_a: CHEBI:26677 ! silicon molecular entity -is_a: CHEBI:36562 ! main-group coordination entity - -[Term] -id: CHEBI:37191 -name: silicon oxoanion -is_a: CHEBI:24834 ! inorganic anion -is_a: CHEBI:35406 ! oxoanion -is_a: CHEBI:37190 ! silicon coordination entity - [Term] id: CHEBI:37193 name: elemental lead @@ -3623,44 +2854,16 @@ id: CHEBI:37217 name: titanium molecular entity is_a: CHEBI:33768 ! titanium group molecular entity -[Term] -id: CHEBI:37332 -name: tropane alkaloid -is_a: CHEBI:22315 ! alkaloid -is_a: CHEBI:38295 ! azabicycloalkane - -[Term] -id: CHEBI:37349 -name: phosphorus oxide -is_a: CHEBI:26082 ! phosphorus molecular entity - -[Term] -id: CHEBI:37376 -name: tetraphosphorus decaoxide -is_a: CHEBI:37349 ! phosphorus oxide - [Term] id: CHEBI:37395 name: mucopolysaccharide is_a: CHEBI:18085 ! glycosaminoglycan -[Term] -id: CHEBI:37403 -name: copper coordination entity -is_a: CHEBI:23377 ! copper molecular entity -is_a: CHEBI:33861 ! transition element coordination entity - [Term] id: CHEBI:37404 name: elemental copper is_a: CHEBI:23377 ! copper molecular entity -[Term] -id: CHEBI:37407 -name: cyclic ether -is_a: CHEBI:25698 ! ether -is_a: CHEBI:38104 ! oxacycle - [Term] id: CHEBI:37527 name: acid @@ -3677,11 +2880,6 @@ name: halide is_a: CHEBI:24471 ! halogen molecular entity is_a: CHEBI:37577 ! heteroatomic molecular entity -[Term] -id: CHEBI:37602 -name: allenes -is_a: CHEBI:78840 ! olefinic compound - [Term] id: CHEBI:37622 name: carboxamide @@ -3700,28 +2898,12 @@ id: CHEBI:37826 name: sulfuric acid derivative is_a: CHEBI:33424 ! sulfur oxoacid derivative -[Term] -id: CHEBI:37997 -name: homopolymer macromolecule -is_a: CHEBI:33839 ! macromolecule - -[Term] -id: CHEBI:38077 -name: polypyrrole -is_a: CHEBI:38101 ! organonitrogen heterocyclic compound - [Term] id: CHEBI:38101 name: organonitrogen heterocyclic compound is_a: CHEBI:24532 ! organic heterocyclic compound is_a: CHEBI:35352 ! organonitrogen compound -[Term] -id: CHEBI:38104 -name: oxacycle -is_a: CHEBI:24532 ! organic heterocyclic compound -is_a: CHEBI:36963 ! organooxygen compound - [Term] id: CHEBI:38166 name: organic heteropolycyclic compound @@ -3733,43 +2915,16 @@ id: CHEBI:38180 name: polycyclic heteroarene is_a: CHEBI:33833 ! heteroarene -[Term] -id: CHEBI:38201 -name: bacteriochlorophyll -is_a: CHEBI:28966 ! chlorophyll - -[Term] -id: CHEBI:38206 -name: chlorophyllide -is_a: CHEBI:28966 ! chlorophyll - [Term] id: CHEBI:38222 name: hydrocarbyl anion is_a: CHEBI:25696 ! organic anion -[Term] -id: CHEBI:38251 -name: magnesium tetrapyrrole -is_a: CHEBI:33909 ! metallotetrapyrrole -is_a: CHEBI:33976 ! magnesium coordination entity - -[Term] -id: CHEBI:38252 -name: phorbines -is_a: CHEBI:36309 ! cyclic tetrapyrrole - [Term] id: CHEBI:38263 name: 2-amino-3-hydroxybutanoic acid is_a: CHEBI:33704 ! alpha-amino acid -[Term] -id: CHEBI:38295 -name: azabicycloalkane -is_a: CHEBI:27171 ! organic heterobicyclic compound -is_a: CHEBI:38101 ! organonitrogen heterocyclic compound - [Term] id: CHEBI:38460 name: methylindole @@ -3785,12 +2940,6 @@ id: CHEBI:38497 name: respiratory-chain inhibitor is_a: CHEBI:38496 ! electron-transport chain inhibitor -[Term] -id: CHEBI:38669 -name: pyrazolopyrimidine -is_a: CHEBI:27171 ! organic heterobicyclic compound -is_a: CHEBI:38101 ! organonitrogen heterocyclic compound - [Term] id: CHEBI:38702 name: inorganic sodium salt @@ -3840,31 +2989,12 @@ name: Bronsted base is_a: CHEBI:15339 ! acceptor is_a: CHEBI:22695 ! base -[Term] -id: CHEBI:39143 -name: Lewis acid -is_a: CHEBI:15339 ! acceptor -is_a: CHEBI:37527 ! acid - [Term] id: CHEBI:39144 name: Lewis base is_a: CHEBI:17891 ! donor is_a: CHEBI:22695 ! base -[Term] -id: CHEBI:39285 -name: chloropicrin -is_a: CHEBI:35716 ! C-nitro compound -is_a: CHEBI:36683 ! organochlorine compound -is_a: CHEBI:64708 ! one-carbon compound - -[Term] -id: CHEBI:39418 -name: straight-chain saturated fatty acid -is_a: CHEBI:26607 ! saturated fatty acid -is_a: CHEBI:59202 ! straight-chain fatty acid - [Term] id: CHEBI:39478 name: buta-1,3-diene @@ -3897,12 +3027,6 @@ name: hydrogenphosphate is_a: CHEBI:35780 ! phosphate ion is_a: CHEBI:79388 ! divalent inorganic anion -[Term] -id: CHEBI:44882 -name: peridinin -is_a: CHEBI:35307 ! epoxycarotenol -is_a: CHEBI:37602 ! allenes - [Term] id: CHEBI:45696 name: hydrogensulfate @@ -3923,87 +3047,6 @@ id: CHEBI:46663 name: silicate mineral is_a: CHEBI:46662 ! mineral -[Term] -id: CHEBI:46664 -name: chrysotile -is_a: CHEBI:46680 ! serpentine asbestos - -[Term] -id: CHEBI:46665 -name: riebeckite -is_a: CHEBI:46663 ! silicate mineral - -[Term] -id: CHEBI:46666 -name: crocidolite asbestos -is_a: CHEBI:46665 ! riebeckite -is_a: CHEBI:46677 ! amphibole asbestos - -[Term] -id: CHEBI:46670 -name: serpentine mineral -is_a: CHEBI:46663 ! silicate mineral - -[Term] -id: CHEBI:46676 -name: tremolite asbestos -is_a: CHEBI:46677 ! amphibole asbestos - -[Term] -id: CHEBI:46677 -name: amphibole asbestos -is_a: CHEBI:46661 ! asbestos - -[Term] -id: CHEBI:46678 -name: amosite asbestos -is_a: CHEBI:46677 ! amphibole asbestos -is_a: CHEBI:46679 ! gruenerite - -[Term] -id: CHEBI:46679 -name: gruenerite -is_a: CHEBI:46663 ! silicate mineral - -[Term] -id: CHEBI:46680 -name: serpentine asbestos -is_a: CHEBI:46661 ! asbestos -is_a: CHEBI:46670 ! serpentine mineral - -[Term] -id: CHEBI:46681 -name: anthophyllite -is_a: CHEBI:46663 ! silicate mineral - -[Term] -id: CHEBI:46682 -name: anthophyllite asbestos -is_a: CHEBI:46677 ! amphibole asbestos -is_a: CHEBI:46681 ! anthophyllite - -[Term] -id: CHEBI:46683 -name: actinolite -is_a: CHEBI:46663 ! silicate mineral - -[Term] -id: CHEBI:46684 -name: actinolite asbestos -is_a: CHEBI:46677 ! amphibole asbestos -is_a: CHEBI:46683 ! actinolite - -[Term] -id: CHEBI:46717 -name: sulfide mineral -is_a: CHEBI:26822 ! sulfide -is_a: CHEBI:46662 ! mineral - -[Term] -id: CHEBI:46718 -name: sulfide salt -is_a: CHEBI:24866 ! salt - [Term] id: CHEBI:46721 name: carbonate salt @@ -4015,34 +3058,6 @@ name: solvent is_a: CHEBI:33232 ! application is_a: CHEBI:51086 ! chemical role -[Term] -id: CHEBI:46890 -name: silicon hydroxide -is_a: CHEBI:26677 ! silicon molecular entity - -[Term] -id: CHEBI:46923 -name: dioxane -is_a: CHEBI:36389 ! saturated organic heteromonocyclic parent -is_a: CHEBI:46926 ! dioxanes - -[Term] -id: CHEBI:46926 -name: dioxanes -is_a: CHEBI:25693 ! organic heteromonocyclic compound -is_a: CHEBI:38104 ! oxacycle - -[Term] -id: CHEBI:47032 -name: 1,4-dioxane -is_a: CHEBI:134179 ! volatile organic compound -is_a: CHEBI:46923 ! dioxane - -[Term] -id: CHEBI:47622 -name: acetate ester -is_a: CHEBI:33308 ! carboxylic ester - [Term] id: CHEBI:47788 name: 3-oxo steroid @@ -4054,11 +3069,6 @@ id: CHEBI:47867 name: indicator is_a: CHEBI:33232 ! application -[Term] -id: CHEBI:47882 -name: cyclic polypyrrole -is_a: CHEBI:38077 ! polypyrrole - [Term] id: CHEBI:47885 name: dinucleotide @@ -4091,11 +3101,6 @@ name: nitrobenzenes is_a: CHEBI:22712 ! benzenes is_a: CHEBI:35716 ! C-nitro compound -[Term] -id: CHEBI:48123 -name: silicate ion -is_a: CHEBI:37191 ! silicon oxoanion - [Term] id: CHEBI:48154 name: sulfur oxide @@ -4145,24 +3150,6 @@ id: CHEBI:48730 name: aluminosilicate mineral is_a: CHEBI:46663 ! silicate mineral -[Term] -id: CHEBI:49202 -name: elemental platinum -is_a: CHEBI:33749 ! platinum molecular entity - -[Term] -id: CHEBI:49470 -name: aluminium(3+) -is_a: CHEBI:27153 ! monoatomic trication -is_a: CHEBI:33627 ! monoatomic aluminium -is_a: CHEBI:63062 ! aluminium cation - -[Term] -id: CHEBI:49475 -name: argon atom -is_a: CHEBI:33309 ! noble gas atom -is_a: CHEBI:33560 ! p-block element atom - [Term] id: CHEBI:49637 name: hydrogen atom @@ -4170,62 +3157,6 @@ is_a: CHEBI:24835 ! inorganic molecular entity is_a: CHEBI:25585 ! nonmetal atom is_a: CHEBI:33559 ! s-block element atom -[Term] -id: CHEBI:49828 -name: praseodymium atom -is_a: CHEBI:33319 ! lanthanoid atom -is_a: CHEBI:33562 ! f-block element atom - -[Term] -id: CHEBI:49936 -name: uranium(0) -is_a: CHEBI:50558 ! monoatomic uranium - -[Term] -id: CHEBI:49976 -name: zinc dichloride -is_a: CHEBI:27364 ! zinc molecular entity -is_a: CHEBI:36093 ! inorganic chloride - -[Term] -id: CHEBI:49986 -name: elemental krypton -is_a: CHEBI:36909 ! krypton molecular entity - -[Term] -id: CHEBI:49987 -name: monoatomic krypton -is_a: CHEBI:33238 ! monoatomic entity -is_a: CHEBI:49986 ! elemental krypton - -[Term] -id: CHEBI:49990 -name: monoatomic argon -is_a: CHEBI:33238 ! monoatomic entity -is_a: CHEBI:49991 ! elemental argon - -[Term] -id: CHEBI:49991 -name: elemental argon -is_a: CHEBI:36908 ! argon molecular entity - -[Term] -id: CHEBI:49992 -name: argon(.1+) -is_a: CHEBI:36879 ! inorganic radical cation -is_a: CHEBI:49990 ! monoatomic argon - -[Term] -id: CHEBI:49994 -name: monoatomic neon -is_a: CHEBI:33238 ! monoatomic entity -is_a: CHEBI:49995 ! elemental neon - -[Term] -id: CHEBI:49995 -name: elemental neon -is_a: CHEBI:36907 ! neon molecular entity - [Term] id: CHEBI:50047 name: organic amino compound @@ -4273,43 +3204,11 @@ id: CHEBI:50406 name: probe is_a: CHEBI:33232 ! application -[Term] -id: CHEBI:50558 -name: monoatomic uranium -is_a: CHEBI:50559 ! elemental uranium - -[Term] -id: CHEBI:50559 -name: elemental uranium -is_a: CHEBI:33499 ! uranium molecular entity - [Term] id: CHEBI:50584 name: alkyl alcohol is_a: CHEBI:2571 ! aliphatic alcohol -[Term] -id: CHEBI:50594 -name: carbon nanotube -is_a: CHEBI:50796 ! nanotube -is_a: CHEBI:50812 ! carbon nanostructure - -[Term] -id: CHEBI:50795 -name: nanostructure -is_a: CHEBI:36357 ! polyatomic entity - -[Term] -id: CHEBI:50796 -name: nanotube -is_a: CHEBI:50795 ! nanostructure - -[Term] -id: CHEBI:50812 -name: carbon nanostructure -is_a: CHEBI:33415 ! elemental carbon -is_a: CHEBI:50795 ! nanostructure - [Term] id: CHEBI:50816 name: iron oxide @@ -4381,64 +3280,23 @@ id: CHEBI:51447 name: organic univalent group is_a: CHEBI:33247 ! organic group -[Term] -id: CHEBI:51580 -name: phthalocyanines -is_a: CHEBI:36309 ! cyclic tetrapyrrole - -[Term] -id: CHEBI:51584 -name: metallophthalocyanines -is_a: CHEBI:33909 ! metallotetrapyrrole -is_a: CHEBI:51580 ! phthalocyanines - -[Term] -id: CHEBI:51585 -name: metallophthalocyanine -is_a: CHEBI:51584 ! metallophthalocyanines - -[Term] -id: CHEBI:51688 -name: enal -is_a: CHEBI:51718 ! alpha,beta-unsaturated aldehyde -is_a: CHEBI:78840 ! olefinic compound - [Term] id: CHEBI:51689 name: enone is_a: CHEBI:51721 ! alpha,beta-unsaturated ketone is_a: CHEBI:78840 ! olefinic compound -[Term] -id: CHEBI:51718 -name: alpha,beta-unsaturated aldehyde -is_a: CHEBI:17478 ! aldehyde - [Term] id: CHEBI:51721 name: alpha,beta-unsaturated ketone is_a: CHEBI:17087 ! ketone -[Term] -id: CHEBI:5186 -name: fucoxanthin -is_a: CHEBI:26878 ! tertiary alcohol -is_a: CHEBI:35307 ! epoxycarotenol -is_a: CHEBI:35681 ! secondary alcohol -is_a: CHEBI:37602 ! allenes -is_a: CHEBI:47622 ! acetate ester - [Term] id: CHEBI:51958 name: organic polycyclic compound is_a: CHEBI:33635 ! polycyclic compound is_a: CHEBI:33832 ! organic cyclic compound -[Term] -id: CHEBI:51959 -name: organic tricyclic compound -is_a: CHEBI:51958 ! organic polycyclic compound - [Term] id: CHEBI:52206 name: biochemical role @@ -4485,51 +3343,6 @@ id: CHEBI:53000 name: epitope is_a: CHEBI:24432 ! biological role -[Term] -id: CHEBI:53225 -name: poly(alkylene) macromolecule -is_a: CHEBI:37997 ! homopolymer macromolecule - -[Term] -id: CHEBI:53226 -name: polyethylene macromolecule -is_a: CHEBI:53225 ! poly(alkylene) macromolecule - -[Term] -id: CHEBI:53242 -name: vinyl polymer macromolecule -is_a: CHEBI:53226 ! polyethylene macromolecule - -[Term] -id: CHEBI:53243 -name: poly(vinyl chloride) -is_a: CHEBI:53242 ! vinyl polymer macromolecule - -[Term] -id: CHEBI:53310 -name: copolymer macromolecule -is_a: CHEBI:33839 ! macromolecule - -[Term] -id: CHEBI:53387 -name: poly(hydroxyalkanoate) -is_a: CHEBI:26178 ! polyester macromolecule - -[Term] -id: CHEBI:53388 -name: poly(hydroxybutyrate) -is_a: CHEBI:53387 ! poly(hydroxyalkanoate) - -[Term] -id: CHEBI:53448 -name: methyl cellulose -is_a: CHEBI:28793 ! beta-D-glucan - -[Term] -id: CHEBI:53550 -name: poly(propylene) -is_a: CHEBI:53226 ! polyethylene macromolecule - [Term] id: CHEBI:5686 name: heterocyclic compound @@ -4540,22 +3353,11 @@ id: CHEBI:58072 name: carbon monoxide(1+) is_a: CHEBI:25697 ! organic cation -[Term] -id: CHEBI:58416 -name: chlorophyll a(1-) -is_a: CHEBI:139291 ! chlorophyll(1-) -is_a: CHEBI:58941 ! cyclic tetrapyrrole anion - [Term] id: CHEBI:58454 name: kynurenate is_a: CHEBI:38773 ! quinolinemonocarboxylate -[Term] -id: CHEBI:58941 -name: cyclic tetrapyrrole anion -is_a: CHEBI:25696 ! organic anion - [Term] id: CHEBI:58950 name: very long-chain fatty acid anion @@ -4576,17 +3378,6 @@ id: CHEBI:59163 name: biomarker is_a: CHEBI:47867 ! indicator -[Term] -id: CHEBI:59202 -name: straight-chain fatty acid -is_a: CHEBI:35366 ! fatty acid - -[Term] -id: CHEBI:59739 -name: electrophilic reagent -is_a: CHEBI:33893 ! reagent -is_a: CHEBI:39143 ! Lewis acid - [Term] id: CHEBI:59740 name: nucleophilic reagent @@ -4608,26 +3399,6 @@ id: CHEBI:60027 name: polymer is_a: CHEBI:60004 ! mixture -[Term] -id: CHEBI:60029 -name: homopolymer -is_a: CHEBI:60027 ! polymer - -[Term] -id: CHEBI:60031 -name: poly(alkylene) polymer -is_a: CHEBI:60029 ! homopolymer - -[Term] -id: CHEBI:60034 -name: polyethylene polymer -is_a: CHEBI:60031 ! poly(alkylene) polymer - -[Term] -id: CHEBI:60160 -name: polyester polymer -is_a: CHEBI:60027 ! polymer - [Term] id: CHEBI:60242 name: monovalent inorganic cation @@ -4644,11 +3415,6 @@ id: CHEBI:60643 name: NMDA receptor antagonist is_a: CHEBI:60798 ! excitatory amino acid antagonist -[Term] -id: CHEBI:60737 -name: polyurethane polymer -is_a: CHEBI:60029 ! homopolymer - [Term] id: CHEBI:60798 name: excitatory amino acid antagonist @@ -4665,16 +3431,6 @@ name: nucleobase-containing molecular entity is_a: CHEBI:33833 ! heteroarene is_a: CHEBI:51143 ! nitrogen molecular entity -[Term] -id: CHEBI:61250 -name: brevetoxin A -is_a: CHEBI:61275 ! ciguatoxin - -[Term] -id: CHEBI:61275 -name: ciguatoxin -is_a: CHEBI:36468 ! polycyclic ether - [Term] id: CHEBI:61292 name: guanyl nucleotide @@ -4697,21 +3453,6 @@ name: adenyl ribonucleotide is_a: CHEBI:26400 ! purine ribonucleotide is_a: CHEBI:61293 ! adenyl nucleotide -[Term] -id: CHEBI:61452 -name: poly(ethylene terephthalate) polymer -is_a: CHEBI:60160 ! polyester polymer - -[Term] -id: CHEBI:61614 -name: vinyl polymer -is_a: CHEBI:60034 ! polyethylene polymer - -[Term] -id: CHEBI:61642 -name: polystyrene polymer -is_a: CHEBI:61614 ! vinyl polymer - [Term] id: CHEBI:62488 name: signalling molecule @@ -4722,18 +3463,6 @@ id: CHEBI:62764 name: reactive nitrogen species is_a: CHEBI:51143 ! nitrogen molecular entity -[Term] -id: CHEBI:62967 -name: amorphous cellulose -is_a: CHEBI:18246 ! (1->4)-beta-D-glucan -is_a: CHEBI:72813 ! exopolysaccharide - -[Term] -id: CHEBI:62968 -name: crystalline cellulose -is_a: CHEBI:18246 ! (1->4)-beta-D-glucan -is_a: CHEBI:72813 ! exopolysaccharide - [Term] id: CHEBI:63046 name: emulsifier @@ -4770,16 +3499,6 @@ id: CHEBI:63471 name: branched-chain amino-acid anion is_a: CHEBI:37022 ! amino-acid anion -[Term] -id: CHEBI:63732 -name: 1,1-diol -is_a: CHEBI:30879 ! alcohol - -[Term] -id: CHEBI:63734 -name: ketone hydrate -is_a: CHEBI:63732 ! 1,1-diol - [Term] id: CHEBI:64047 name: food additive @@ -4830,18 +3549,6 @@ id: CHEBI:72813 name: exopolysaccharide is_a: CHEBI:33694 ! biomacromolecule -[Term] -id: CHEBI:73113 -name: divinyl chlorophyll a -is_a: CHEBI:25248 ! methyl ester -is_a: CHEBI:28966 ! chlorophyll - -[Term] -id: CHEBI:73115 -name: divinyl chlorophyll b -is_a: CHEBI:25248 ! methyl ester -is_a: CHEBI:28966 ! chlorophyll - [Term] id: CHEBI:75763 name: eukaryotic metabolite @@ -4862,17 +3569,6 @@ id: CHEBI:75787 name: prokaryotic metabolite is_a: CHEBI:25212 ! metabolite -[Term] -id: CHEBI:75896 -name: iron sulfides -is_a: CHEBI:24873 ! iron molecular entity -is_a: CHEBI:46718 ! sulfide salt - -[Term] -id: CHEBI:75897 -name: iron(2+) sulfides -is_a: CHEBI:75896 ! iron sulfides - [Term] id: CHEBI:76413 name: greenhouse gas @@ -4943,11 +3639,6 @@ id: CHEBI:77941 name: EC 3.5.1.4 (amidase) inhibitor is_a: CHEBI:76807 ! EC 3.5.1.* (non-peptide linear amide C-N hydrolase) inhibitor -[Term] -id: CHEBI:77971 -name: raising agent -is_a: CHEBI:64047 ! food additive - [Term] id: CHEBI:77974 name: food packaging gas @@ -4959,11 +3650,6 @@ name: food propellant is_a: CHEBI:64047 ! food additive is_a: CHEBI:76414 ! propellant -[Term] -id: CHEBI:78130 -name: fatty acid anion 28:0 -is_a: CHEBI:58953 ! saturated fatty acid anion - [Term] id: CHEBI:78295 name: food component @@ -5004,43 +3690,6 @@ id: CHEBI:79389 name: monovalent inorganic anion is_a: CHEBI:24834 ! inorganic anion -[Term] -id: CHEBI:80043 -name: Nodularin -is_a: CHEBI:25698 ! ether - -[Term] -id: CHEBI:8006 -name: Peptidoglycan(N-acetyl-D-glucosamine) -is_a: CHEBI:26191 ! polyol - -[Term] -id: CHEBI:80770 -name: Brevetoxin B -is_a: CHEBI:61275 ! ciguatoxin - -[Term] -id: CHEBI:8108 -name: pheophytin -is_a: CHEBI:38252 ! phorbines - -[Term] -id: CHEBI:82661 -name: diatomaceous earth -is_a: CHEBI:30563 ! silicon dioxide -is_a: CHEBI:46662 ! mineral - -[Term] -id: CHEBI:82663 -name: elemental iron -is_a: CHEBI:24873 ! iron molecular entity -is_a: CHEBI:33259 ! elemental molecular entity - -[Term] -id: CHEBI:82664 -name: iron(0) -is_a: CHEBI:82663 ! elemental iron - [Term] id: CHEBI:83039 name: crustacean metabolite @@ -5056,13 +3705,6 @@ id: CHEBI:83057 name: Daphnia metabolite is_a: CHEBI:83039 ! crustacean metabolite -[Term] -id: CHEBI:83348 -name: chlorophyllide a(2-) -is_a: CHEBI:139292 ! chlorophyllide(2-) -is_a: CHEBI:35757 ! monocarboxylic acid anion -is_a: CHEBI:58941 ! cyclic tetrapyrrole anion - [Term] id: CHEBI:83628 name: N-acylammonia @@ -5095,12 +3737,6 @@ name: pentose phosphate is_a: CHEBI:33447 ! phospho sugar is_a: CHEBI:63409 ! pentose derivative -[Term] -id: CHEBI:86471 -name: pyrite -is_a: CHEBI:46717 ! sulfide mineral -is_a: CHEBI:75897 ! iron(2+) sulfides - [Term] id: CHEBI:88184 name: metal allergen diff --git a/src/envo/imports/chebi_import.owl b/src/envo/imports/chebi_import.owl index f05de546..c4ce241b 100644 --- a/src/envo/imports/chebi_import.owl +++ b/src/envo/imports/chebi_import.owl @@ -60,18 +60,6 @@ - - - - - - - - - - - - - - - - - pyrrolopurine - - - - @@ -241,42 +219,6 @@ - - - - - ultra-long-chain fatty acid - - - - - - - - - ultra-long-chain fatty acid anion - - - - - - - - - manganese dihydroxide - - - - - - - - - manganese hydroxide - - - - @@ -315,18 +257,6 @@ - - - - - - - - hydron - - - - @@ -505,16 +435,6 @@ - - - - - - chitosan - - - - @@ -642,18 +562,6 @@ - - - - - - - - paralytic shellfish toxin - - - - @@ -685,15 +593,6 @@ - - - - - heteroglycan - - - - @@ -793,17 +692,6 @@ - - - - - - - alginic acid - - - - @@ -1141,15 +1029,6 @@ - - - - - alkaloid - - - - @@ -1289,15 +1168,6 @@ - - - - - carbamate ester - - - - @@ -1537,15 +1407,6 @@ - - - - - guanidines - - - - @@ -1613,16 +1474,6 @@ - - - - - - proton - - - - @@ -1919,15 +1770,6 @@ - - - - - monoatomic monocation - - - - @@ -2386,15 +2228,6 @@ - - - - - radical - - - - @@ -2423,15 +2256,6 @@ - - - - - saturated fatty acid - - - - @@ -2582,17 +2406,6 @@ - - - - - - - organic heterotricyclic compound - - - - @@ -2641,15 +2454,6 @@ - - - - - Anatoxin a - - - - @@ -2688,15 +2492,6 @@ - - - - - very long-chain fatty acid - - - - @@ -3045,24 +2840,6 @@ - - - - - deuteron - - - - - - - - - deuterium atom - - - - @@ -3138,15 +2915,6 @@ - - - - - gold(0) - - - - @@ -3183,16 +2951,6 @@ - - - - - - alpha-particle - - - - @@ -3212,24 +2970,6 @@ - - - - - neutron - - - - - - - - - positron - - - - @@ -3240,15 +2980,6 @@ - - - - - monoatomic dication - - - - @@ -3331,27 +3062,6 @@ - - - - - - octacosanoic acid - - - - - - - - - - - octacosanoate - - - - @@ -3558,35 +3268,6 @@ - - - - - - monoatomic hydrogen - - - - - - - - - atomic nucleus - - - - - - - - - - nucleon - - - - @@ -3840,26 +3521,6 @@ - - - - - - monoatomic helium - - - - - - - - - - helium(2+) - - - - @@ -4113,15 +3774,6 @@ - - - - - platinum(0) - - - - @@ -4535,16 +4187,6 @@ - - - - - - monoatomic aluminium - - - - @@ -4781,24 +4423,6 @@ - - - - - elemental helium - - - - - - - - - diatomic helium - - - - @@ -4841,6 +4465,7 @@ + amino-acid cation @@ -5088,15 +4713,6 @@ - - - - - elemental gold - - - - @@ -5107,20 +4723,6 @@ - - - - - - - - - - saxitoxin - - - - @@ -5168,24 +4770,6 @@ - - - - - vanadium(0) - - - - - - - - - elemental vanadium - - - - @@ -5378,16 +4962,6 @@ - - - - - - fatty acid - - - - @@ -5700,16 +5274,6 @@ - - - - - - baryon - - - - @@ -5736,43 +5300,7 @@ - - - - - composite particle - - - - - - - - - hadron - - - - - - - - - nuclear particle - - - - - - - - - neutrino - - - - - + @@ -5839,16 +5367,6 @@ - - - - - - polycyclic ether - - - - @@ -5888,15 +5406,6 @@ - - - - - heterotricyclic compound - - - - @@ -5925,56 +5434,6 @@ - - - - - - inorganic radical - - - - - - - - - - radical cation - - - - - - - - - - radical ion - - - - - - - - - - inorganic radical ion - - - - - - - - - - inorganic radical cation - - - - @@ -6003,15 +5462,6 @@ - - - - - neon molecular entity - - - - @@ -6021,15 +5471,6 @@ - - - - - krypton molecular entity - - - - @@ -6077,15 +5518,6 @@ - - - - - nitrogen-15 atom - - - - @@ -6305,16 +5737,6 @@ - - - - - - tropane alkaloid - - - - @@ -6438,15 +5860,6 @@ - - - - - homopolymer macromolecule - - - - @@ -6532,15 +5945,6 @@ - - - - - phorbines - - - - @@ -6550,16 +5954,6 @@ - - - - - - azabicycloalkane - - - - @@ -6713,16 +6107,6 @@ - - - - - - straight-chain saturated fatty acid - - - - @@ -6825,147 +6209,6 @@ - - - - - chrysotile - - - - - - - - - riebeckite - - - - - - - - - - crocidolite asbestos - - - - - - - - - serpentine mineral - - - - - - - - - tremolite asbestos - - - - - - - - - amphibole asbestos - - - - - - - - - - amosite asbestos - - - - - - - - - gruenerite - - - - - - - - - - serpentine asbestos - - - - - - - - - anthophyllite - - - - - - - - - - anthophyllite asbestos - - - - - - - - - actinolite - - - - - - - - - - actinolite asbestos - - - - - - - - - - sulfide mineral - - - - - - - - - sulfide salt - - - - @@ -7211,26 +6454,6 @@ - - - - - elemental platinum - - - - - - - - - - - aluminium(3+) - - - - @@ -7262,15 +6485,6 @@ - - - - - uranium(0) - - - - @@ -7281,73 +6495,6 @@ - - - - - elemental krypton - - - - - - - - - - monoatomic krypton - - - - - - - - - - monoatomic argon - - - - - - - - - elemental argon - - - - - - - - - - argon(.1+) - - - - - - - - - - monoatomic neon - - - - - - - - - elemental neon - - - - @@ -7431,24 +6578,6 @@ - - - - - monoatomic uranium - - - - - - - - - elemental uranium - - - - @@ -7712,15 +6841,6 @@ - - - - - organic tricyclic compound - - - - @@ -7803,51 +6923,6 @@ - - - - - poly(alkylene) macromolecule - - - - - - - - - polyethylene macromolecule - - - - - - - - - vinyl polymer macromolecule - - - - - - - - - poly(vinyl chloride) - - - - - - - - - copolymer macromolecule - - - - @@ -7875,15 +6950,6 @@ - - - - - poly(propylene) - - - - @@ -7966,15 +7032,6 @@ - - - - - straight-chain fatty acid - - - - @@ -8022,42 +7079,6 @@ - - - - - homopolymer - - - - - - - - - poly(alkylene) polymer - - - - - - - - - polyethylene polymer - - - - - - - - - polyester polymer - - - - @@ -8086,15 +7107,6 @@ - - - - - polyurethane polymer - - - - @@ -8123,24 +7135,6 @@ - - - - - brevetoxin A - - - - - - - - - ciguatoxin - - - - @@ -8179,33 +7173,6 @@ - - - - - poly(ethylene terephthalate) polymer - - - - - - - - - vinyl polymer - - - - - - - - - polystyrene polymer - - - - @@ -8224,26 +7191,6 @@ - - - - - - amorphous cellulose - - - - - - - - - - crystalline cellulose - - - - @@ -8308,24 +7255,6 @@ - - - - - 1,1-diol - - - - - - - - - ketone hydrate - - - - @@ -8468,25 +7397,6 @@ - - - - - - iron sulfides - - - - - - - - - iron(2+) sulfides - - - - @@ -8641,15 +7551,6 @@ - - - - - fatty acid anion 28:0 - - - - @@ -8722,42 +7623,6 @@ - - - - - Nodularin - - - - - - - - - Peptidoglycan(N-acetyl-D-glucosamine) - - - - - - - - - Brevetoxin B - - - - - - - - - pheophytin - - - - @@ -8768,25 +7633,6 @@ - - - - - - elemental iron - - - - - - - - - iron(0) - - - - @@ -8881,16 +7727,6 @@ - - - - - - pyrite - - - - @@ -8919,5 +7755,5 @@ - + diff --git a/src/envo/imports/fao_import.owl b/src/envo/imports/fao_import.owl index 07c3e38b..6c5db9bf 100644 --- a/src/envo/imports/fao_import.owl +++ b/src/envo/imports/fao_import.owl @@ -298,5 +298,5 @@ - + diff --git a/src/envo/imports/foodon_import.obo b/src/envo/imports/foodon_import.obo index f3b73eb3..7a762d39 100644 --- a/src/envo/imports/foodon_import.obo +++ b/src/envo/imports/foodon_import.obo @@ -1,6 +1,5 @@ format-version: 1.2 ontology: envo/imports/foodon_import -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\nDeclaration(Datatype(rdfs:anyURI))\n\n\nAnnotationAssertion( \"https://orcid.org/0000-0001-5275-8866\"^^rdfs:anyURI)\nAnnotationAssertion( \"http://orcid.org/0000-0002-8844-9165\"^^rdfs:anyURI)\nAnnotationAssertion( \"http://orcid.org/0000-0002-8844-9165\"^^rdfs:anyURI)\n) [Term] id: FOODON:00001001 @@ -43,30 +42,28 @@ is_a: FOODON:00001096 ! fermented elaeis palm beverage id: FOODON:00001006 name: mammalian meat food product def: "A food product made of meat, the skeletal muscle and associated fat, and other edible tissues such as organs, livers, skin, brains, bone marrow, kidneys, or lungs, of mammals." [] -xref: SUBSET_SIREN:F17332 +xref: https://bioregistry.io/reference/siren\:F17332 is_a: FOODON:00001092 ! vertebrate animal food product property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Meat +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Meat [Term] id: FOODON:00001007 -name: sausage food product +name: meat sausage food product def: "A processed meat food product that is made from a sausage." [] is_a: FOODON:00001010 ! processed meat food product -property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-5275-8866 -property_value: http://purl.org/dc/elements/1.1/date 2022-10-28T11:02:42Z xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 +property_value: http://purl.org/dc/terms/date 2022-10-28T11:02:42Z xsd:dateTime [Term] id: FOODON:00001008 name: liver paste -comment: SIREN DB annotation:\n* has quality 'semisolid with smooth consistency' (http://purl.obolibrary.org/obo/FOODON_03430119)\n* derives from 'liver' (http://purl.obolibrary.org/obo/UBERON_0002107)\n -subset: subset_siren -xref: SUBSET_SIREN:F17604 +comment: SIREN DB annotation:\n* semisolid with smooth consistency FOODON:03430119\n* liver UBERON:0002107 +xref: https://bioregistry.io/reference/siren\:F17604 is_a: FOODON:00002819 ! liver food product is_a: FOODON:03315925 ! pate -property_value: http://purl.org/dc/elements/1.1/date 2019-06-11T23:00:48Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-06-11T23:00:48Z xsd:dateTime property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000412 http://langual.org xsd:string property_value: seeAlso https://madison.com/lifestyles/chicken-liver-paste-is-still-a-tasty-treat/article_2194b8cb-82b5-5112-9a97-0042571e90d1.html xsd:string [Term] @@ -75,7 +72,7 @@ name: hot dog def: "A hot dog is a moist sausage of soft, even texture and flavor, often made from advanced meat recovery or meat slurry. Most types are fully cooked, cured or smoked. It is often placed hot in a special purpose soft, sliced hot dog bun." [] synonym: "frankfurter" NARROW [] synonym: "hotdog" EXACT [] -is_a: FOODON:00001224 ! sausage (cooked) +is_a: FOODON:00001224 ! meat sausage (cooked) property_value: http://schema.org/image https://upload.wikimedia.org/wikipedia/commons/thumb/f/fb/Hotdog_-_Evan_Swigart.jpg/640px-Hotdog_-_Evan_Swigart.jpg property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string @@ -98,8 +95,8 @@ id: FOODON:00001013 name: cheese food product def: "Cheese is a food derived from milk that is produced in a wide range of flavors, textures, and forms by coagulation of the milk protein casein." [] synonym: "cheese" EXACT [] +xref: https://bioregistry.io/reference/siren\:F1076 xref: https://en.wikipedia.org/wiki/Cheese -xref: SUBSET_SIREN:F1076 is_a: FOODON:00001256 ! dairy food product property_value: IAO:0000114 IAO:0000428 property_value: seeAlso https://www.asmscience.org/content/book/10.1128/9781555818593.chap3 @@ -143,6 +140,7 @@ is_a: FOODON:00001014 ! yogurt food product [Term] id: FOODON:00001019 name: wort food product +def: "The liquid extracted from the mashing process during the brewing of beer or whiskey. Wort contains the sugars that will be fermented by the brewing yeast to produce alcohol." [Wikipedia:Wort_%28brewing%29] is_a: FOODON:00001102 ! fermented grain beverage [Term] @@ -159,11 +157,10 @@ is_a: FOODON:00001020 ! beer wort food product id: FOODON:00001023 name: mammalian milk butter def: "Cream component produced by churning and containing not less than 80% milkfat." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=C0179 +xref: langual:thesaurus.asp?termid=C0179 is_a: FOODON:00001243 ! animal lipid food product is_a: FOODON:03315150 ! mammalian milk product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:00001024 @@ -192,28 +189,36 @@ is_a: FOODON:00001127 ! cow milk cheese [Term] id: FOODON:00001028 name: Brie cheese food product +def: "A large disc of smooth, soft, even runny cheese made with cow's milk." [http://www.whatamieating.com/?b=1&d=1&t=main&s=brie&r=All] is_a: FOODON:00001127 ! cow milk cheese [Term] id: FOODON:00001029 name: gouda cheese food product +def: "A hard cow's milk cheese with an almost orange yellow paste. Older cheeses are coated in black wax." [http://www.whatamieating.com/?b=1&d=1&t=main&s=gouda&r=All] is_a: FOODON:00001127 ! cow milk cheese [Term] id: FOODON:00001031 name: gorgonzola cheese food product +def: "A drum of very rich, creamy, pungent blue-veined cow's milk cheese. It has a white paste with blue veining and a brined rind. It is made in Gorgonzola, near Milan." [http://www.whatamieating.com/?b=1&d=1&t=main&s=Gorgonzola&r=All] is_a: FOODON:00001065 ! blue cheese food product is_a: FOODON:00001127 ! cow milk cheese [Term] id: FOODON:00001032 name: swiss cheese food product +def: "A generic cheese common to many countries for several related varieties of cheese which resemble the Swiss Emmental. Three types of bacteria are used in the production of Emmental cheese: Streptococcus salivarius subsp. thermophilus, Lactobacillus (L. helveticus or Lactobacillus delbrueckii subsp. bulgaricus), and Propionibacter (P. freudenreichii or P. shermani). In a late stage of cheese production, the Propionibacter consumes the lactic acid excreted by the other bacteria, and releases carbon dioxide gas, which slowly forms the bubbles that develop the eyes. Swiss cheese without eyes is known as \"blind.\"" [Wikipedia:Swiss_cheese] is_a: FOODON:00001127 ! cow milk cheese [Term] id: FOODON:00001033 -name: emmenthal cheese food product -is_a: FOODON:00001127 ! cow milk cheese +name: emmenthal cheese +def: "A semi-hard, yellow cheese that has mild flavor that is slightly buttery." [] +synonym: "Emmental cheese" EXACT [] +synonym: "Emmentaler cheese" EXACT [] +is_a: FOODON:00001032 ! swiss cheese food product +property_value: seeAlso http://www.whatamieating.com/?b=1&d=1&t=main&s=Emmental&r=All [Term] id: FOODON:00001035 @@ -223,11 +228,13 @@ is_a: FOODON:00001027 ! cheddar cheese food product [Term] id: FOODON:00001036 name: pont ieveque cheese food product +def: "A small, sweetish, soft, square cow's milk cheese from Normandy with a yellowish-orange rind." [http://www.whatamieating.com/?b=1&d=1&t=main&s=Pont+l%27Eveque&r=All] is_a: FOODON:00001127 ! cow milk cheese [Term] id: FOODON:00001037 name: vacherin mont dor cheese food product +def: "A disc of soft cheese made with cow's milk. It has a soft to runny paste and a smooth, pink rind." [http://www.whatamieating.com/?b=1&d=1&t=main&s=vacherin+Mont+d%27Or&r=All] is_a: FOODON:00002252 ! soft cheese food product [Term] @@ -235,7 +242,7 @@ id: FOODON:00001038 name: pork meat food product def: "A food product made from domestic pig meat (Sus domesticus or Sus scrofa scrofa)." [] synonym: "pork" EXACT [] -is_a: FOODON:00002663 ! pork food product +is_a: FOODON:00002663 ! pig food product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Pork xsd:anyURI @@ -243,6 +250,7 @@ property_value: IAO:0000119 http://en.wikipedia.org/wiki/Pork xsd:anyURI [Term] id: FOODON:00001039 name: cured meat food product +def: "A meat that is preserved by the addition of a combination of salt, sugar, nitrates or nitrite and or is smoked." [http://en.wikipedia.org/wiki/Cured_meat] is_a: FOODON:00001010 ! processed meat food product [Term] @@ -252,12 +260,17 @@ is_a: FOODON:00001131 ! poultry meat food product [Term] id: FOODON:00001041 -name: beef food product +name: cow food product +def: "A food product that is derived from some cow." [] is_a: FOODON:00001134 ! bovine meat food product +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 xsd:string +property_value: http://purl.org/dc/terms/date 2024-06-27T22:43:12Z xsd:dateTime +property_value: IAO:0000114 IAO:0000122 [Term] id: FOODON:00001045 name: ice cream food product +def: "A frozen dessert usually made from dairy products, such as milk and cream, and often combined with fruits or other ingredients and flavours. Most varieties contain sugar, although some are made with other sweeteners. In some cases, artificial flavourings and colourings are used in addition to (or in replacement of) the natural ingredients. This mixture is stirred slowly while cooling to prevent large ice crystals from forming; the result is a smoothly textured ice cream." [Wikipedia:Ice_cream] synonym: "ice cream" EXACT [] synonym: "ice-cream" EXACT [] is_a: FOODON:00001149 ! confectionery food product @@ -288,6 +301,7 @@ is_a: FOODON:00001013 ! cheese food product [Term] id: FOODON:00001049 name: pork chop food product +def: "A cut of meat (a meat chop) cut perpendicularly to the spine of the pig and usually containing a rib or part of a vertebra, served as an individual portion." [http://en.wikipedia.org/wiki/Pork_chop] is_a: FOODON:00001038 ! pork meat food product [Term] @@ -332,10 +346,8 @@ is_a: FOODON:03315173 ! fish product (unspecified species) [Term] id: FOODON:00001056 name: flour food product -def: "A fine powder made from cereals or other starchy food sources." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=H0152 -is_a: FOODON:00001093 ! cereal grain food product -property_value: hasSynonym "flour added" xsd:string +def: "A food product made from flour." [] +is_a: FOODON:00004509 ! milled food product property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000119 Wikipedia:Flour xsd:anyURI @@ -354,16 +366,15 @@ is_a: FOODON:00001057 ! plant fruit food product id: FOODON:00001059 name: apple juice def: "Apple juice is a fruit juice made by the maceration and pressing of an apple." [] -subset: subset_siren +comment: SIREN DB annotation:\n* liquid, low viscosity, with no visible particles FOODON:03430123\n* fruit, peel present, core, pit or seed present FOODON:03420140 synonym: "apple juice" EXACT [] -xref: SUBSET_SIREN:F1419 +xref: https://bioregistry.io/reference/siren\:F1419 is_a: FOODON:00001140 ! fruit juice food product is_a: FOODON:00001611 ! apple food product intersection_of: FOODON:00001140 ! fruit juice food product intersection_of: FOODON:00001611 ! apple food product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Apple_juice xsd:anyURI -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:00001060 @@ -399,9 +410,9 @@ is_a: FOODON:00001260 ! beer beverage [Term] id: FOODON:00001065 name: blue cheese food product -comment: SIREN DB annotation:\n* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151)\n* derives from 'curd' (http://purl.obolibrary.org/obo/FOODON_03420245)\n* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)\n* formed as a result of 'interior mold curing process' (http://purl.obolibrary.org/obo/FOODON_03460331) -subset: subset_siren -xref: SUBSET_SIREN:F1128 +def: "A class of cow's milk, sheep's milk, or goat's milk cheeses that have had Penicillium cultures added so that the final product is spotted or veined throughout with blue, blue-gray or blue-green mould, and carries a distinct smell." [Wikipedia:Blue_cheese] +comment: SIREN DB annotation:\n* solid FOODON:03430151\n* curd FOODON:03420245\n* curing or aging process FOODON:03460253\n* interior mold curing process FOODON:03460331 +xref: https://bioregistry.io/reference/siren\:F1128 is_a: FOODON:00001013 ! cheese food product property_value: IAO:0000114 IAO:0000122 property_value: seeAlso https://en.wikipedia.org/wiki/List_of_blue_cheeses xsd:anyURI @@ -409,6 +420,7 @@ property_value: seeAlso https://en.wikipedia.org/wiki/List_of_blue_cheeses xsd:a [Term] id: FOODON:00001067 name: buttermilk food product +def: "The liquid left over after producing butter from cream during the churning process." [Wikipedia:Buttermilk] is_a: FOODON:00001107 ! bovine dairy food product property_value: IAO:0000114 IAO:0000428 @@ -421,9 +433,8 @@ is_a: FOODON:00001258 ! food (fermented) id: FOODON:00001070 name: miso food product def: "A food produced by fermenting rice, barley and/or soybeans, with salt and the mold koji-kin (Aspergillus oryzae)." [] -comment: SIREN DB annotation:\n* has quality 'semisolid' (http://purl.obolibrary.org/obo/FOODON_03430144)\n* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014)\n* derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133)\n* formed as a result of 'fermentation/modification process, multiple component' (http://purl.obolibrary.org/obo/FOODON_03460128)\n* formed as a result of 'salted' (http://purl.obolibrary.org/obo/FOODON_03460173)\n* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)\n* formed as a result of 'preservation by fermentation' (http://purl.obolibrary.org/obo/FOODON_03470104) -subset: subset_siren -xref: SUBSET_SIREN:F1971 +comment: SIREN DB annotation:\n* semisolid FOODON:03430144\n* fully heat-treated FOODON:03440014\n* seed, skin present, germ present FOODON:03420133\n* fermentation/modification process, multiple component FOODON:03460128\n* salted FOODON:03460173\n* curing or aging process FOODON:03460253\n* preservation by fermentation FOODON:03470104 +xref: https://bioregistry.io/reference/siren\:F1971 is_a: FOODON:00001078 ! fermented soybean food product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string @@ -440,12 +451,14 @@ property_value: IAO:0000119 https://en.wikipedia.org/wiki/Must#Winemaking xsd:st [Term] id: FOODON:00001073 name: vinegar food product +def: "A liquid produced from the fermentation of ethanol in a process that yields its key ingredient, acetic acid." [Wikipedia:Vinegar] is_a: FOODON:00001133 ! condiment food product is_a: FOODON:00001258 ! food (fermented) [Term] id: FOODON:00001074 name: barley malt vinegar +def: "Vinegar is made by malting barley, causing the starch in the grain to turn to maltose." [Wikipedia:Malt_vinegar#Malt] is_a: FOODON:00001191 ! barley food product is_a: FOODON:00001919 ! grain based vinegar food product intersection_of: FOODON:00001073 ! vinegar food product @@ -479,7 +492,7 @@ property_value: IAO:0000114 IAO:0000122 id: FOODON:00001079 name: food (pickled) def: "A food preserved by soaking and storing it in vinegar or brine." [] -comment: SIREN DB annotation:\n* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151)\n* formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190) +comment: SIREN DB annotation:\n* solid FOODON:03430151\n* pickling process FOODON:03460190 subset: subset_siren synonym: "pickled" EXACT [] xref: SUBSET_SIREN:F1302 @@ -496,6 +509,7 @@ is_a: FOODON:00001051 ! fermented rice beverage [Term] id: FOODON:00001081 name: Bondon cheese food product +def: "A soft cheese made with cow's milk. It has a creamy paste and a greyish-red and downy white penicillin rind and is sometimes foil-wrapped." [http://www.whatamieating.com/?b=1&d=1&t=main&s=bondon&r=All] is_a: FOODON:00001127 ! cow milk cheese [Term] @@ -511,6 +525,7 @@ is_a: FOODON:00001133 ! condiment food product [Term] id: FOODON:00001086 name: kefir food product +def: "A fermented milk drink made from milk. It is prepared by inoculating cow, goat, or sheep's milk with kefir grains, a combination of bacteria and yeasts in a matrix of proteins, lipids, and sugars. This symbiotic matrix forms \"grains\" that resemble cauliflower. Many different bacteria and yeasts are found in the kefir grains, which are a complex and highly variable community of micro-organisms termed probiotics." [Wikipedia:Kefir] is_a: FOODON:03303909 ! cultured dairy product [Term] @@ -521,7 +536,7 @@ is_a: FOODON:03310387 ! oil is_a: FOODON:03460263 ! vegetable fat or oil property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Vegetable_fats_and_oils +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Vegetable_fats_and_oils [Term] id: FOODON:00001088 @@ -531,19 +546,19 @@ comment: Food-grade flaxseed oil is cold-pressed, obtained without solvent extra synonym: "flax oil" EXACT [] synonym: "flax seed oil" EXACT [] synonym: "linseed oil" EXACT [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=H0852 +xref: langual:H0852 is_a: FOODON:00001859 ! flaxseed food product is_a: FOODON:03420307 ! seed oil -property_value: http://purl.org/dc/elements/1.1/date 2019-09-19T21:51:42Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-09-19T21:51:42Z xsd:dateTime property_value: IAO:0000117 http://orcid.org/0000-0002-8844-9165 property_value: IAO:0000119 "Nutritional_supplement_and_food" -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:00001089 -name: corn flour food product -is_a: FOODON:00001056 ! flour food product +name: milled corn food product +def: "A food product made from milling corn." [] is_a: FOODON:00001142 ! maize (corn) food product +is_a: FOODON:00004509 ! milled food product [Term] id: FOODON:00001090 @@ -574,17 +589,15 @@ is_a: FOODON:00001173 ! plant seed food product [Term] id: FOODON:00001094 name: fermented beverage -comment: SIREN DB annotation:\n* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)\n* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)\n* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)\n -subset: subset_siren +comment: SIREN DB annotation:\n* liquid FOODON:03430130\n* microbial/enzymatic modification process FOODON:03460119\n* curing or aging process FOODON:03460253 synonym: "alcoholic beverage" EXACT [] -xref: SUBSET_SIREN:F5644 +xref: https://bioregistry.io/reference/siren\:F5644 is_a: FOODON:00001258 ! food (fermented) is_a: FOODON:03301977 ! beverage food product intersection_of: FOODON:00001258 ! food (fermented) intersection_of: FOODON:03301977 ! beverage food product -property_value: http://purl.org/dc/elements/1.1/date 2019-06-11T07:25:19Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-06-11T07:25:19Z xsd:dateTime property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:00001096 @@ -613,16 +626,14 @@ is_a: FOODON:00001157 ! pomaceous fruit juice beverage [Term] id: FOODON:00001100 name: orange fruit beverage -comment: SIREN DB annotation:\n* has quality 'liquid, low viscosity' (http://purl.obolibrary.org/obo/FOODON_03430109)\n* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200)\n* has substance added 'water addition process' (http://purl.obolibrary.org/obo/FOODON_03460148)\n* has substance added 'sweetener added' (http://purl.obolibrary.org/obo/FOODON_03460202)\n* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227)\n -subset: subset_siren -xref: SUBSET_SIREN:F2385 +comment: SIREN DB annotation:\n* liquid, low viscosity FOODON:03430109\n* acidified FOODON:03460200\n* ingredient: water addition process FOODON:03460148\n* ingredient: sweetener added FOODON:03460202\n* ingredient: flavoring, spice or herb added FOODON:03460227 +xref: https://bioregistry.io/reference/siren\:F2385 is_a: FOODON:00001156 ! citrus fruit juice is_a: FOODON:00002071 ! orange food product intersection_of: FOODON:00001156 ! citrus fruit juice intersection_of: FOODON:00002071 ! orange food product -property_value: http://purl.org/dc/elements/1.1/date 2019-06-20T07:47:47Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-06-20T07:47:47Z xsd:dateTime property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:00001102 @@ -649,7 +660,7 @@ is_a: FOODON:00001250 ! fish egg food product id: FOODON:00001105 name: avian egg food product def: "A food product made from an avian egg." [] -is_a: FOODON:00001251 ! avian food product +is_a: FOODON:00001251 ! avian animal food product is_a: FOODON:00001274 ! egg food product property_value: IAO:0000114 IAO:0000122 @@ -805,7 +816,11 @@ is_a: FOODON:03315552 ! juice beverage [Term] id: FOODON:00001141 name: wheat food product +comment: SIREN DB annotation:\n* seed (anatomical part) FOODON:03420155 +xref: https://bioregistry.io/reference/siren\:F10142 is_a: FOODON:00001093 ! cereal grain food product +property_value: http://purl.org/dc/terms/date 2023-05-03T04:59:00Z xsd:dateTime +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 [Term] id: FOODON:00001142 @@ -843,7 +858,7 @@ id: FOODON:00001149 name: confectionery food product def: "Food items that are rich in sugar, any one or type of which is called a confection. Modern usage may include substances rich in artificial sweeteners as well." [] is_a: FOODON:00002373 ! food product by meal type -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Confectionery +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Confectionery [Term] id: FOODON:00001150 @@ -882,7 +897,6 @@ property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: FOODON:00001155 name: obsolete: watermelon plant -property_value: IAO:0000412 http://langual.org xsd:string is_obsolete: true replaced_by: NCBITaxon:3654 @@ -983,7 +997,7 @@ is_a: FOODON:00001169 ! cruciferous food product [Term] id: FOODON:00001172 name: nut food product -xref: SUBSET_SIREN:F16972 +xref: https://bioregistry.io/reference/siren\:F16972 is_a: FOODON:00001262 ! botanical fruit food product is_a: FOODON:03460177 ! plant seed or nut food product property_value: IAO:0000114 IAO:0000122 @@ -1014,6 +1028,7 @@ is_a: FOODON:00004242 ! animal food product [Term] id: FOODON:00001177 name: insect food product +def: "A food product with insects as a defining ingredient." [] is_a: FOODON:00001176 ! invertebrate animal food product [Term] @@ -1029,16 +1044,20 @@ id: FOODON:00001180 name: prepared food product def: "Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked." [] synonym: "prepared" BROAD [] -is_a: FOODON:00001002 ! food product +is_a: FOODON:03311737 ! processed food product property_value: IAO:0000119 langual:thesaurus.asp?termid=A0172 +property_value: seeAlso https://www.fns.usda.gov/snap/retailer-eligibility-prepared-foods-and-heated-foods [Term] id: FOODON:00001181 name: food (cooked) +def: "A food product which is an output of a food cooking process." [] synonym: "cooked" EXACT [] is_a: FOODON:00002645 ! food product by process +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Cooking xsd:string [Term] id: FOODON:00001182 @@ -1049,17 +1068,16 @@ is_a: FOODON:00002333 ! vegetable pickle food product [Term] id: FOODON:00001183 name: bread food product +def: "A staple food prepared from a dough of flour (usually wheat) and water, usually by baking" [] is_a: FOODON:00002456 ! food (baked) -is_a: FOODON:00003395 ! multi-component wheat food product +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Bread [Term] id: FOODON:00001184 name: algal food product def: "This food product type includes food products which are derived from a large, diverse group of photosynthetic organisms." [] -subset: subset_siren -xref: SUBSET_SIREN:F10419 +xref: https://bioregistry.io/reference/siren\:F10419 is_a: FOODON:00002381 ! food product by organism -property_value: IAO:0000412 http://langual.org xsd:string property_value: seeAlso https://ungc-communications-assets.s3.amazonaws.com/docs/publications/The-Seaweed-Manifesto.pdf [Term] @@ -1087,6 +1105,7 @@ replaced_by: http://purl.obolibrary.org/obo/FOODON_00002038 [Term] id: FOODON:00001189 name: oat food product +def: "A food product made from oats." [] synonym: "common oat food product" EXACT [] is_a: FOODON:00001093 ! cereal grain food product @@ -1103,6 +1122,7 @@ is_a: FOODON:00001093 ! cereal grain food product [Term] id: FOODON:00001192 name: quinoa food product +def: "A food product made from quinoa" [] is_a: FOODON:00001093 ! cereal grain food product [Term] @@ -1130,13 +1150,13 @@ replaced_by: http://purl.obolibrary.org/obo/FOODON_00001997 [Term] id: FOODON:00001196 -name: pigeon pea (whole, dried) +name: pigeon pea (dried) def: "A product of the dry seeds of Cajanus cajan." [] -is_a: FOODON:00001194 ! dry pea food product -is_a: FOODON:00002752 ! bean (whole, dried) -is_a: FOODON:00002781 ! pigeon pea (whole) -intersection_of: FOODON:00002752 ! bean (whole, dried) -intersection_of: FOODON:00002781 ! pigeon pea (whole) +is_a: FOODON:00001209 ! pulse food product +is_a: FOODON:00002752 ! bean (dried) +is_a: FOODON:00002781 ! pigeon pea +intersection_of: FOODON:00002752 ! bean (dried) +intersection_of: FOODON:00002781 ! pigeon pea property_value: IAO:0000119 http://en.wikipedia.org/wiki/Legume xsd:anyURI [Term] @@ -1157,14 +1177,14 @@ property_value: IAO:0000119 https://en.wikipedia.org/wiki/Vigna_subterranea xsd: [Term] id: FOODON:00001198 -name: broad bean (whole, dried) +name: broad bean (dried) def: "A product of the dry seeds of plants of the genus Vicia." [] synonym: "dried fava bean" EXACT [] -is_a: FOODON:00001209 ! pulse food product -is_a: FOODON:00002752 ! bean (whole, dried) -is_a: FOODON:03301227 ! broad bean (whole) -intersection_of: FOODON:00002752 ! bean (whole, dried) -intersection_of: FOODON:03301227 ! broad bean (whole) +is_a: FOODON:00001203 ! vetch seed (dried) +is_a: FOODON:00002752 ! bean (dried) +is_a: FOODON:03301227 ! broad bean +intersection_of: FOODON:00002752 ! bean (dried) +intersection_of: FOODON:03301227 ! broad bean property_value: IAO:0000116 http://en.wikipedia.org/wiki/Legume xsd:string [Term] @@ -1176,7 +1196,7 @@ synonym: "Egyptian pea" NARROW [] synonym: "garbanzo bean food product" EXACT [] synonym: "gram" NARROW [] is_a: FOODON:00001209 ! pulse food product -is_a: FOODON:03301467 ! bean substance +is_a: FOODON:03301467 ! bean (whole or pieces) property_value: IAO:0000119 http://en.wikipedia.org/wiki/Legume xsd:string [Term] @@ -1205,20 +1225,19 @@ property_value: seeAlso http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef0 [Term] id: FOODON:00001202 name: winged bean food product -def: "The winged bean food category covers beans of the winged bean plant" [] +def: "A bean food product which derives from a winged bean plant (Psophocarpus tetragonolobus)." [] is_a: FOODON:00001635 ! bean food product -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Winged_bean xsd:anyURI +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-8844-9165 xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Winged_bean xsd:string [Term] id: FOODON:00001203 -name: vetch seed (whole, dried) +name: vetch seed (dried) def: "A product of the dry seeds of Vicia sativa." [] is_a: FOODON:00001209 ! pulse food product -is_a: FOODON:00002791 ! vetch seed (whole) +is_a: FOODON:00002791 ! vetch seed is_a: FOODON:03307539 ! food (dried) -intersection_of: FOODON:00002791 ! vetch seed (whole) +intersection_of: FOODON:00002791 ! vetch seed intersection_of: FOODON:03307539 ! food (dried) [Term] @@ -1234,35 +1253,37 @@ property_value: IAO:0000119 https://en.wikipedia.org/wiki/Pachyrhizus_erosus xsd [Term] id: FOODON:00001205 -name: velvet bean (whole, dried) +name: velvet bean (dried) def: "A product of the dry seeds of Mucuna pruriens var. utilis." [] is_a: FOODON:00001209 ! pulse food product -is_a: FOODON:00002752 ! bean (whole, dried) -is_a: FOODON:00002786 ! velvet bean (whole) -intersection_of: FOODON:00002752 ! bean (whole, dried) -intersection_of: FOODON:00002786 ! velvet bean (whole) +is_a: FOODON:00002752 ! bean (dried) +is_a: FOODON:00002786 ! velvet bean +intersection_of: FOODON:00002752 ! bean (dried) +intersection_of: FOODON:00002786 ! velvet bean property_value: IAO:0000119 http://en.wikipedia.org/wiki/Legume xsd:anyURI [Term] id: FOODON:00001206 name: lupin seed food product +def: "A product of the dry seeds of Lupinus spp." [http://en.wikipedia.org/wiki/Pulse_%28legume%29] is_a: FOODON:00001209 ! pulse food product is_a: FOODON:00002012 ! lupine bean food product [Term] id: FOODON:00001207 -name: jack bean (whole, dried) +name: jack bean (dried) def: "A dry seed of the jack-bean plant." [] is_a: FOODON:00001209 ! pulse food product -is_a: FOODON:00002752 ! bean (whole, dried) -is_a: FOODON:00002778 ! jack bean (whole) -intersection_of: FOODON:00002752 ! bean (whole, dried) -intersection_of: FOODON:00002778 ! jack bean (whole) +is_a: FOODON:00002752 ! bean (dried) +is_a: FOODON:00002778 ! jack bean +intersection_of: FOODON:00002752 ! bean (dried) +intersection_of: FOODON:00002778 ! jack bean property_value: IAO:0000119 http://en.wikipedia.org/wiki/Legume xsd:anyURI [Term] id: FOODON:00001208 name: hyacinth bean food product +def: "A product of the dry seeds of Lablab purpureus." [http://en.wikipedia.org/wiki/Pulse_%28legume%29] is_a: FOODON:00001209 ! pulse food product is_a: FOODON:00001635 ! bean food product @@ -1287,11 +1308,14 @@ is_a: FOODON:00001141 ! wheat food product [Term] id: FOODON:00001211 name: pasta food product -is_a: FOODON:00001141 ! wheat food product +def: "A food made from an unleavened dough of wheat or buckwheat flour and water, sometimes with other ingredients such as eggs and vegetable extracts." [] +is_a: FOODON:03311737 ! processed food product +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Pasta [Term] id: FOODON:00001212 name: pastry food product +def: "A pastry food product is a food product containing a pastry component. The food may be ready for consumption or may require further cooking." [http://en.wikipedia.org/wiki/Pastry] is_a: FOODON:00002125 ! plant based bakery food product is_a: FOODON:00003395 ! multi-component wheat food product @@ -1302,7 +1326,7 @@ def: "A confection made from a concentrated solution of sugar in water, to which is_a: FOODON:00001149 ! confectionery food product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Candy +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Candy [Term] id: FOODON:00001215 @@ -1314,7 +1338,8 @@ is_a: FOODON:00001173 ! plant seed food product [Term] id: FOODON:00001216 name: cream food product -xref: LANGUAL:C0195 +def: "A dairy product that is composed of the higher-butterfat layer skimmed from the top of milk before homogenization." [http://en.wikipedia.org/wiki/Cream] +xref: langual:thesaurus.asp?termid=C0195 is_a: FOODON:00001257 ! milk or milk based food product property_value: hasSynonym "sweet cream" xsd:string property_value: IAO:0000114 IAO:0000428 @@ -1322,33 +1347,40 @@ property_value: IAO:0000114 IAO:0000428 [Term] id: FOODON:00001217 name: mammalian milk beverage +def: "An opague white dairy product produced by the mammary glands of female mammals." [http://en.wikipedia.org/wiki/Milk] is_a: FOODON:00001252 ! animal derived beverage is_a: FOODON:03315150 ! mammalian milk product [Term] id: FOODON:00001218 name: bee food product +def: "A food product with bees or bee substances as a defining ingredient." [] is_a: FOODON:00001177 ! insect food product [Term] id: FOODON:00001219 name: sausage (cooked, smoked) +def: "A sausage that is cooked and then smoked or smoke-cooked." [http://en.wikipedia.org/wiki/Sausage] is_a: FOODON:00001220 ! sausage (smoked) -is_a: FOODON:00001224 ! sausage (cooked) +is_a: FOODON:00001224 ! meat sausage (cooked) intersection_of: FOODON:00001220 ! sausage (smoked) -intersection_of: FOODON:00001224 ! sausage (cooked) +intersection_of: FOODON:00001224 ! meat sausage (cooked) [Term] id: FOODON:00001220 name: sausage (smoked) +def: "Sausage which is cured with a food smoking process." [] +xref: SUBSET_SIREN:F10756 is_a: FOODON:00001225 ! smoked meat food product -is_a: FOODON:03315904 ! sausage (whole) +is_a: FOODON:03315904 ! meat sausage intersection_of: FOODON:00001225 ! smoked meat food product -intersection_of: FOODON:03315904 ! sausage (whole) +intersection_of: FOODON:03315904 ! meat sausage +property_value: IAO:0000119 http://en.wikipedia.org/wiki/Sausage [Term] id: FOODON:00001221 name: sausage (raw, smoked) +def: "A raw sausage that is smoked." [http://en.wikipedia.org/wiki/Sausage] is_a: FOODON:00001220 ! sausage (smoked) is_a: FOODON:00001222 ! sausage (raw) intersection_of: FOODON:00001220 ! sausage (smoked) @@ -1358,29 +1390,30 @@ intersection_of: FOODON:00001222 ! sausage (raw) id: FOODON:00001222 name: sausage (raw) def: "A sausage made from meats that have not been previously cured." [] -xref: SUBSET_SIREN:F1113 -is_a: FOODON:03315904 ! sausage (whole) +xref: https://bioregistry.io/reference/siren\:F1113 +is_a: FOODON:03315904 ! meat sausage property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Sausage xsd:anyURI [Term] id: FOODON:00001223 -name: sausage (dried, fermented) +name: meat sausage (dried, fermented) def: "A cured sausage that is fermented and dried." [] -is_a: FOODON:03315904 ! sausage (whole) +is_a: FOODON:03315904 ! meat sausage property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Sausage xsd:anyURI [Term] id: FOODON:00001224 -name: sausage (cooked) +name: meat sausage (cooked) def: "A sausage made with fresh meats, and then fully cooked." [] +xref: SUBSET_SIREN:F10754 is_a: FOODON:00001181 ! food (cooked) -is_a: FOODON:03315904 ! sausage (whole) +is_a: FOODON:03315904 ! meat sausage property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Sausage +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Sausage [Term] id: FOODON:00001225 @@ -1390,24 +1423,29 @@ is_a: FOODON:00001039 ! cured meat food product [Term] id: FOODON:00001229 name: processed cheese food product +def: "A cheese product made from traditional cheese and emulsifying salts, often with the addition of milk, more salt, preservatives, and food coloring." [] is_a: FOODON:00001013 ! cheese food product is_a: FOODON:03311737 ! processed food product +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Cheese [Term] id: FOODON:00001230 name: mustard seed food product def: "A product made from the seeds of a mustard plant (white or yellow mustard, Sinapis hirta; brown or Indian mustard, Brassica juncea; or black mustard, Brassica nigra)." [] -is_a: FOODON:00001242 ! spice or herb +is_a: FOODON:00001173 ! plant seed food product is_a: FOODON:00002053 ! mustard food product +is_a: FOODON:03303380 ! spice food product [Term] id: FOODON:00001231 name: creamy salad dressing +def: "A salad dressing that is usually mayonnaise-based, but which may also contain yogurt, sour cream, or creme fraiche." [http://en.wikipedia.org/wiki/Salad_dressing#Dressings] is_a: FOODON:00001290 ! salad dressing [Term] id: FOODON:00001232 name: vinaigrette dressing food product +def: "A salad dressing that is an emulsion of a vegetable oil and vinegar, often flavored with herbs, spices, and other ingredients." [http://en.wikipedia.org/wiki/Vinaigrette] is_a: FOODON:00001290 ! salad dressing [Term] @@ -1418,11 +1456,13 @@ is_a: FOODON:00001087 ! vegetable oil food product [Term] id: FOODON:00001234 name: mayonnaise food product +def: "A stable emulsion of oil, and vinegar or lemon juice, with many options for embellishment with other herbs and spices. Egg yolk is the traditional emulsifier." [http://en.wikipedia.org/wiki/Mayonnaise] is_a: FOODON:00001231 ! creamy salad dressing [Term] id: FOODON:00001235 name: soy sauce food product +def: "A condiment produced by fermenting soybeans with Aspergillus oryzae and Aspergillus soyae molds along with roasted grain, water, and salt." [http://en.wikipedia.org/wiki/Soy_sauce] is_a: FOODON:00001078 ! fermented soybean food product is_a: FOODON:00002262 ! soybean condiment @@ -1437,12 +1477,15 @@ intersection_of: FOODON:00001038 ! pork meat food product [Term] id: FOODON:00001242 name: spice or herb +def: "A food product that has some spice or herb as a defining ingredient." [] def: "A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment." [] -synonym: "herb and spice" EXACT [] synonym: "herb or spice" EXACT [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=H0151 +xref: langual:thesaurus.asp?termid=H0151 is_a: FOODON:00001015 ! plant food product -is_a: FOODON:00001133 ! condiment food product +union_of: FOODON:00003042 ! herb food product +union_of: FOODON:03303380 ! spice food product +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 xsd:string +property_value: http://purl.org/dc/terms/date 2023-08-16T10:14:35Z xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000119 http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef10e.htm#1.01 xsd:anyURI @@ -1460,7 +1503,7 @@ def: "A brewed drink prepared from roasted seeds, commonly called coffee beans, is_a: FOODON:00001139 ! coffee based beverage product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Coffee +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Coffee [Term] id: FOODON:00001245 @@ -1469,16 +1512,18 @@ def: "A beverage prepared from the cured leaves of Camellia sinensis by combinat is_a: FOODON:00001138 ! tea based beverage product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Tea +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Tea [Term] id: FOODON:00001246 name: hot chocolate food product +def: "A heated beverage typically consisting of shaved chocolate or cocoa powder, heated milk or water, and sugar." [http://en.wikipedia.org/wiki/Hot_chocolate] is_a: FOODON:00001255 ! nonfermented plant derived beverage product [Term] id: FOODON:00001247 name: mate food product +def: "A beverage prepated by steeping dry leaves (and twigs) of yerba mate in hot water." [http://en.wikipedia.org/wiki/Yerba_Mate] is_a: FOODON:00001255 ! nonfermented plant derived beverage product [Term] @@ -1498,8 +1543,12 @@ is_a: FOODON:03315173 ! fish product (unspecified species) [Term] id: FOODON:00001251 -name: avian food product +name: avian animal food product +def: "A food product that is derived from some avian animal." [] is_a: FOODON:00001092 ! vertebrate animal food product +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 xsd:string +property_value: http://purl.org/dc/terms/date 2024-06-27T22:43:12Z xsd:dateTime +property_value: IAO:0000114 IAO:0000122 [Term] id: FOODON:00001252 @@ -1510,6 +1559,7 @@ is_a: FOODON:03301977 ! beverage food product [Term] id: FOODON:00001253 name: plant derived beverage +def: "A beverage derived from plants." [] is_a: FOODON:00001015 ! plant food product is_a: FOODON:03301977 ! beverage food product @@ -1532,7 +1582,7 @@ name: dairy food product def: "A dairy food product has mammilian milk or a milk component as an ingredient." [] synonym: "dairy product" EXACT [] synonym: "milk product" EXACT [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=H0242 +xref: langual:thesaurus.asp?termid=H0242 is_a: FOODON:00001092 ! vertebrate animal food product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string @@ -1567,21 +1617,21 @@ property_value: IAO:0000119 https://en.wikipedia.org/wiki/Beer xsd:anyURI [Term] id: FOODON:00001261 name: vegetable food product -def: "Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food." [] +def: "A plant food product which derives from one or more vegetables." [] +comment: FAO definition for vegetable: "Vegetables are plants cultivated both as field crops and garden crops, both in the open and under glass." and also: "Vegetables are grouped according to botanic characteristics as follows: leafy or stem vegetables (e.g., cabbage); fruit-bearing vegetables (e.g., melons); flower vegetables (e.g., cauliflowers); root, bulb and tuberous vegetables (e.g., onion); leguminous vegetables (e.g., green peas); other vegetables (e.g., green maize and mushrooms)." is_a: FOODON:00001015 ! plant food product -property_value: IAO:0000119 "7.01" +property_value: seeAlso https://www.fao.org/economic/the-statistics-division-ess/methodology/methodology-systems/crops-statistics-concepts-definitions-and-classifications/en/ [Term] id: FOODON:00001262 name: botanical fruit food product +def: "Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits." [http://eurovoc.europa.eu/drupal/?q=request&uri=http\://eurovoc.europa.eu/1115, http://oek1.fao.org/skosmos/agrovoc/en/page/c_3119, http://www.fao.org/pollination/resources/glossary/en/, https://en.wikipedia.org/wiki/Fruit] is_a: FOODON:00001015 ! plant food product [Term] id: FOODON:00001264 name: legume food product def: "A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995)" [] -synonym: "http://purl.obolibrary.org/obo/FOODON_03411254" NARROW [] -synonym: "http://purl.obolibrary.org/obo/FOODON_03411338" NARROW [] synonym: "legume" EXACT [] is_a: FOODON:00001262 ! botanical fruit food product property_value: IAO:0000119 http://www.fao.org/pollination/resources/glossary/en/ xsd:anyURI @@ -1601,14 +1651,15 @@ is_a: FOODON:00001121 ! equine milk beverage [Term] id: FOODON:00001274 name: egg food product +def: "A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves." [Wikipedia:Egg_%28food%29] comment: Regarding American regulatory aspects of egg products, see this summary:\nhttps://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-graphic-000077 is_a: FOODON:00001092 ! vertebrate animal food product [Term] id: FOODON:00001275 -name: hen egg food product -def: "A hen egg food product is any food product consisting mainly of hen eggs or derivatives." [] -xref: SUBSET_SIREN:F1074 +name: chicken egg food product +def: "An avian egg food product having chicken eggs or derivatives as a defining ingredient." [] +xref: https://bioregistry.io/reference/siren\:F1074 is_a: FOODON:00001105 ! avian egg food product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Egg_as_food xsd:anyURI @@ -1630,6 +1681,7 @@ is_a: FOODON:00001001 ! orange juice (liquid) [Term] id: FOODON:00001278 name: cake food product +def: "A food that is usually sweet and often baked. Cakes normally combine some kind of flour, a sweetening agent (commonly sugar), a binding agent (generally egg, though gluten or starch are often used by lacto-vegetarians and vegans), fats (usually butter, shortening, or margarine, although a fruit puree such as applesauce is sometimes substituted to avoid using fat), a liquid (milk, water or fruit juice), flavors and some form of leavening agent (such as yeast or baking powder), though many cakes lack these ingredients and instead rely on air bubbles in the dough to expand and cause the cake to rise. Cake is often frosted with buttercream or marzipan, and finished with piped borders and crystallized fruit." [Wikipedia:Cake] is_a: FOODON:00001626 ! bakery food product [Term] @@ -1656,30 +1708,37 @@ property_value: seeAlso https://en.wikipedia.org/wiki/List_of_custard_desserts [Term] id: FOODON:00001282 -name: ground beef food product -def: "A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese." [] +name: beef (ground) +def: "Beef that has been ground." [] +comment: A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese. synonym: "beef mince" EXACT [] synonym: "ground beef" EXACT [] synonym: "hamburger meat" EXACT [] synonym: "minced beef" EXACT [] -is_a: FOODON:00001041 ! beef food product +is_a: FOODON:00001041 ! cow food product +is_a: FOODON:02000412 ! piece(s) of beef property_value: http://schema.org/image https://upload.wikimedia.org/wikipedia/commons/thumb/d/d1/Hackfleisch-1.jpg/631px-Hackfleisch-1.jpg property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000119 Ground:beef +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Ground_beef xsd:string [Term] id: FOODON:00001283 name: poultry food product def: "A food product from a category of domestic birds kept for meat, eggs, and feathers including fowl such as chickens, turkeys, and waterfowls such as domestic ducks and geese and other meat birds such as pigeons and doves and games birds including pheasants." [] -is_a: FOODON:00001251 ! avian food product +def: "A food product that is derived from some poultry." [] +is_a: FOODON:00001251 ! avian animal food product +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 xsd:string +property_value: http://purl.org/dc/terms/date 2024-06-27T22:43:12Z xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Poultry property_value: IAO:0000119 Wikipedia:Poultry [Term] id: FOODON:00001284 name: duck meat food product is_a: FOODON:00001131 ! poultry meat food product +is_a: FOODON:02020114 ! duck food product [Term] id: FOODON:00001285 @@ -1745,7 +1804,7 @@ def: "A family of hard Italian cheeses made from sheep milk." [] is_a: FOODON:00001130 ! sheep milk cheese food product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000119 http://en.wikipedia.org/wiki/Pecorino +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Pecorino [Term] id: FOODON:00001296 @@ -1781,14 +1840,6 @@ id: FOODON:00001626 name: bakery food product is_a: FOODON:00002645 ! food product by process -[Term] -id: FOODON:00001632 -name: barley flour food product -is_a: FOODON:00001056 ! flour food product -is_a: FOODON:00001191 ! barley food product -intersection_of: FOODON:00001056 ! flour food product -intersection_of: FOODON:00001191 ! barley food product - [Term] id: FOODON:00001635 name: bean food product @@ -1797,9 +1848,9 @@ is_a: FOODON:00001264 ! legume food product is_a: FOODON:00002153 ! plant seed vegetable food product property_value: IAO:0000116 "Note, this was previously labelled \"Bean (vegetable) food product\". We have been listing both dry and freshly harvested moist beans here, so have broadened the name scope." xsd:string property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: seeAlso http://purl.obolibrary.org/obo/FOODON_00002428 xsd:anyURI -property_value: seeAlso http://www.fao.org/es/faodef/fdef04e.htm#4.02 xsd:anyURI -property_value: seeAlso https://oconto.extension.wisc.edu/files/2011/02/The-Importance-of-Dry-Beans-in-Your-Diet.pdf xsd:string +property_value: seeAlso "4.02" +property_value: seeAlso FOODON:00002428 +property_value: seeAlso https://oconto.extension.wisc.edu/files/2011/02/The-Importance-of-Dry-Beans-in-Your-Diet.pdf [Term] id: FOODON:00001640 @@ -1826,9 +1877,9 @@ intersection_of: FOODON:03301444 ! vegetable juice food product id: FOODON:00001696 name: cattle cured meat food product is_a: FOODON:00001039 ! cured meat food product -is_a: FOODON:00001041 ! beef food product +is_a: FOODON:00001041 ! cow food product intersection_of: FOODON:00001039 ! cured meat food product -intersection_of: FOODON:00001041 ! beef food product +intersection_of: FOODON:00001041 ! cow food product [Term] id: FOODON:00001714 @@ -1891,6 +1942,7 @@ is_a: FOODON:00001173 ! plant seed food product [Term] id: FOODON:00001867 name: food dressing product +def: "A mix or ready made sauce for dipping or adding to food, especially salad." [] is_a: FOODON:00001714 ! food product component [Term] @@ -1919,14 +1971,6 @@ id: FOODON:00001919 name: grain based vinegar food product is_a: FOODON:00001073 ! vinegar food product -[Term] -id: FOODON:00001994 -name: leguminous vegetable food product -def: "A food product made from legumes that are considered vegetables, such as immature raw legume pods or seeds." [] -is_a: FOODON:00001264 ! legume food product -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Damion Dooley" xsd:string - [Term] id: FOODON:00002012 name: lupine bean food product @@ -1964,17 +2008,6 @@ id: FOODON:00002071 name: orange food product is_a: FOODON:00001151 ! citrus fruit food product -[Term] -id: FOODON:00002115 -name: pigeon pea vegetable food product -def: "A product containing primarily immature ripe pigeon peas." [] -is_a: FOODON:00001994 ! leguminous vegetable food product -is_a: FOODON:00002780 ! pigeon pea food product -is_a: FOODON:00002813 ! pea food product -property_value: http://purl.org/dc/elements/1.1/date 2019-07-14T10:26:00 xsd:dateTime -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "Damion Dooley" xsd:string - [Term] id: FOODON:00002125 name: plant based bakery food product @@ -2042,7 +2075,8 @@ is_a: FOODON:00001261 ! vegetable food product [Term] id: FOODON:00002156 -name: plant stem or spear vegetable food product +name: plant stem or spear food product +def: "A food product deriving from a plant stem or spear part." [] is_a: FOODON:00001175 ! plant stem food product is_a: FOODON:00001261 ! vegetable food product intersection_of: FOODON:00001175 ! plant stem food product @@ -2064,16 +2098,16 @@ property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: FOODON:00002165 name: organ meat product -is_a: FOODON:03317170 ! meat (whole or parts) +is_a: FOODON:03317170 ! meat (whole or pieces) [Term] id: FOODON:00002175 -name: prepared hen egg product +name: prepared chicken egg product def: "A prepared hen egg product is a product predominantly made of hen egg that has been cooked and may only require defrosting or reheating for consumption." [] is_a: FOODON:00001180 ! prepared food product -is_a: FOODON:00001275 ! hen egg food product +is_a: FOODON:00001275 ! chicken egg food product intersection_of: FOODON:00001180 ! prepared food product -intersection_of: FOODON:00001275 ! hen egg food product +intersection_of: FOODON:00001275 ! chicken egg food product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: seeAlso https://www.eggnutritioncenter.org/articles/nutritional-benefits-cooked-vs-raw-eggs/ @@ -2123,9 +2157,9 @@ is_a: FOODON:00001253 ! plant derived beverage [Term] id: FOODON:00002300 name: sweetener food product +xref: langual:thesaurus.asp?termid=H0202 is_a: FOODON:00001133 ! condiment food product is_a: FOODON:00001857 ! food flavoring or seasoning product -replaced_by: http://www.langual.org/langual_thesaurus.asp?termid=H0202 [Term] id: FOODON:00002301 @@ -2146,6 +2180,7 @@ intersection_of: FOODON:03301444 ! vegetable juice food product [Term] id: FOODON:00002333 name: vegetable pickle food product +def: "A vegetable food product containing one or more pickled vegetables." [] is_a: FOODON:00001079 ! food (pickled) is_a: FOODON:00001261 ! vegetable food product @@ -2179,7 +2214,6 @@ synonym: "foodstuff" EXACT [] synonym: "nourishment" EXACT [] synonym: "sustenance" EXACT [] property_value: IAO:0000119 https://en.wikipedia.org/wiki/Food -property_value: IAO:0000412 http://purl.obolibrary.org/obo/envo.owl [Term] id: FOODON:00002423 @@ -2196,9 +2230,10 @@ intersection_of: FOODON:00002501 ! multi-component food product [Term] id: FOODON:00002454 -name: food product by quality -def: "A class which contains food product categories qualified by a quality such as granularity or temperature, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like \"food (frozen)\" are both a quality descriptor and the output of a process." [] -is_a: FOODON:00001002 ! food product +name: food material by characteristic +def: "Food material which has been categorized by a characteristic such as granularity or temperature." [] +comment: This term was renamed from "food product by quality" to align better with COB "characteristic" label, and as well to disambiguate from other use of "quality" as a food grading. This term is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. +is_a: FOODON:00002403 ! food material property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string @@ -2216,7 +2251,7 @@ def: "A food product consisting of food material derived from ingredients source comment: The definition of this is being discussed in issue: https://github.com/FoodOntology/foodon/issues/57\n\nNamely, how to characterize the threshold of ingredients that make for multi-component classification? Salt, pepper, spices wouldn't normally make a food multi-component? is_a: FOODON:00001002 ! food product property_value: hasSynonym "multi-ingredient" xsd:string -property_value: http://purl.org/dc/elements/1.1/date 2019-01-23T22:40:32Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-01-23T22:40:32Z xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string @@ -2226,8 +2261,8 @@ name: food (dehydrated) def: "A preserved food, where the moisture levels in the food product have been reduced to low levels to improve shelf life." [] is_a: FOODON:00002158 ! food (preserved) property_value: hasSynonym "food (dessicated)" xsd:string -property_value: http://purl.org/dc/elements/1.1/contributor "https://orcid.org/0000-0002-8844-9165 | https://orcid.org/0000-0001-5193-0062 | https://orcid.org/0000-0001-8008-8249" xsd:string -property_value: http://purl.org/dc/elements/1.1/date 2019-05-23T19:53:09Z xsd:dateTime +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-8844-9165 | https://orcid.org/0000-0001-5193-0062 | https://orcid.org/0000-0001-8008-8249" xsd:string +property_value: http://purl.org/dc/terms/date 2019-05-23T19:53:09Z xsd:dateTime property_value: IAO:0000114 "requires discussion" xsd:string property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000119 https://www.sciencedirect.com/topics/food-science/food-dehydration xsd:string @@ -2237,15 +2272,19 @@ id: FOODON:00002645 name: food product by process def: "A food product organized by the process which it results from." [] is_a: FOODON:00001002 ! food product -property_value: http://purl.org/dc/elements/1.1/date 2019-05-23T23:02:07Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-05-23T23:02:07Z xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: FOODON:00002663 +name: pig food product name: pork food product +def: "A food product that is derived from some pig." [] is_a: FOODON:00001132 ! swine food product -property_value: http://purl.org/dc/elements/1.1/date 2019-06-14T04:23:35Z xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 xsd:string +property_value: http://purl.org/dc/terms/date 2019-06-14T04:23:35Z xsd:dateTime +property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] @@ -2255,31 +2294,33 @@ def: "A lipid food product is a food product made primarily of plant or animal f synonym: "fats and oils" EXACT [] synonym: "oils and fats" EXACT [] is_a: FOODON:03420228 ! extract, concentrate or isolate of plant or animal -property_value: http://purl.org/dc/elements/1.1/date 2019-06-11T09:18:41Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-06-11T09:18:41Z xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: FOODON:00002752 -name: bean (whole, dried) +name: bean (dried) def: "A whole dried bean is a bean resulting from natural or mechanical air drying applied to a bean or bean pod." [] synonym: "dried bean" EXACT [] -is_a: FOODON:00002753 ! bean (whole) +is_a: FOODON:00002753 ! bean is_a: FOODON:03307539 ! food (dried) -intersection_of: FOODON:00002753 ! bean (whole) +intersection_of: FOODON:00002753 ! bean intersection_of: FOODON:03307539 ! food (dried) -property_value: http://purl.org/dc/elements/1.1/date 2019-06-29T14:48:10Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-06-29T14:48:10Z xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: seeAlso http://www.fao.org/es/faodef/fdef04e.htm#4.02 xsd:anyURI [Term] id: FOODON:00002753 -name: bean (whole) +name: bean def: "A seed of a bean plant from one of several genera of the flowering plant family (Fabaceae)." [] synonym: "bean" EXACT [] is_a: FOODON:00001635 ! bean food product -property_value: http://purl.org/dc/elements/1.1/date 2020-10-14T07:28:59 xsd:dateTime +is_a: FOODON:03310646 ! legume +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 xsd:string +property_value: http://purl.org/dc/terms/date 2020-10-14T07:28:59 xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "Damion Dooley's note. This could be enhanced to explicitly state the anatomical parts of a seed - seed coat, cotyledons, embryo etc. Currently the Plant Ontology is not explicit about this yet." xsd:string property_value: IAO:0000117 "Damion Dooley" xsd:string @@ -2289,21 +2330,21 @@ id: FOODON:00002762 name: bean (cooked) def: "Cooked bean material is the bean material output of a cooking process applied to dry, rehydrated, or raw (fresh) beans." [] is_a: FOODON:00001181 ! food (cooked) -is_a: FOODON:03301467 ! bean substance +is_a: FOODON:03301467 ! bean (whole or pieces) intersection_of: FOODON:00001181 ! food (cooked) -intersection_of: FOODON:03301467 ! bean substance -property_value: http://purl.org/dc/elements/1.1/date 2019-07-08T21:47:07Z xsd:dateTime +intersection_of: FOODON:03301467 ! bean (whole or pieces) +property_value: http://purl.org/dc/terms/date 2019-07-08T21:47:07Z xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: FOODON:00002778 -name: jack bean (whole) +name: jack bean def: "A seed of a jack seed plant (Canavalia ensiformis)." [] synonym: "jack bean" EXACT [] -is_a: FOODON:00002753 ! bean (whole) +is_a: FOODON:00002753 ! bean is_a: FOODON:00002779 ! jack-bean food product -property_value: http://purl.org/dc/elements/1.1/date 2019-07-09T22:17:36 xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-07-09T22:17:36 xsd:dateTime property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Canavalia_ensiformis xsd:string @@ -2311,7 +2352,7 @@ property_value: IAO:0000119 https://en.wikipedia.org/wiki/Canavalia_ensiformis x id: FOODON:00002779 name: jack-bean food product is_a: FOODON:00001635 ! bean food product -property_value: http://purl.org/dc/elements/1.1/date 2019-07-09T22:21:16Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-07-09T22:21:16Z xsd:dateTime property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] @@ -2319,30 +2360,32 @@ id: FOODON:00002780 name: pigeon pea food product def: "A pigeon pea food product is a food product derived from the pigeon pea plant" [] is_a: FOODON:00001264 ! legume food product -property_value: http://purl.org/dc/elements/1.1/date 2019-07-09T22:29:17Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-07-09T22:29:17Z xsd:dateTime property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: seeAlso https://en.wikipedia.org/wiki/Pigeon_pea xsd:anyURI [Term] id: FOODON:00002781 -name: pigeon pea (whole) +name: pigeon pea def: "A seed of a pigeon pea plant (Cajanus cajan)." [] synonym: "pigeon pea" EXACT [] -is_a: FOODON:00002115 ! pigeon pea vegetable food product -property_value: http://purl.org/dc/elements/1.1/date 2019-07-09T22:29:49 xsd:dateTime +is_a: FOODON:00002780 ! pigeon pea food product +is_a: FOODON:03310646 ! legume +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-8844-9165 xsd:string +property_value: http://purl.org/dc/terms/date 2019-07-09T22:29:49 xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Pigeon_pea xsd:string [Term] id: FOODON:00002786 -name: velvet bean (whole) +name: velvet bean def: "A seed of a velvet bean plant (Mucuna pruriens)" [] synonym: "tericopelo bean" EXACT [] synonym: "velvet bean" EXACT [] -is_a: FOODON:00002753 ! bean (whole) +is_a: FOODON:00002753 ! bean is_a: FOODON:00004156 ! velvet bean food product -property_value: http://purl.org/dc/elements/1.1/date 2019-07-10T00:00:22 xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-07-10T00:00:22 xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Legume xsd:anyURI @@ -2352,16 +2395,17 @@ property_value: IAO:0000119 https://en.wikipedia.org/wiki/Mucuna_pruriens xsd:st id: FOODON:00002787 name: vetch food product is_a: FOODON:00002153 ! plant seed vegetable food product -property_value: http://purl.org/dc/elements/1.1/date 2019-07-10T00:16:38Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-07-10T00:16:38Z xsd:dateTime property_value: IAO:0000117 "Damion Dooley" xsd:string [Term] id: FOODON:00002791 -name: vetch seed (whole) +name: vetch seed def: "A seed of a vetch plant." [] synonym: "vetch seed" EXACT [] is_a: FOODON:00002787 ! vetch food product -property_value: http://purl.org/dc/elements/1.1/date 2019-07-10T01:33:15Z xsd:dateTime +is_a: FOODON:03310646 ! legume +property_value: http://purl.org/dc/terms/date 2019-07-10T01:33:15Z xsd:dateTime property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Vicia xsd:string @@ -2369,7 +2413,7 @@ property_value: IAO:0000119 https://en.wikipedia.org/wiki/Vicia xsd:string id: FOODON:00002813 name: pea food product is_a: FOODON:00001264 ! legume food product -property_value: http://purl.org/dc/elements/1.1/date 2019-07-12T17:18:31Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-07-12T17:18:31Z xsd:dateTime property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string @@ -2378,10 +2422,22 @@ id: FOODON:00002819 name: liver food product def: "A liver food product is a food product that derives from one or more liver organs." [] is_a: FOODON:00002165 ! organ meat product -property_value: http://purl.org/dc/elements/1.1/date 2019-08-02T18:22:37Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-08-02T18:22:37Z xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string +[Term] +id: FOODON:00003042 +name: herb food product +def: "A leaf of a plant that is used for flavoring." [] +def: "The leaves, flowers, or stems of plants, typically excluding vegetables, used for flavoring or as a garnish." [] +is_a: FOODON:00001242 ! spice or herb +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 xsd:string +property_value: http://purl.org/dc/terms/date 2019-08-24T15:26:51Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2023-08-16T10:14:35Z xsd:dateTime +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 http://orcid.org/0000-0002-8844-9165 + [Term] id: FOODON:00003341 name: brassica food product @@ -2389,7 +2445,6 @@ def: "A genus of plants in the mustard family (Brassicaceae). The members of the synonym: "bok choy vegetable food product" NARROW [] synonym: "bomdong vegetable food product" NARROW [] synonym: "broccolini vegetable food product" NARROW [] -synonym: "chinese cabbage vegetable food product" NARROW [] synonym: "choy sum vegetable food product" NARROW [] synonym: "cole crop vegetable food product" RELATED [] synonym: "collard greens vegetable food product" NARROW [] @@ -2408,7 +2463,7 @@ property_value: IAO:0000119 https://en.wikipedia.org/wiki/Brassica id: FOODON:00003395 name: multi-component wheat food product is_a: FOODON:03316579 ! multi-component plant food product -property_value: http://purl.org/dc/elements/1.1/date 2020-09-06T15:59:54Z xsd:dateTime +property_value: http://purl.org/dc/terms/date 2020-09-06T15:59:54Z xsd:dateTime property_value: IAO:0000117 http://orcid.org/0000-0002-8844-9165 [Term] @@ -2416,43 +2471,98 @@ id: FOODON:00004156 name: velvet bean food product def: "A bean food product made from velvet bean." [] is_a: FOODON:00001635 ! bean food product -property_value: http://purl.org/dc/elements/1.1/date 2021-12-24T00:12:16Z xsd:string +property_value: http://purl.org/dc/terms/date 2021-12-24T00:12:16Z xsd:string property_value: IAO:0000117 https://orcid.org/0000-0001-5275-8866 [Term] id: FOODON:00004242 name: animal food product -def: "A food product deriving from one or more animals." [] +def: "A food product that is derived from some animal." [] is_a: FOODON:00002381 ! food product by organism -property_value: http://purl.org/dc/elements/1.1/date 2022-09-01T16:31:09Z xsd:dateTime -property_value: IAO:0000117 http://orcid.org/0000-0002-8844-9165 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-8844-9165 xsd:string +property_value: http://purl.org/dc/terms/date 2023-08-01T21:25:29Z xsd:dateTime +property_value: IAO:0000114 IAO:0000122 + +[Term] +id: FOODON:00004335 +name: piece(s) of animal +def: "One or more pieces of animals." [] +is_a: FOODON:03420164 ! animal material +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 xsd:string +property_value: http://purl.org/dc/terms/date 2023-08-01T21:25:29Z xsd:dateTime +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 + +[Term] +id: FOODON:00004509 +name: milled food product +def: "A food product made from milling plant material." [] +is_a: FOODON:00001015 ! plant food product +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 +property_value: http://purl.org/dc/terms/date 2023-10-07T13:41:10Z xsd:dateTime +property_value: IAO:0000114 IAO:0000122 + +[Term] +id: FOODON:00004532 +name: piece(s) of cow +def: "One or more pieces of cows." [] +is_a: FOODON:00004335 ! piece(s) of animal +is_a: FOODON:02020889 ! cow material +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 +property_value: http://purl.org/dc/terms/date 2023-12-15T22:55:22Z xsd:dateTime +property_value: IAO:0000114 IAO:0000122 + +[Term] +id: FOODON:02000412 +name: piece(s) of beef +def: "One or more pieces of beef." [] +is_a: FOODON:00004532 ! piece(s) of cow + +[Term] +id: FOODON:02020114 +name: duck food product +def: "A food product that is derived from some duck." [] +is_a: FOODON:00004242 ! animal food product +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3410-4655 xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 xsd:string +property_value: http://purl.org/dc/terms/date 2024-02-12T14:11:19Z xsd:dateTime +property_value: IAO:0000114 IAO:0000122 + +[Term] +id: FOODON:02020889 +name: cow material +def: "Material that derives from some cow." [] +comment: This branch isn't necessarily food material +is_a: FOODON:03420164 ! animal material +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3410-4655 xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8844-9165 xsd:string +property_value: http://purl.org/dc/terms/date 2024-02-12T14:11:19Z xsd:dateTime +property_value: IAO:0000114 IAO:0000122 [Term] id: FOODON:03301073 name: sugar (granulated) -comment: SIREN DB annotation:\n* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143)\n* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014)\n* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108)\n* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138)\n* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)\n -subset: subset_siren -xref: SUBSET_SIREN:F1073 +comment: SIREN DB annotation:\n* crystal FOODON:03430143\n* fully heat-treated FOODON:03440014\n* sugar FOODON:03420108\n* water removal process FOODON:03460138\n* preservation by dehydration or drying FOODON:03470116 +xref: https://bioregistry.io/reference/siren\:F1073 is_a: FOODON:03307345 ! sugar (refined) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03301103 name: orange juice -comment: SIREN DB annotation:\n* has quality 'liquid, low viscosity, with small particles' (http://purl.obolibrary.org/obo/FOODON_03430114)\n* derives from 'fruit, peel removed, core, pit or seed removed' (http://purl.obolibrary.org/obo/FOODON_03420229)\n -subset: subset_siren -xref: SUBSET_SIREN:F1103 -xref: SUBSET_SIREN:F11069 +comment: SIREN DB annotation:\n* liquid, low viscosity, with small particles FOODON:03430114\n* fruit, peel removed, core, pit or seed removed FOODON:03420229 +xref: https://bioregistry.io/reference/siren\:F1103 +xref: https://bioregistry.io/reference/siren\:F11069 is_a: FOODON:00001100 ! orange fruit beverage property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03301227 -name: broad bean (whole) +name: broad bean def: "A seed of a broad bean plant (Vicia faba)." [] -subset: subset_siren synonym: "broad bean" EXACT [] synonym: "broadbean" EXACT [] synonym: "faba bean" EXACT [] @@ -2462,788 +2572,730 @@ synonym: "Horse bean" NARROW [] synonym: "tic bean" NARROW [] synonym: "tick bean" NARROW [] synonym: "Windsor bean" EXACT [] -xref: SUBSET_SIREN:F1227 +xref: https://bioregistry.io/reference/siren\:F1227 is_a: FOODON:00001665 ! broad bean food product -is_a: FOODON:00002753 ! bean (whole) +is_a: FOODON:00002753 ! bean +is_a: FOODON:00002791 ! vetch seed +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-8844-9165 xsd:string property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03301444 name: vegetable juice food product -comment: SIREN DB annotation:\n* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)\n* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174)\n -subset: subset_siren -xref: SUBSET_SIREN:F1444 +comment: SIREN DB annotation:\n* liquid FOODON:03430130\n* part of plant FOODON:03420174 +xref: https://bioregistry.io/reference/siren\:F1444 is_a: FOODON:00001253 ! plant derived beverage property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03301467 -name: bean substance +name: bean (whole or pieces) def: "A bean substance is a substance made by processing seed from a bean plant." [] -comment: SIREN DB annotation:\n* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155)\n -subset: subset_siren -xref: SUBSET_SIREN:F1467 +comment: SIREN DB annotation:\n* seed (anatomical part) FOODON:03420155 +xref: https://bioregistry.io/reference/siren\:F1467 is_a: FOODON:00001635 ! bean food product property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "Damion Dooley's note: This class is intended to provide the most generic reference to bean, as it does not imply any more information about the state of a bean - whether it is whole or in fragments, or fragments of several beans, whether it is dry, raw, or cooked etc." xsd:string property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Bean xsd:string -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03301977 name: beverage food product def: "A liquid prepared for consumption, or a product that can be combined with water or milk to make one." [] is_a: FOODON:00002373 ! food product by meal type -property_value: http://purl.org/dc/elements/1.1/date 2019-09-12T00:00:00 xsd:dateTime +property_value: http://purl.org/dc/terms/date 2019-09-12T00:00:00 xsd:dateTime property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03302001 name: animal-derived food -comment: SIREN DB annotation:\n* derives from 'part of animal' (http://purl.obolibrary.org/obo/FOODON_03420164)\n -subset: subset_siren -xref: SUBSET_SIREN:F2001 -is_a: FOODON:00004242 ! animal food product +comment: SIREN DB annotation:\n* part of animal FOODON:03420164 +xref: https://bioregistry.io/reference/siren\:F2001 +is_a: FOODON:00001092 ! vertebrate animal food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03302082 name: beef (dehydrated) -comment: SIREN DB annotation:\n* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151)\n* derives from 'skeletal meat part, without bone or shell' (http://purl.obolibrary.org/obo/FOODON_03420125)\n* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138)\n* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)\n -subset: subset_siren -xref: SUBSET_SIREN:F2082 -is_a: FOODON:00001041 ! beef food product +comment: SIREN DB annotation:\n* solid FOODON:03430151\n* skeletal meat part, without bone or shell FOODON:03420125\n* water removal process FOODON:03460138\n* preservation by dehydration or drying FOODON:03470116 +xref: https://bioregistry.io/reference/siren\:F2082 +is_a: FOODON:00001041 ! cow food product is_a: FOODON:00002643 ! food (dehydrated) -intersection_of: FOODON:00001041 ! beef food product +intersection_of: FOODON:00001041 ! cow food product intersection_of: FOODON:00002643 ! food (dehydrated) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03303220 name: dessert food -comment: SIREN DB annotation:\n* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136)\n -subset: subset_siren +def: "A food product served during the dessert course of a meal." [] +comment: SIREN DB annotation:\n* ingredient: sugar or sugar syrup added FOODON:03460136 synonym: "desert preparation" EXACT [] synonym: "dessert" EXACT [] -xref: SUBSET_SIREN:F3220 +xref: https://bioregistry.io/reference/siren\:F3220 is_a: FOODON:00002373 ! food product by meal type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Dessert + +[Term] +id: FOODON:03303380 +name: spice food product +def: "A food product derived from a spice." [] +comment: SIREN DB annotation:\n* whole, natural shape FOODON:03430150\n* not heat-treated FOODON:03440003\n* part of plant FOODON:03420174 +xref: https://bioregistry.io/reference/siren\:F3380 +is_a: FOODON:00001242 ! spice or herb +property_value: IAO:0000114 IAO:0000122 +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Spice xsd:string [Term] id: FOODON:03303909 name: cultured dairy product def: "A cultured dairy product is a fermented dairy product in which a microbial starter was introduced to the fermentation process." [] -comment: SIREN DB annotation:\n* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913)\n* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)\n -subset: subset_siren -xref: SUBSET_SIREN:F3909 +comment: SIREN DB annotation:\n* milk (mammary secretion) UBERON:0001913\n* microbial/enzymatic modification process FOODON:03460119 +xref: https://bioregistry.io/reference/siren\:F3909 is_a: FOODON:00001053 ! fermented dairy food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03304497 name: edible seed food product -comment: SIREN DB annotation:\n* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150)\n* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155)\n -subset: subset_siren -xref: SUBSET_SIREN:F4497 +comment: SIREN DB annotation:\n* whole, natural shape FOODON:03430150\n* seed (anatomical part) FOODON:03420155 +xref: https://bioregistry.io/reference/siren\:F4497 is_a: FOODON:00001173 ! plant seed food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03305536 name: honey blend table syrup -comment: SIREN DB annotation:\n* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139)\n* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014)\n* derives from 'sugar syrup or syrup solids' (http://purl.obolibrary.org/obo/FOODON_03420271)\n* has substance added 'honey added' (http://purl.obolibrary.org/obo/FOODON_03460149)\n -subset: subset_siren -xref: SUBSET_SIREN:F5536 +comment: SIREN DB annotation:\n* liquid, high viscosity, with no visible particles FOODON:03430139\n* fully heat-treated FOODON:03440014\n* sugar syrup or syrup solids FOODON:03420271\n* ingredient: honey added FOODON:03460149 +xref: https://bioregistry.io/reference/siren\:F5536 is_a: FOODON:00002157 ! plant sweetener is_a: FOODON:00002450 ! multi-component honey product intersection_of: FOODON:00002157 ! plant sweetener intersection_of: FOODON:00002450 ! multi-component honey product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03307345 name: sugar (refined) -comment: SIREN DB annotation:\n* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143)\n* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014)\n* derives from 'white sugar' (http://purl.obolibrary.org/obo/FOODON_03420157)\n -subset: subset_siren -xref: SUBSET_SIREN:F7345 +comment: SIREN DB annotation:\n* crystal FOODON:03430143\n* fully heat-treated FOODON:03440014\n* white sugar FOODON:03420157 +xref: https://bioregistry.io/reference/siren\:F7345 is_a: FOODON:03316271 ! sugar product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03307539 name: food (dried) -comment: SIREN DB annotation:\n* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138)\n* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)\n -subset: subset_siren -xref: SUBSET_SIREN:F7539 +comment: SIREN DB annotation:\n* water removal process FOODON:03460138\n* preservation by dehydration or drying FOODON:03470116 +xref: https://bioregistry.io/reference/siren\:F7539 is_a: FOODON:00002643 ! food (dehydrated) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03310006 name: fermented bean product -comment: SIREN DB annotation:\n* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155)\n* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)\n* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)\n -subset: subset_siren -xref: SUBSET_SIREN:F10006 +comment: SIREN DB annotation:\n* seed (anatomical part) FOODON:03420155\n* microbial/enzymatic modification process FOODON:03460119\n* curing or aging process FOODON:03460253 +xref: https://bioregistry.io/reference/siren\:F10006 is_a: FOODON:00001258 ! food (fermented) is_a: FOODON:00001635 ! bean food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03310387 name: oil -comment: SIREN DB annotation:\n* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139)\n* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190)\n -subset: subset_siren -xref: SUBSET_SIREN:F10387 +comment: SIREN DB annotation:\n* liquid, high viscosity, with no visible particles FOODON:03430139\n* fat or oil FOODON:03420190 +xref: https://bioregistry.io/reference/siren\:F10387 is_a: FOODON:00002664 ! lipid food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string + +[Term] +id: FOODON:03310646 +name: legume +def: "A seed of a legume plant in the family Fabaceae." [] +comment: SIREN DB annotation:\n* whole, natural shape FOODON:03430150\n* not heat-treated FOODON:03440003\n* seed (anatomical part) FOODON:03420155 +xref: https://bioregistry.io/reference/siren\:F10646 +is_a: FOODON:00001264 ! legume food product +is_a: FOODON:00002153 ! plant seed vegetable food product +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 xsd:string +property_value: http://purl.org/dc/terms/date 2020-10-21T09:28:28 xsd:dateTime +property_value: IAO:0000114 IAO:0000428 [Term] id: FOODON:03311737 name: processed food product -subset: subset_siren -xref: SUBSET_SIREN:F11737 +xref: https://bioregistry.io/reference/siren\:F11737 is_a: FOODON:00001002 ! food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03312053 name: pork (dehydrated) -comment: SIREN DB annotation:\n* has quality 'divided or disintegrated' (http://purl.obolibrary.org/obo/FOODON_03430122)\n* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014)\n* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268)\n* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)\n* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138)\n* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116)\n -subset: subset_siren -xref: SUBSET_SIREN:F12053 +comment: SIREN DB annotation:\n* divided or disintegrated FOODON:03430122\n* fully heat-treated FOODON:03440014\n* skeletal meat part, without bone, without skin FOODON:03420268\n* microbial/enzymatic modification process FOODON:03460119\n* water removal process FOODON:03460138\n* preservation by dehydration or drying FOODON:03470116 +xref: https://bioregistry.io/reference/siren\:F12053 is_a: FOODON:00001038 ! pork meat food product is_a: FOODON:00002643 ! food (dehydrated) intersection_of: FOODON:00001038 ! pork meat food product intersection_of: FOODON:00002643 ! food (dehydrated) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03315150 name: mammalian milk product -comment: SIREN DB annotation:\n* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913)\n -subset: subset_siren -xref: SUBSET_SIREN:F15150 +comment: SIREN DB annotation:\n* milk (mammary secretion) UBERON:0001913 +xref: https://bioregistry.io/reference/siren\:F15150 is_a: FOODON:00001257 ! milk or milk based food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03315173 name: fish product (unspecified species) def: "A fish product is a home-made or commercially produced or retail or wholesale product containing substantial amounts of freshwater or saltwater fish and/or shellfish flesh. Note that this category should avoid items that mention a particular species of fish or shellfish." [] -comment: SIREN DB annotation:\n* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175)\n -subset: subset_siren -xref: SUBSET_SIREN:F15173 +comment: SIREN DB annotation:\n* skeletal meat part FOODON:03420175 +xref: https://bioregistry.io/reference/siren\:F15173 is_a: FOODON:00001248 ! fish food product property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000412 http://langual.org xsd:string property_value: seeAlso https://en.wikipedia.org/wiki/Fish_products xsd:string [Term] id: FOODON:03315302 name: cocoa food product -comment: SIREN DB annotation:\n* derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133)\n* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119)\n* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253)\n -subset: subset_siren -xref: SUBSET_SIREN:F15302 +comment: SIREN DB annotation:\n* seed, skin present, germ present FOODON:03420133\n* microbial/enzymatic modification process FOODON:03460119\n* curing or aging process FOODON:03460253 +xref: https://bioregistry.io/reference/siren\:F15302 is_a: FOODON:03460231 ! chocolate or cocoa property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03315552 name: juice beverage -subset: subset_siren synonym: "juice" EXACT [] -xref: SUBSET_SIREN:F15552 +xref: https://bioregistry.io/reference/siren\:F15552 is_a: FOODON:03301977 ! beverage food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03315904 -name: sausage (whole) +name: meat sausage def: "A food product that is highly seasoned minced meat and is encased in a skin in the shape of a cylinder." [] -comment: SIREN DB annotation:\n* has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147)\n* derives from 'meat part of animal' (http://purl.obolibrary.org/obo/FOODON_03420103)\n* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227)\n -subset: subset_siren +comment: SIREN DB annotation:\n* whole, shape achieved by forming FOODON:03430147\n* meat part of animal FOODON:03420103\n* ingredient: flavoring, spice or herb added FOODON:03460227 synonym: "sausage" EXACT [] -xref: SUBSET_SIREN:F15904 -is_a: FOODON:00001007 ! sausage food product -property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0001-5275-8866 +xref: https://bioregistry.io/reference/siren\:F15904 +is_a: FOODON:00001007 ! meat sausage food product +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Sausage xsd:string -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03315925 name: pate -comment: SIREN DB annotation:\n* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151)\n* derives from 'meat part of animal' (http://purl.obolibrary.org/obo/FOODON_03420103)\n -subset: subset_siren -xref: SUBSET_SIREN:F15925 +comment: SIREN DB annotation:\n* solid FOODON:03430151\n* meat part of animal FOODON:03420103 +xref: https://bioregistry.io/reference/siren\:F15925 is_a: FOODON:00001010 ! processed meat food product is_a: FOODON:03302001 ! animal-derived food property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03316079 name: herbal infusion -comment: SIREN DB annotation:\n* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)\n* has quality 'heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440022)\n* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174)\n* formed as a result of 'steeping' (http://purl.obolibrary.org/obo/FOODON_03450036)\n -subset: subset_siren -xref: SUBSET_SIREN:F16079 +comment: SIREN DB annotation:\n* liquid FOODON:03430130\n* heat-treated FOODON:03440022\n* part of plant FOODON:03420174\n* steeping FOODON:03450036 +xref: https://bioregistry.io/reference/siren\:F16079 is_a: FOODON:00002275 ! steeped beverage product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03316271 name: sugar product -comment: SIREN DB annotation:\n* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108)\n -subset: subset_siren -xref: SUBSET_SIREN:F16271 +comment: SIREN DB annotation:\n* sugar FOODON:03420108 +xref: https://bioregistry.io/reference/siren\:F16271 is_a: FOODON:00002157 ! plant sweetener property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03316579 name: multi-component plant food product -comment: SIREN DB annotation:\n* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174)\n -subset: subset_siren -xref: SUBSET_SIREN:F16579 +comment: SIREN DB annotation:\n* part of plant FOODON:03420174 +xref: https://bioregistry.io/reference/siren\:F16579 is_a: FOODON:00002501 ! multi-component food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03316694 name: vegetable fat food product -comment: SIREN DB annotation:\n* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190)\n -subset: subset_siren -xref: SUBSET_SIREN:F16694 +comment: SIREN DB annotation:\n* fat or oil FOODON:03420190 +xref: https://bioregistry.io/reference/siren\:F16694 is_a: FOODON:00002139 ! plant fat or oil refined food product is_a: FOODON:03460263 ! vegetable fat or oil property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03317170 -name: meat (whole or parts) +name: meat (whole or pieces) def: "A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean)." [] -comment: SIREN DB annotation:\n* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127)\n -subset: subset_siren -xref: SUBSET_SIREN:F17170 +comment: SIREN DB annotation:\n* animal body or body part FOODON:03420127 +xref: https://bioregistry.io/reference/siren\:F17170 is_a: FOODON:00001006 ! mammalian meat food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400115 name: cheese or cheese product (us cfr) def: "Natural cheese, cured or uncured, cheese product (which is further processed), or cheese product analog." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0115 +xref: langual:thesaurus.asp?termid=A0115 is_a: FOODON:03400164 ! dairy product (us cfr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string property_value: seeAlso https://www.ecfr.gov/cgi-bin/text-idx?node=pt21.2.133 [Term] id: FOODON:03400143 name: fruit or fruit product (us cfr) def: "Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0143 +xref: langual:thesaurus.asp?termid=A0143 is_a: FOODON:03400257 ! fruit or vegetable product (us cfr) property_value: hasSynonym "pie filling, fruit" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400147 name: milk or milk product analog (us cfr) def: "Food product having functional characteristics similar to milk or milk products, including cream product analogs, margarine, and milk analogs. Certain alternate ingredients are substituted for those components that are responsible for specific functional properties." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0147 +xref: langual:thesaurus.asp?termid=A0147 is_a: FOODON:03400148 ! milk or milk product (us cfr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400148 name: milk or milk product (us cfr) def: "Milk in all forms, milk-based beverage, cultured milk product, or milk or milk product analog. Index infant formula under *MEAL REPLACEMENT*." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0148 +xref: langual:thesaurus.asp?termid=A0148 is_a: FOODON:03400164 ! dairy product (us cfr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400155 name: fruit butter, jelly, preserve or related product (us cfr) def: "Semisolid or jelled food prepared from fruit or fruit juice and other ingredients prescribed for the individual products (21 CFR 150)." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0155 +xref: langual:thesaurus.asp?termid=A0155 is_a: FOODON:03400143 ! fruit or fruit product (us cfr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400164 name: dairy product (us cfr) def: "Milk, a product derived from milk, or a dairy product analog; includes cheese and frozen dairy desserts. [FDA CFSAN 1995]" [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0164 +xref: langual:thesaurus.asp?termid=A0164 is_a: FOODON:03401270 ! U.S. code of federal regulations, title 21 food product type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400187 name: natural cheese (us cfr) def: "Cheese made from milk or milk components, such as cream, by the following process: (1) produce curd through coagulation of milk by bacterial action and/or enzymes and/or acidification and draining of whey. (2) For cured cheese only: cure the curd. Excludes products made through further processing, such as comminuting (see *CHEESE PRODUCT*)." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0187 +xref: langual:thesaurus.asp?termid=A0187 is_a: FOODON:03400115 ! cheese or cheese product (us cfr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400188 name: confectionery (us cfr) def: "Candy or other food product made with sweeteners and frequently containing nuts, fruits, starches, flavorings and other foods (21 CFR 170.3(n)(9). [FDA CFSAN 1995]" [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0188 +xref: langual:thesaurus.asp?termid=A0188 is_a: FOODON:03401270 ! U.S. code of federal regulations, title 21 food product type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400204 name: candy (us cfr) def: "Food product prepared by heating a mixture of sweeteners and other optional ingredients according to the specific formula for each subgroup." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0204 +xref: langual:thesaurus.asp?termid=A0204 is_a: FOODON:03400188 ! confectionery (us cfr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400209 name: fruit jelly (us cfr) def: "Jelled product made from one or more fruit juices and optional ingredients. Includes both fruit jelly, which may be sweetened with nutritive carbohydrate sweeteners, (21 CFR 150.140), and artificially sweetened fruit jelly (21 CFR 150.141). The finished fruit jelly must have a soluble solid content of no less than 65% and the ratio by weight of the fruit ingredient to sweetener in the starting mixture must be no less than 45:55. Artificially sweetened fruit jelly must contain no less than 55% fruit ingredient by weight." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0209 +xref: langual:thesaurus.asp?termid=A0209 is_a: FOODON:03400155 ! fruit butter, jelly, preserve or related product (us cfr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400213 name: fudge (us cfr) def: "Soft candy prepared by boiling milk, sugar, salt and optional ingredients to the soft-ball stage (238 degrees F.)." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0213 +xref: langual:thesaurus.asp?termid=A0213 is_a: FOODON:03400293 ! soft candy (us cfr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400231 name: margarine (us cfr) def: "Food product having functional characteristics similar to those of butter; it is in plastic form or liquid emulsion and contains not less than 80% fat whose origin is vegetable or rendered animal carcass fats or a mixture of these as well as other optional ingredients specified by 21 CFR 166.110." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0231 +xref: langual:thesaurus.asp?termid=A0231 is_a: FOODON:03400294 ! butter product analog (us cfr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400257 name: fruit or vegetable product (us cfr) def: "Fruits and vegetables in all forms. [FDA CFSAN 1995]" [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0257 +xref: langual:thesaurus.asp?termid=A0257 is_a: FOODON:03401270 ! U.S. code of federal regulations, title 21 food product type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400289 name: USA agency food product type def: "Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995]" [] comment: LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0289 +xref: langual:thesaurus.asp?termid=A0289 is_a: FOODON:03400361 ! agency food product type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400293 name: soft candy (us cfr) def: "Candy prepared by cooking a mixture of water, sugars and optional ingredients to a temperature of 250 degrees F. or less." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0293 +xref: langual:thesaurus.asp?termid=A0293 is_a: FOODON:03400204 ! candy (us cfr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400294 name: butter product analog (us cfr) def: "Food product having functional characteristics similar to a butter product; it may be nutritionally equivalent or inferior to the product it purports to resemble." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0294 +xref: langual:thesaurus.asp?termid=A0294 is_a: FOODON:03400147 ! milk or milk product analog (us cfr) property_value: hasSynonym "butter substitute" xsd:string property_value: hasSynonym "butter, imitation" xsd:string property_value: hasSynonym "imitation butter" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400352 name: international agency food product type def: "Renamed from *PRODUCT TYPE, CODEX ALIMENTARIUS* in LanguaL 2008." [] comment: LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0352 +xref: langual:thesaurus.asp?termid=A0352 is_a: FOODON:03400361 ! agency food product type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400356 name: European Union agency food product type comment: LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0356 +xref: langual:thesaurus.asp?termid=A0356 is_a: FOODON:03400361 ! agency food product type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400361 name: agency food product type def: "An agency food product type is a class of food product defined by an agency or consortium." [] comment: This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible. -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0361 +xref: langual:thesaurus.asp?termid=A0361 is_a: FOODON:00002403 ! food material property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Damion Dooley" xsd:string -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400643 name: Codex Alimentarius classification of food and feed commodities def: "Codex Alimentarius, Volume 2 - 1993, Section 2: Pesticide Residues in Food.\n\nThe Codex Classification of food and animal feed commodities moving in trade and the description of the various items and groups of food and animal feedstuffs included in the present document have been developed by the Codex Committee on Pesticide Residues. It was first adopted by the 18th Session of the Codex Alimentarius Commission, (1989).\n\nThe Codex Classification includes food commodities and animal feedstuffs for which Codex maximum residue limits will not necessarily be established. The Classification is intended to be as complete a listing of food commodities in trade as possible, classified into groups on the basis of the commodity's similar potential for pesticide residues.\n\nThe Classification may also be appropriate for other purposes such as setting maximum levels for other types of residues or for other contaminants in food. The Codex Classification should be consulted in order to obtain a precise description of the food or animal feed commodities and, especially, in cases where Codex maximum residue limits have been set for groups of food and groups of animal feedstuffs. The Codex Classification is intended to promote harmonization of the terms used to describe commodities which are subject to maximum residue limits and of the approach to grouping commodities with similar potential for residue for which a common group maximum residue limit can be set." [] comment: LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0643 +xref: langual:thesaurus.asp?termid=A0643 is_a: FOODON:03400352 ! international agency food product type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400644 name: a. primary food commodities of plant origin (ccpr) comment: LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0644 +xref: langual:thesaurus.asp?termid=A0644 is_a: FOODON:03400643 ! Codex Alimentarius classification of food and feed commodities property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400650 name: 02 vegetables (ccpr) def: "Vegetables are foods derived from many different kinds of plants mostly annual and usually cultivated, commonly known by custom and tradition as \"vegetables\".\nIn several countries, some of these commodities grown on large areas are distinguished as \"field crops\" or arable crops e.g. sugar beet. For the sake of convenience in this guide such crops are classified under Type 2 Vegetables.\nExposure to pesticides is dependent on the particular part of the plant used for food and the growing practices.\nVegetables may be consumed in whole or in part and in the form of fresh, dried or processed foods." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0650 +xref: langual:thesaurus.asp?termid=A0650 is_a: FOODON:03400644 ! a. primary food commodities of plant origin (ccpr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400680 name: 015 pulses (vd) (ccpr) def: "Pulses are derived from the mature seeds naturally or artificially dried, of leguminous plants known as beans (dry) and peas (dry).\nThe seeds in the pods are protected from most pesticides applied during the growing season except pesticides which show a systemic action. The dried beans and peas however are often exposed to post-harvest treatments.\nThe dry pulses are consumed after processing or household cooking." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0680 +xref: langual:thesaurus.asp?termid=A0680 is_a: FOODON:03400650 ! 02 vegetables (ccpr) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400777 name: eurofir food classification comment: LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0777 +xref: langual:thesaurus.asp?termid=A0777 is_a: FOODON:03400356 ! European Union agency food product type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400801 name: seafood or related product (eurofir) def: "The group includes marine or freshwater fish, molluscs, crustaceans, and other fauna such as reptiles, insects or frogs not in the “Meats” group. The group also includes seafood product analogs and seafood-based sausage or luncheon meat as well as such products as squid ink and clam juice." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0801 +xref: langual:thesaurus.asp?termid=A0801 is_a: FOODON:03400777 ! eurofir food classification property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400803 name: seafood product (eurofir) def: "includes fish offal; a food product whose predominant constituent is fish (e.g. dried and salted fish, smoked fish, canned fish, pickled fish, restructured fish and fish analogues, surimi; fish paste, pâté)." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0803 +xref: langual:thesaurus.asp?termid=A0803 is_a: FOODON:03400801 ! seafood or related product (eurofir) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400840 name: beverage (non-milk) (eurofir) def: "Alcoholic or non-alcoholic beverage; excludes milk and milk-based beverages." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0840 +xref: langual:thesaurus.asp?termid=A0840 is_a: FOODON:03400777 ! eurofir food classification property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400842 name: non alcoholic beverage (eurofir) def: "Beverage containing no more than 0.5% alcohol; it may be flavoured, sweetened or carbonated; includes soft drinks and steeped beverages; excludes milk in all forms, fruit juices and vegetable juices." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0842 +xref: langual:thesaurus.asp?termid=A0842 is_a: FOODON:03400840 ! beverage (non-milk) (eurofir) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400845 name: coffee, tea, cocoa or infusion (eurofir) def: "Beverage prepared by extracting flavour and other components from food sources by percolation and/or immersion in water, usually at near-boiling temperature. The group includes coffee (e.g. instant coffee, coffee and chicory essence), tea, herbal tea (e.g. green tea, black tea, tisane), cocoa beverage and beverage powder." [] comment: LanguaL curation note: Renamed from *COFFEE, TEA, COCOA (EUROFIR)* (LanguaL 2010). -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0845 +xref: langual:thesaurus.asp?termid=A0845 is_a: FOODON:03400842 ! non alcoholic beverage (eurofir) property_value: hasSynonym "infusion" xsd:string property_value: hasSynonym "steeped beverage" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400852 name: miscellaneous food product (eurofir) def: "EFG group 32, Eurocode-2 group 12." [] comment: LanguaL curation note: Use for foods and ingredients that could not fit into any of the above classes. -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0852 +xref: langual:thesaurus.asp?termid=A0852 is_a: FOODON:03400777 ! eurofir food classification property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400861 name: prepared food product (eurofir) def: "This subgroup includes multicomponent meals, sauces, retail salads, desserts, soups, snacks and other foods where similarity of the product type is more significant than the source of the principal ingredient(s)." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0861 +xref: langual:thesaurus.asp?termid=A0861 is_a: FOODON:03400852 ! miscellaneous food product (eurofir) property_value: hasSynonym "soup, sauce or miscellaneous food product" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400865 name: soup (eurofir) def: "A liquid food made by simmering meat, poultry, seafood or vegetables, being clear or thickened to the consistency of a thin puree or having milk or cream added, and often containing pieces of solid food such as meat, shellfish, pasta or vegetables. Soup takes precedence over other food products. Examples are egg and lemon soup, oxtail soup, fish soup, rice soup, lentil soup, minestrone, cherry soup." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0865 +xref: langual:thesaurus.asp?termid=A0865 is_a: FOODON:03400861 ! prepared food product (eurofir) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400874 name: GS1 Global Product Classification (GPC) def: "The Global System 1 (GS1) Global Product Classification (GPC) is a system that gives buyers and sellers a common language for grouping products in the same way, everywhere in the world.$br/$\nThe GS1 GPC classification in facet A is currently updated based on June 2017 release of GS1 GPC Standard for Food/Beverage/Tobacco, except for codes pertaining to tobacco. See the GS1 site for details [https://www.gs1.org/standards/gpc]." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0874 +xref: langual:thesaurus.asp?termid=A0874 is_a: FOODON:03400352 ! international agency food product type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string property_value: seeAlso https://www.gs1.org/docs/gdsn/support/it/GDSN_Mandatory_Attributes_Simplified_TK.ppt property_value: seeAlso https://www.gs1.org/docs/gdsn/tiig/3_1/GDSN_Trade_Item_Implementation_Guide.pdf [Term] id: FOODON:03400960 name: 50220000 - cereal/grain/pulse products (gs1 gpc) -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0960 +xref: langual:thesaurus.asp?termid=A0960 is_a: FOODON:03400874 ! GS1 Global Product Classification (GPC) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03400969 name: 50221200 - processed cereal products (gs1 gpc) -xref: http://www.langual.org/langual_thesaurus.asp?termid=A0969 +xref: langual:thesaurus.asp?termid=A0969 is_a: FOODON:03400960 ! 50220000 - cereal/grain/pulse products (gs1 gpc) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03401061 name: 50190000 - prepared/preserved foods (gs1 gpc) -xref: http://www.langual.org/langual_thesaurus.asp?termid=A1061 +xref: langual:thesaurus.asp?termid=A1061 is_a: FOODON:03400874 ! GS1 Global Product Classification (GPC) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03401095 name: 50192900 - pasta/noodles (gs1 gpc) -xref: http://www.langual.org/langual_thesaurus.asp?termid=A1095 +xref: langual:thesaurus.asp?termid=A1095 is_a: FOODON:03401061 ! 50190000 - prepared/preserved foods (gs1 gpc) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03401270 name: U.S. code of federal regulations, title 21 food product type def: "Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL." [] comment: LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. -xref: http://www.langual.org/langual_thesaurus.asp?termid=A1270 +xref: langual:A1270 is_a: FOODON:03400289 ! USA agency food product type property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string property_value: seeAlso https://www.ecfr.gov/cgi-bin/text-idx?SID=87f720ce0d0b6c4548f4bbfd1f8e4c3d&mc=true&tpl=/ecfrbrowse/Title21/21chapterI.tpl xsd:anyURI [Term] id: FOODON:03411009 name: polysaccharide-producing plant -xref: http://www.langual.org/langual_thesaurus.asp?termid=B1009 +xref: langual:thesaurus.asp?termid=B1009 is_a: FOODON:03411048 ! carbohydrate-producing plant property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03411013 name: plant used for producing extract or concentrate -xref: http://www.langual.org/langual_thesaurus.asp?termid=B1013 +xref: langual:thesaurus.asp?termid=B1013 property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03411016 name: starch-producing plant -xref: http://www.langual.org/langual_thesaurus.asp?termid=B1016 +xref: langual:thesaurus.asp?termid=B1016 is_a: FOODON:03411009 ! polysaccharide-producing plant property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03411048 name: carbohydrate-producing plant -xref: http://www.langual.org/langual_thesaurus.asp?termid=B1048 +xref: langual:thesaurus.asp?termid=B1048 is_a: FOODON:03411013 ! plant used for producing extract or concentrate property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03412344 name: devils tongue plant -xref: http://www.langual.org/langual_thesaurus.asp?termid=B2344 +xref: langual:thesaurus.asp?termid=B2344 is_a: FOODON:03411016 ! starch-producing plant property_value: hasSynonym "amorphophallus konjac" xsd:string property_value: hasSynonym "amorphophallus rivieri" xsd:string property_value: hasSynonym "hydrosme rivieri" xsd:string property_value: hasSynonym "leopard palm" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03412637 name: konjac plant -xref: http://www.langual.org/langual_thesaurus.asp?termid=B2637 +xref: langual:thesaurus.asp?termid=B2637 is_a: FOODON:03412344 ! devils tongue plant property_value: hasSynonym "amorphophallus rivieri var. konjac" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03420108 name: sugar def: "A broad term that includes the nutritive sweeteners dextrose, fructose, galactose, lactose, maltose and sucrose, which are simple carbohydrates with molecules composed of one or two saccharide units. Note that on a product label or in a recipe, 'sugar' means *SUCROSE* and should be so indexed. Use the broad term *SUGAR* only if the specific sugar used is not known or not listed in the vocabulary." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=C0108 +xref: langual:thesaurus.asp?termid=C0108 is_a: FOODON:03420152 ! carbohydrate extract, concentrate, or isolate property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string + +[Term] +id: FOODON:03420116 +name: organism material +def: "Anatomical or other part(s) or substances derived from plant or animal or fungal organisms." [] +comment: LanguaL curation note: "e.g. *LEAF*, *ROOT OR TUBER*, *ORGAN MEAT*, *MILK* OR *EGG*; it also includes components of parts, such as *CREAM*, and extracts, concentrates or isolates, such as *PROTEIN EXTRACT* or *SUGAR*." +xref: langual:thesaurus.asp?termid=C0116 +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "This was renamed from \"part of organism\" (and from LanguaL's original \"part of plant or animal\") to encompass organism material that is produced by an animal or plant rather than \"part of\" it, such as an egg, and might not be countable per se, such as milk. Additionally the existing definition's \"from which a food product or its major ingredient is derived.\" was removed as an unnecessary constraint. [2023/03/02]" xsd:string [Term] id: FOODON:03420152 name: carbohydrate extract, concentrate, or isolate def: "Extract, concentrate or isolate high in sugar, oligosaccharide or polysaccharide." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=C0152 +xref: langual:thesaurus.asp?termid=C0152 is_a: FOODON:03420228 ! extract, concentrate or isolate of plant or animal -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03420156 name: brown sugar def: "Soft sugar whose crystals are covered by a film of refined dark syrup that imparts color, flavor, and moisture." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=C0156 +xref: langual:C0156 is_a: FOODON:00001083 ! sugar condiment is_a: FOODON:03301073 ! sugar (granulated) property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string + +[Term] +id: FOODON:03420164 +name: animal material +def: "Material that derives from some animal." [] +comment: Langual note: Includes eggs and milk that, although separated from the animal, are produced as integral parts and are affected by the animal's food intake and metabolism. +comment: This branch isn't necessarily food material +xref: langual:thesaurus.asp?termid=C0164 +is_a: FOODON:03420116 ! organism material +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5275-8866 xsd:string +property_value: http://purl.org/dc/terms/date 2023-08-01T21:25:29Z xsd:dateTime +property_value: IAO:0000114 IAO:0000122 [Term] id: FOODON:03420228 name: extract, concentrate or isolate of plant or animal def: "A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed." [] comment: Damion Dooley's note: Items in this branch will be merged into foodon food product branch. -xref: http://www.langual.org/langual_thesaurus.asp?termid=C0228 +xref: langual:C0228 is_a: FOODON:00001714 ! food product component property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03420244 name: mammalian milk whey def: "The serum or watery part of milk that is separated from the thicker or more coagulable part or curd, espcially in the process of making cheese; it contains lactose, minerals and lactalbumin." [] synonym: "whey" EXACT [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=C0244 +xref: langual:thesaurus.asp?termid=C0244 is_a: FOODON:03315150 ! mammalian milk product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03420307 name: seed oil def: "The oil produced by pressing or extracting lipids from plant seeds (e.g. grapeseed oil, rapeseed oil, linseed oil) /AM" [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=C0307 +xref: langual:thesaurus.asp?termid=C0307 is_a: FOODON:00001087 ! vegetable oil food product property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03430109 name: food (liquid, low viscosity) def: "A liquid that flows very easily at room temperature. Examples are: water, apple juice, sherry, acidophilus milk, whipping cream and some heavy liqueurs. The range of low viscosity liquid spans sucrose solutions between 0 and 45% solids (viscosity range from 1 to 10 centipoise). Prefer 'solid pieces' factor term to 'small particles' if both appear in the food." [] -xref: http://www.langual.org/langual_thesaurus.asp?termid=E0109 +xref: langual:thesaurus.asp?termid=E0109 is_a: FOODON:03430130 ! food (liquid) property_value: hasSynonym "liquid, thin" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03430130 name: food (liquid) def: "A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*." [] -comment: SIREN DB annotation:\n* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130)\n -xref: http://www.langual.org/langual_thesaurus.asp?termid=E0130 -xref: SUBSET_SIREN:F5105 -is_a: FOODON:00002454 ! food product by quality +comment: SIREN DB annotation:\n* liquid FOODON:03430130 +xref: https://bioregistry.io/reference/siren\:F5105 +xref: langual:thesaurus.asp?termid=E0130 +is_a: FOODON:00002454 ! food material by characteristic property_value: hasSynonym "fluid" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03460156 name: obsolete: molasses added -property_value: IAO:0000412 http://langual.org xsd:string is_obsolete: true replaced_by: http://purl.obolibrary.org/obo/CHEBI_83163 @@ -3251,37 +3303,34 @@ replaced_by: http://purl.obolibrary.org/obo/CHEBI_83163 id: FOODON:03460177 name: plant seed or nut food product comment: LanguaL curation note: With the exception of peanut (see *PEANUT OR PEANUT BUTTER ADDED*), used when a nut or seed ingredient is the second ingredient in order of predominance. -xref: http://www.langual.org/langual_thesaurus.asp?termid=H0177 +xref: langual:H0177 is_a: FOODON:00001015 ! plant food product union_of: FOODON:00001172 ! nut food product union_of: FOODON:00001173 ! plant seed food product property_value: IAO:0000116 "This disjunction is provided for food indexers who used the LanguaL category per guidelines. Currently, by specifying the more specific nut or seed as ingredient instead, this category can be inferred." xsd:string property_value: IAO:0000118 "nut or seed added" xsd:string -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03460231 name: chocolate or cocoa comment: LanguaL curation note: Used when chocolate or cocoa is added at any level or when chocolate is used as a coating. -xref: http://www.langual.org/langual_thesaurus.asp?termid=H0231 +xref: langual:thesaurus.asp?termid=H0231 is_a: FOODON:00001215 ! cacao food product union_of: FOODON:00001280 ! chocolate food product union_of: FOODON:03315302 ! cocoa food product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000118 "chocolate or cocoa added" xsd:string -property_value: IAO:0000412 http://langual.org xsd:string [Term] id: FOODON:03460263 name: vegetable fat or oil def: "A fat or oil derived from vegetable material" [] comment: This is a convenience class inherited from LanguaL -xref: http://www.langual.org/langual_thesaurus.asp?termid=H0263 +xref: langual:H0263 is_a: FOODON:00001174 ! plant lipid food product union_of: FOODON:00001087 ! vegetable oil food product union_of: FOODON:03316694 ! vegetable fat food product property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Damion Dooley" xsd:string property_value: IAO:0000118 "vegetable fat or oil added" xsd:string -property_value: IAO:0000412 http://langual.org xsd:string diff --git a/src/envo/imports/foodon_import.owl b/src/envo/imports/foodon_import.owl index 70276272..02df532b 100644 --- a/src/envo/imports/foodon_import.owl +++ b/src/envo/imports/foodon_import.owl @@ -1,7 +1,6 @@ + - + - + - - - - - - - + @@ -134,6 +127,12 @@ + + + + + + @@ -188,23 +187,6 @@ - - - - - - - - - - - - - emmenthal cheese food product + + A semi-hard, yellow cheese that has mild flavor that is slightly buttery. + Emmental cheese + Emmentaler cheese + emmenthal cheese + @@ -573,8 +590,15 @@ + A small, sweetish, soft, square cow's milk cheese from Normandy with a yellowish-orange rind. pont ieveque cheese food product + + + + A small, sweetish, soft, square cow's milk cheese from Normandy with a yellowish-orange rind. + http://www.whatamieating.com/?b=1&d=1&t=main&s=Pont+l%27Eveque&r=All + @@ -582,8 +606,15 @@ + A disc of soft cheese made with cow's milk. It has a soft to runny paste and a smooth, pink rind. vacherin mont dor cheese food product + + + + A disc of soft cheese made with cow's milk. It has a soft to runny paste and a smooth, pink rind. + http://www.whatamieating.com/?b=1&d=1&t=main&s=vacherin+Mont+d%27Or&r=All + @@ -605,8 +636,15 @@ + A meat that is preserved by the addition of a combination of salt, sugar, nitrates or nitrite and or is smoked. cured meat food product + + + + A meat that is preserved by the addition of a combination of salt, sugar, nitrates or nitrite and or is smoked. + http://en.wikipedia.org/wiki/Cured_meat + @@ -623,7 +661,11 @@ - beef food product + + A food product that is derived from some cow. + https://orcid.org/0000-0001-5275-8866 + 2024-06-27T22:43:12Z + cow food product @@ -634,10 +676,17 @@ + A frozen dessert usually made from dairy products, such as milk and cream, and often combined with fruits or other ingredients and flavours. Most varieties contain sugar, although some are made with other sweeteners. In some cases, artificial flavourings and colourings are used in addition to (or in replacement of) the natural ingredients. This mixture is stirred slowly while cooling to prevent large ice crystals from forming; the result is a smoothly textured ice cream. ice cream ice-cream ice cream food product + + + + A frozen dessert usually made from dairy products, such as milk and cream, and often combined with fruits or other ingredients and flavours. Most varieties contain sugar, although some are made with other sweeteners. In some cases, artificial flavourings and colourings are used in addition to (or in replacement of) the natural ingredients. This mixture is stirred slowly while cooling to prevent large ice crystals from forming; the result is a smoothly textured ice cream. + Wikipedia:Ice_cream + @@ -678,8 +727,15 @@ + A cut of meat (a meat chop) cut perpendicularly to the spine of the pig and usually containing a rib or part of a vertebra, served as an individual portion. pork chop food product + + + + A cut of meat (a meat chop) cut perpendicularly to the spine of the pig and usually containing a rib or part of a vertebra, served as an individual portion. + http://en.wikipedia.org/wiki/Pork_chop + @@ -755,12 +811,10 @@ - - A fine powder made from cereals or other starchy food sources. + + A food product made from flour. Damion Dooley Wikipedia:Flour - http://www.langual.org/langual_thesaurus.asp?termid=H0152 - flour added flour food product @@ -801,10 +855,11 @@ Apple juice is a fruit juice made by the maceration and pressing of an apple. https://en.wikipedia.org/wiki/Apple_juice - http://langual.org - SUBSET_SIREN:F1419 + apple juice - subset_siren + SIREN DB annotation: +* liquid, low viscosity, with no visible particles FOODON:03430123 +* fruit, peel present, core, pit or seed present FOODON:03420140 apple juice @@ -866,16 +921,22 @@ - SUBSET_SIREN:F1128 - subset_siren + A class of cow's milk, sheep's milk, or goat's milk cheeses that have had Penicillium cultures added so that the final product is spotted or veined throughout with blue, blue-gray or blue-green mould, and carries a distinct smell. + SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'curd' (http://purl.obolibrary.org/obo/FOODON_03420245) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) -* formed as a result of 'interior mold curing process' (http://purl.obolibrary.org/obo/FOODON_03460331) +* solid FOODON:03430151 +* curd FOODON:03420245 +* curing or aging process FOODON:03460253 +* interior mold curing process FOODON:03460331 blue cheese food product https://en.wikipedia.org/wiki/List_of_blue_cheeses + + + + A class of cow's milk, sheep's milk, or goat's milk cheeses that have had Penicillium cultures added so that the final product is spotted or veined throughout with blue, blue-gray or blue-green mould, and carries a distinct smell. + Wikipedia:Blue_cheese + @@ -884,8 +945,15 @@ + The liquid left over after producing butter from cream during the churning process. buttermilk food product + + + + The liquid left over after producing butter from cream during the churning process. + Wikipedia:Buttermilk + @@ -906,16 +974,15 @@ A food produced by fermenting rice, barley and/or soybeans, with salt and the mold koji-kin (Aspergillus oryzae). Damion Dooley - SUBSET_SIREN:F1971 - subset_siren + SIREN DB annotation: -* has quality 'semisolid' (http://purl.obolibrary.org/obo/FOODON_03430144) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) -* formed as a result of 'fermentation/modification process, multiple component' (http://purl.obolibrary.org/obo/FOODON_03460128) -* formed as a result of 'salted' (http://purl.obolibrary.org/obo/FOODON_03460173) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) -* formed as a result of 'preservation by fermentation' (http://purl.obolibrary.org/obo/FOODON_03470104) +* semisolid FOODON:03430144 +* fully heat-treated FOODON:03440014 +* seed, skin present, germ present FOODON:03420133 +* fermentation/modification process, multiple component FOODON:03460128 +* salted FOODON:03460173 +* curing or aging process FOODON:03460253 +* preservation by fermentation FOODON:03470104 miso food product @@ -938,8 +1005,15 @@ + A liquid produced from the fermentation of ethanol in a process that yields its key ingredient, acetic acid. vinegar food product + + + + A liquid produced from the fermentation of ethanol in a process that yields its key ingredient, acetic acid. + Wikipedia:Vinegar + @@ -956,8 +1030,15 @@ + Vinegar is made by malting barley, causing the starch in the grain to turn to maltose. barley malt vinegar + + + + Vinegar is made by malting barley, causing the starch in the grain to turn to maltose. + Wikipedia:Malt_vinegar#Malt + @@ -1011,11 +1092,10 @@ SUBSET_SIREN:F1302 SUBSET_SIREN:F16510 pickled - subset_siren subset_siren SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* formed as a result of 'pickling process' (http://purl.obolibrary.org/obo/FOODON_03460190) +* solid FOODON:03430151 +* pickling process FOODON:03460190 food (pickled) @@ -1034,8 +1114,15 @@ + A soft cheese made with cow's milk. It has a creamy paste and a greyish-red and downy white penicillin rind and is sometimes foil-wrapped. Bondon cheese food product + + + + A soft cheese made with cow's milk. It has a creamy paste and a greyish-red and downy white penicillin rind and is sometimes foil-wrapped. + http://www.whatamieating.com/?b=1&d=1&t=main&s=bondon&r=All + @@ -1061,8 +1148,15 @@ + A fermented milk drink made from milk. It is prepared by inoculating cow, goat, or sheep's milk with kefir grains, a combination of bacteria and yeasts in a matrix of proteins, lipids, and sugars. This symbiotic matrix forms "grains" that resemble cauliflower. Many different bacteria and yeasts are found in the kefir grains, which are a complex and highly variable community of micro-organisms termed probiotics. kefir food product + + + + A fermented milk drink made from milk. It is prepared by inoculating cow, goat, or sheep's milk with kefir grains, a combination of bacteria and yeasts in a matrix of proteins, lipids, and sugars. This symbiotic matrix forms "grains" that resemble cauliflower. Many different bacteria and yeasts are found in the kefir grains, which are a complex and highly variable community of micro-organisms termed probiotics. + Wikipedia:Kefir + @@ -1074,7 +1168,7 @@ A lipid material derived from plants. Physically, oils are liquid at room temperature. Damion Dooley - + vegetable oil food product @@ -1088,9 +1182,8 @@ An oil used as a nutritional supplement and is a traditional European ethnic food, highly regarded for its nutty flavor. - http://langual.org - 2019-09-19T21:51:42Z - http://www.langual.org/langual_thesaurus.asp?termid=H0852 + 2019-09-19T21:51:42Z + langual:H0852 flax oil flax seed oil linseed oil @@ -1104,9 +1197,10 @@ - - corn flour food product + + A food product made from milling corn. + milled corn food product @@ -1173,16 +1267,13 @@ Damion Dooley - http://langual.org - 2019-06-11T07:25:19Z - SUBSET_SIREN:F5644 + 2019-06-11T07:25:19Z + alcoholic beverage - subset_siren SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) -* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) - +* liquid FOODON:03430130 +* microbial/enzymatic modification process FOODON:03460119 +* curing or aging process FOODON:03460253 fermented beverage @@ -1248,17 +1339,14 @@ Damion Dooley - http://langual.org - 2019-06-20T07:47:47Z - SUBSET_SIREN:F2385 - subset_siren + 2019-06-20T07:47:47Z + SIREN DB annotation: -* has quality 'liquid, low viscosity' (http://purl.obolibrary.org/obo/FOODON_03430109) -* formed as a result of 'acidified' (http://purl.obolibrary.org/obo/FOODON_03460200) -* has substance added 'water addition process' (http://purl.obolibrary.org/obo/FOODON_03460148) -* has substance added 'sweetener added' (http://purl.obolibrary.org/obo/FOODON_03460202) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - +* liquid, low viscosity FOODON:03430109 +* acidified FOODON:03460200 +* ingredient: water addition process FOODON:03460148 +* ingredient: sweetener added FOODON:03460202 +* ingredient: flavoring, spice or herb added FOODON:03460227 orange fruit beverage @@ -1564,6 +1652,11 @@ + + 2023-05-03T04:59:00Z + + SIREN DB annotation: +* seed (anatomical part) FOODON:03420155 wheat food product @@ -1621,7 +1714,7 @@ Food items that are rich in sugar, any one or type of which is called a confection. Modern usage may include substances rich in artificial sweeteners as well. - + confectionery food product @@ -1684,7 +1777,6 @@ - http://langual.org obsolete: watermelon plant true @@ -1866,7 +1958,7 @@ The default nut product is a whole, raw nut - meaning that the kernel is whole, and moderately or significantly dried, but not baked. Minimal references to nuts often leave ambiguous whether the shell is on or off. "I ate a peanut" doesn't clarify whether I ate a shell-off nut or whether I did the shelling. Damion Dooley - SUBSET_SIREN:F16972 + nut food product @@ -1913,6 +2005,7 @@ + A food product with insects as a defining ingredient. insect food product @@ -1939,11 +2032,12 @@ - + Food product that is 1) ready or nearly ready for consumption; 2) usually a composite of several foods or ingredients that often belong to distinct product types; 3) usually formulated, mixed and partially or fully cooked. prepared prepared food product + @@ -1953,7 +2047,10 @@ + A food product which is an output of a food cooking process. Damion Dooley + https://en.wikipedia.org/wiki/Cooking + cooked food (cooked) @@ -1974,7 +2071,8 @@ - + A staple food prepared from a dough of flour (usually wheat) and water, usually by baking + bread food product @@ -1985,9 +2083,7 @@ This food product type includes food products which are derived from a large, diverse group of photosynthetic organisms. - http://langual.org - SUBSET_SIREN:F10419 - subset_siren + algal food product @@ -2036,6 +2132,7 @@ + A food product made from oats. common oat food product oat food product @@ -2064,6 +2161,7 @@ + A food product made from quinoa quinoa food product @@ -2115,12 +2213,12 @@ - + A product of the dry seeds of Cajanus cajan. http://en.wikipedia.org/wiki/Legume - pigeon pea (whole, dried) + pigeon pea (dried) @@ -2156,13 +2254,13 @@ - + A product of the dry seeds of plants of the genus Vicia. http://en.wikipedia.org/wiki/Legume dried fava bean - broad bean (whole, dried) + broad bean (dried) @@ -2226,10 +2324,9 @@ tepary bean (Ph. acutifolius) - - The winged bean food category covers beans of the winged bean plant - Damion Dooley - https://en.wikipedia.org/wiki/Winged_bean + A bean food product which derives from a winged bean plant (Psophocarpus tetragonolobus). + https://en.wikipedia.org/wiki/Winged_bean + http://orcid.org/0000-0002-8844-9165 winged bean food product @@ -2250,7 +2347,7 @@ tepary bean (Ph. acutifolius) A product of the dry seeds of Vicia sativa. - vetch seed (whole, dried) + vetch seed (dried) @@ -2290,7 +2387,7 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth A product of the dry seeds of Mucuna pruriens var. utilis. http://en.wikipedia.org/wiki/Legume - velvet bean (whole, dried) + velvet bean (dried) @@ -2300,8 +2397,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A product of the dry seeds of Lupinus spp. lupin seed food product + + + + A product of the dry seeds of Lupinus spp. + http://en.wikipedia.org/wiki/Pulse_%28legume%29 + @@ -2321,7 +2425,7 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth A dry seed of the jack-bean plant. http://en.wikipedia.org/wiki/Legume - jack bean (whole, dried) + jack bean (dried) @@ -2331,8 +2435,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A product of the dry seeds of Lablab purpureus. hyacinth bean food product + + + + A product of the dry seeds of Lablab purpureus. + http://en.wikipedia.org/wiki/Pulse_%28legume%29 + @@ -2365,7 +2476,9 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth - + + A food made from an unleavened dough of wheat or buckwheat flour and water, sometimes with other ingredients such as eggs and vegetable extracts. + pasta food product @@ -2376,8 +2489,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A pastry food product is a food product containing a pastry component. The food may be ready for consumption or may require further cooking. pastry food product + + + + A pastry food product is a food product containing a pastry component. The food may be ready for consumption or may require further cooking. + http://en.wikipedia.org/wiki/Pastry + @@ -2388,7 +2508,7 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth A confection made from a concentrated solution of sugar in water, to which flavorings and colorants are added. Damion Dooley - + candy food product @@ -2410,10 +2530,17 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth - LANGUAL:C0195 + A dairy product that is composed of the higher-butterfat layer skimmed from the top of milk before homogenization. + sweet cream cream food product + + + + A dairy product that is composed of the higher-butterfat layer skimmed from the top of milk before homogenization. + http://en.wikipedia.org/wiki/Cream + @@ -2422,8 +2549,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + An opague white dairy product produced by the mammary glands of female mammals. mammalian milk beverage + + + + An opague white dairy product produced by the mammary glands of female mammals. + http://en.wikipedia.org/wiki/Milk + @@ -2431,6 +2565,7 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A food product with bees or bee substances as a defining ingredient. bee food product @@ -2449,8 +2584,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A sausage that is cooked and then smoked or smoke-cooked. sausage (cooked, smoked) + + + + A sausage that is cooked and then smoked or smoke-cooked. + http://en.wikipedia.org/wiki/Sausage + @@ -2467,6 +2609,9 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + Sausage which is cured with a food smoking process. + + SUBSET_SIREN:F10756 sausage (smoked) @@ -2485,8 +2630,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A raw sausage that is smoked. sausage (raw, smoked) + + + + A raw sausage that is smoked. + http://en.wikipedia.org/wiki/Sausage + @@ -2497,7 +2649,7 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth A sausage made from meats that have not been previously cured. https://en.wikipedia.org/wiki/Sausage - SUBSET_SIREN:F1113 + sausage (raw) @@ -2511,7 +2663,7 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth A cured sausage that is fermented and dried. Damion Dooley http://en.wikipedia.org/wiki/Sausage - sausage (dried, fermented) + meat sausage (dried, fermented) @@ -2524,8 +2676,9 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth A sausage made with fresh meats, and then fully cooked. Damion Dooley - - sausage (cooked) + + SUBSET_SIREN:F10754 + meat sausage (cooked) @@ -2544,6 +2697,8 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A cheese product made from traditional cheese and emulsifying salts, often with the addition of milk, more salt, preservatives, and food coloring. + processed cheese food product @@ -2552,8 +2707,9 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth - + + A product made from the seeds of a mustard plant (white or yellow mustard, Sinapis hirta; brown or Indian mustard, Brassica juncea; or black mustard, Brassica nigra). mustard seed food product @@ -2564,8 +2720,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A salad dressing that is usually mayonnaise-based, but which may also contain yogurt, sour cream, or creme fraiche. creamy salad dressing + + + + A salad dressing that is usually mayonnaise-based, but which may also contain yogurt, sour cream, or creme fraiche. + http://en.wikipedia.org/wiki/Salad_dressing#Dressings + @@ -2573,8 +2736,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A salad dressing that is an emulsion of a vegetable oil and vinegar, often flavored with herbs, spices, and other ingredients. vinaigrette dressing food product + + + + A salad dressing that is an emulsion of a vegetable oil and vinegar, often flavored with herbs, spices, and other ingredients. + http://en.wikipedia.org/wiki/Vinaigrette + @@ -2591,8 +2761,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A stable emulsion of oil, and vinegar or lemon juice, with many options for embellishment with other herbs and spices. Egg yolk is the traditional emulsifier. mayonnaise food product + + + + A stable emulsion of oil, and vinegar or lemon juice, with many options for embellishment with other herbs and spices. Egg yolk is the traditional emulsifier. + http://en.wikipedia.org/wiki/Mayonnaise + @@ -2601,8 +2778,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A condiment produced by fermenting soybeans with Aspergillus oryzae and Aspergillus soyae molds along with roasted grain, water, and salt. soy sauce food product + + + + A condiment produced by fermenting soybeans with Aspergillus oryzae and Aspergillus soyae molds along with roasted grain, water, and salt. + http://en.wikipedia.org/wiki/Soy_sauce + @@ -2627,14 +2811,23 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + + + + + + + + - + A food product that has some spice or herb as a defining ingredient. A vegetable product such as leaves, flowers, seeds and roots that is rich in essential oils and aromatic principles. Used mainly a a condiment. Damion Dooley http://www.fao.org/WAICENT/faoinfo/economic/faodef/fdef10e.htm#1.01 - http://www.langual.org/langual_thesaurus.asp?termid=H0151 - herb and spice + https://orcid.org/0000-0001-5275-8866 + 2023-08-16T10:14:35Z + herb or spice spice or herb @@ -2658,7 +2851,7 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth A brewed drink prepared from roasted seeds, commonly called coffee beans, of the coffee plant. Damion Dooley - + coffee beverage @@ -2671,7 +2864,7 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth A beverage prepared from the cured leaves of Camellia sinensis by combination with hot or boiling water. Damion Dooley - + tea beverage (liquid) @@ -2681,8 +2874,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A heated beverage typically consisting of shaved chocolate or cocoa powder, heated milk or water, and sugar. hot chocolate food product + + + + A heated beverage typically consisting of shaved chocolate or cocoa powder, heated milk or water, and sugar. + http://en.wikipedia.org/wiki/Hot_chocolate + @@ -2690,8 +2890,15 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A beverage prepated by steeping dry leaves (and twigs) of yerba mate in hot water. mate food product + + + + A beverage prepated by steeping dry leaves (and twigs) of yerba mate in hot water. + http://en.wikipedia.org/wiki/Yerba_Mate + @@ -2722,7 +2929,11 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth - avian food product + + A food product that is derived from some avian animal. + https://orcid.org/0000-0001-5275-8866 + 2024-06-27T22:43:12Z + avian animal food product @@ -2742,6 +2953,7 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A beverage derived from plants. plant derived beverage @@ -2781,7 +2993,7 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth A dairy food product has mammilian milk or a milk component as an ingredient. Damion Dooley - http://www.langual.org/langual_thesaurus.asp?termid=H0242 + dairy product milk product dairy food product @@ -2836,9 +3048,10 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth - Any plant food product which, typically, is constituted by intact parts from one or more annual plants cultivated as field and garden crops in the open and under glass, and used almost exclusively for food. - + A plant food product which derives from one or more vegetables. + FAO definition for vegetable: "Vegetables are plants cultivated both as field crops and garden crops, both in the open and under glass." and also: "Vegetables are grouped according to botanic characteristics as follows: leafy or stem vegetables (e.g., cabbage); fruit-bearing vegetables (e.g., melons); flower vegetables (e.g., cauliflowers); root, bulb and tuberous vegetables (e.g., onion); leguminous vegetables (e.g., green peas); other vegetables (e.g., green maize and mushrooms)." vegetable food product + @@ -2847,8 +3060,18 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. botanical fruit food product + + + + Mature ovary of a plant, with a fleshy part of the carpel that develops with the seed to attract animals for aid in dispersal. Botanically, nuts are considered fruits. + http://eurovoc.europa.eu/drupal/?q=request&amp;uri=http://eurovoc.europa.eu/1115 + http://oek1.fao.org/skosmos/agrovoc/en/page/c_3119 + http://www.fao.org/pollination/resources/glossary/en/ + https://en.wikipedia.org/wiki/Fruit + @@ -2859,8 +3082,6 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth A one-celled fruit (pod) usually dehiscing down both sutures, and having the seed attached along a ventral suture. (Roubik 1995) http://www.fao.org/pollination/resources/glossary/en/ legume - http://purl.obolibrary.org/obo/FOODON_03411338 - http://purl.obolibrary.org/obo/FOODON_03411254 legume food product @@ -2890,10 +3111,17 @@ FAO: The yam bean is a legume but unlike its close relatives the soybean and oth + A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. Regarding American regulatory aspects of egg products, see this summary: https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-graphic-000077 egg food product + + + + A food consisting of a round or oval body laid by the female of many animals, consisting of an ovum surrounded by layers of membranes and an outer casing, which acts to nourish and protect a developing embryo and its nutrient reserves. + Wikipedia:Egg_%28food%29 + @@ -2902,10 +3130,10 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr - A hen egg food product is any food product consisting mainly of hen eggs or derivatives. + An avian egg food product having chicken eggs or derivatives as a defining ingredient. https://en.wikipedia.org/wiki/Egg_as_food - SUBSET_SIREN:F1074 - hen egg food product + + chicken egg food product @@ -2936,8 +3164,15 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr + A food that is usually sweet and often baked. Cakes normally combine some kind of flour, a sweetening agent (commonly sugar), a binding agent (generally egg, though gluten or starch are often used by lacto-vegetarians and vegans), fats (usually butter, shortening, or margarine, although a fruit puree such as applesauce is sometimes substituted to avoid using fat), a liquid (milk, water or fruit juice), flavors and some form of leavening agent (such as yeast or baking powder), though many cakes lack these ingredients and instead rely on air bubbles in the dough to expand and cause the cake to rise. Cake is often frosted with buttercream or marzipan, and finished with piped borders and crystallized fruit. cake food product + + + + A food that is usually sweet and often baked. Cakes normally combine some kind of flour, a sweetening agent (commonly sugar), a binding agent (generally egg, though gluten or starch are often used by lacto-vegetarians and vegans), fats (usually butter, shortening, or margarine, although a fruit puree such as applesauce is sometimes substituted to avoid using fat), a liquid (milk, water or fruit juice), flavors and some form of leavening agent (such as yeast or baking powder), though many cakes lack these ingredients and instead rely on air bubbles in the dough to expand and cause the cake to rise. Cake is often frosted with buttercream or marzipan, and finished with piped borders and crystallized fruit. + Wikipedia:Cake + @@ -2979,16 +3214,18 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr + - A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese. - + Beef that has been ground. + https://en.wikipedia.org/wiki/Ground_beef beef mince beef mince ground beef hamburger meat minced beef - ground beef food product + A ground beef product is made of beef that has been finely chopped with a knife or a meat grinder (American English) or mincing machine (British English). Ground beef is used in many recipes including hamburgers and spaghetti Bolognese. + beef (ground) @@ -2999,8 +3236,12 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr A food product from a category of domestic birds kept for meat, eggs, and feathers including fowl such as chickens, turkeys, and waterfowls such as domestic ducks and geese and other meat birds such as pigeons and doves and games birds including pheasants. + A food product that is derived from some poultry. Damion Dooley + + https://orcid.org/0000-0002-8844-9165 + 2024-06-27T22:43:12Z poultry food product @@ -3010,6 +3251,7 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr + duck meat food product @@ -3115,7 +3357,7 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr A family of hard Italian cheeses made from sheep milk. Damion Dooley - + pecorino cheese @@ -3185,24 +3427,6 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr - - - - - - - - - - - - - - barley flour food product - - - - @@ -3212,9 +3436,9 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr Note, this was previously labelled "Bean (vegetable) food product". We have been listing both dry and freshly harvested moist beans here, so have broadened the name scope. Damion Dooley bean food product - https://oconto.extension.wisc.edu/files/2011/02/The-Importance-of-Dry-Beans-in-Your-Diet.pdf - http://purl.obolibrary.org/obo/FOODON_00002428 - http://www.fao.org/es/faodef/fdef04e.htm#4.02 + + + @@ -3384,6 +3608,7 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr + A mix or ready made sauce for dipping or adding to food, especially salad. food dressing product @@ -3443,18 +3668,6 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr - - - - - - A food product made from legumes that are considered vegetables, such as immature raw legume pods or seeds. - Damion Dooley - leguminous vegetable food product - - - - @@ -3520,21 +3733,6 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr - - - - - - - - A product containing primarily immature ripe pigeon peas. - Damion Dooley - 2019-07-14T10:26:00 - pigeon pea vegetable food product - - - - @@ -3673,7 +3871,8 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr - plant stem or spear vegetable food product + A food product deriving from a plant stem or spear part. + plant stem or spear food product @@ -3724,7 +3923,7 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr A prepared hen egg product is a product predominantly made of hen egg that has been cooked and may only require defrosting or reheating for consumption. Damion Dooley - prepared hen egg product + prepared chicken egg product @@ -3805,7 +4004,7 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr - http://www.langual.org/langual_thesaurus.asp?termid=H0202 + sweetener food product @@ -3852,6 +4051,7 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr + A vegetable food product containing one or more pickled vegetables. vegetable pickle food product @@ -3894,7 +4094,6 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience - food foodstuff nourishment @@ -3935,11 +4134,12 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr - + - A class which contains food product categories qualified by a quality such as granularity or temperature, which is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. + Food material which has been categorized by a characteristic such as granularity or temperature. Damion Dooley - food product by quality + This term was renamed from "food product by quality" to align better with COB "characteristic" label, and as well to disambiguate from other use of "quality" as a food grading. This term is useful for tasks like food inspection where little prior knowledge of how the food came to be is available. Some terms like "food (frozen)" are both a quality descriptor and the output of a process. + food material by characteristic @@ -3962,7 +4162,7 @@ https://www.politico.com/agenda/story/2016/03/crazy-us-chicken-egg-regulation-gr A food product consisting of food material derived from ingredients sourced from multiple organisms. Damion Dooley - 2019-01-23T22:40:32Z + 2019-01-23T22:40:32Z multi-ingredient The definition of this is being discussed in issue: https://github.com/FoodOntology/foodon/issues/57 @@ -3980,8 +4180,8 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A preserved food, where the moisture levels in the food product have been reduced to low levels to improve shelf life. Damion Dooley https://www.sciencedirect.com/topics/food-science/food-dehydration - https://orcid.org/0000-0002-8844-9165 | https://orcid.org/0000-0001-5193-0062 | https://orcid.org/0000-0001-8008-8249 - 2019-05-23T19:53:09Z + https://orcid.org/0000-0002-8844-9165 | https://orcid.org/0000-0001-5193-0062 | https://orcid.org/0000-0001-8008-8249 + 2019-05-23T19:53:09Z food (dessicated) food (dehydrated) @@ -3995,7 +4195,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A food product organized by the process which it results from. Damion Dooley - 2019-05-23T23:02:07Z + 2019-05-23T23:02:07Z food product by process @@ -4005,8 +4205,12 @@ Namely, how to characterize the threshold of ingredients that make for multi-com + + A food product that is derived from some pig. Damion Dooley - 2019-06-14T04:23:35Z + https://orcid.org/0000-0002-8844-9165 + 2019-06-14T04:23:35Z + pig food product pork food product @@ -4019,7 +4223,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A lipid food product is a food product made primarily of plant or animal fat or oil Damion Dooley - 2019-06-11T09:18:41Z + 2019-06-11T09:18:41Z fats and oils oils and fats lipid food product @@ -4043,9 +4247,9 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A whole dried bean is a bean resulting from natural or mechanical air drying applied to a bean or bean pod. Damion Dooley - 2019-06-29T14:48:10Z + 2019-06-29T14:48:10Z dried bean - bean (whole, dried) + bean (dried) http://www.fao.org/es/faodef/fdef04e.htm#4.02 @@ -4055,14 +4259,15 @@ Namely, how to characterize the threshold of ingredients that make for multi-com + A seed of a bean plant from one of several genera of the flowering plant family (Fabaceae). Damion Dooley's note. This could be enhanced to explicitly state the anatomical parts of a seed - seed coat, cotyledons, embryo etc. Currently the Plant Ontology is not explicit about this yet. Damion Dooley - https://orcid.org/0000-0001-5275-8866 - 2020-10-14T07:28:59 + https://orcid.org/0000-0001-5275-8866 + 2020-10-14T07:28:59 bean - bean (whole) + bean @@ -4083,7 +4288,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Cooked bean material is the bean material output of a cooking process applied to dry, rehydrated, or raw (fresh) beans. Damion Dooley - 2019-07-08T21:47:07Z + 2019-07-08T21:47:07Z bean (cooked) @@ -4097,9 +4302,9 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A seed of a jack seed plant (Canavalia ensiformis). Damion Dooley https://en.wikipedia.org/wiki/Canavalia_ensiformis - 2019-07-09T22:17:36 + 2019-07-09T22:17:36 jack bean - jack bean (whole) + jack bean @@ -4109,7 +4314,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Damion Dooley - 2019-07-09T22:21:16Z + 2019-07-09T22:21:16Z jack-bean food product @@ -4122,7 +4327,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A pigeon pea food product is a food product derived from the pigeon pea plant Damion Dooley - 2019-07-09T22:29:17Z + 2019-07-09T22:29:17Z pigeon pea food product https://en.wikipedia.org/wiki/Pigeon_pea @@ -4132,14 +4337,15 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - + + A seed of a pigeon pea plant (Cajanus cajan). - http://orcid.org/0000-0002-8844-9165 https://en.wikipedia.org/wiki/Pigeon_pea - 2019-07-09T22:29:49 + http://orcid.org/0000-0002-8844-9165 + 2019-07-09T22:29:49 pigeon pea - pigeon pea (whole) + pigeon pea @@ -4154,11 +4360,11 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Damion Dooley https://en.wikipedia.org/wiki/Mucuna_pruriens http://en.wikipedia.org/wiki/Legume - 2019-07-10T00:00:22 + 2019-07-10T00:00:22 tericopelo bean tericopelo bean velvet bean - velvet bean (whole) + velvet bean @@ -4168,7 +4374,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Damion Dooley - 2019-07-10T00:16:38Z + 2019-07-10T00:16:38Z vetch food product @@ -4178,12 +4384,13 @@ Namely, how to characterize the threshold of ingredients that make for multi-com + A seed of a vetch plant. Damion Dooley https://en.wikipedia.org/wiki/Vicia - 2019-07-10T01:33:15Z + 2019-07-10T01:33:15Z vetch seed - vetch seed (whole) + vetch seed @@ -4194,7 +4401,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Damion Dooley - 2019-07-12T17:18:31Z + 2019-07-12T17:18:31Z pea food product @@ -4207,12 +4414,28 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A liver food product is a food product that derives from one or more liver organs. Damion Dooley - 2019-08-02T18:22:37Z + 2019-08-02T18:22:37Z liver food product + + + + + + A leaf of a plant that is used for flavoring. + The leaves, flowers, or stems of plants, typically excluding vegetables, used for flavoring or as a garnish. + + https://orcid.org/0000-0001-5275-8866 + 2019-08-24T15:26:51Z + 2023-08-16T10:14:35Z + herb food product + + + + @@ -4223,7 +4446,6 @@ Namely, how to characterize the threshold of ingredients that make for multi-com bok choy vegetable food product bomdong vegetable food product broccolini vegetable food product - chinese cabbage vegetable food product choy sum vegetable food product collard greens vegetable food product gai lan vegetable food product @@ -4244,7 +4466,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - 2020-09-06T15:59:54Z + 2020-09-06T15:59:54Z multi-component wheat food product @@ -4256,7 +4478,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A bean food product made from velvet bean. - 2021-12-24T00:12:16Z + 2021-12-24T00:12:16Z velvet bean food product @@ -4266,29 +4488,110 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - A food product deriving from one or more animals. - - 2022-09-01T16:31:09Z + + A food product that is derived from some animal. + http://orcid.org/0000-0002-8844-9165 + 2023-08-01T21:25:29Z animal food product + + + + + + One or more pieces of animals. + + https://orcid.org/0000-0002-8844-9165 + 2023-08-01T21:25:29Z + piece(s) of animal + + + + + + + + + + A food product made from milling plant material. + + 2023-10-07T13:41:10Z + milled food product + + + + + + + + + + + One or more pieces of cows. + + https://orcid.org/0000-0002-8844-9165 + 2023-12-15T22:55:22Z + piece(s) of cow + + + + + + + + + One or more pieces of beef. + piece(s) of beef + + + + + + + + + + A food product that is derived from some duck. + https://orcid.org/0000-0001-5275-8866 + https://orcid.org/0000-0002-3410-4655 + https://orcid.org/0000-0002-8844-9165 + 2024-02-12T14:11:19Z + duck food product + + + + + + + + + + Material that derives from some cow. + https://orcid.org/0000-0001-5275-8866 + https://orcid.org/0000-0002-3410-4655 + https://orcid.org/0000-0002-8844-9165 + 2024-02-12T14:11:19Z + This branch isn't necessarily food material + cow material + + + + - http://langual.org - SUBSET_SIREN:F1073 - subset_siren + SIREN DB annotation: -* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - +* crystal FOODON:03430143 +* fully heat-treated FOODON:03440014 +* sugar FOODON:03420108 +* water removal process FOODON:03460138 +* preservation by dehydration or drying FOODON:03470116 sugar (granulated) @@ -4299,14 +4602,11 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F1103 - SUBSET_SIREN:F11069 - subset_siren + + SIREN DB annotation: -* has quality 'liquid, low viscosity, with small particles' (http://purl.obolibrary.org/obo/FOODON_03430114) -* derives from 'fruit, peel removed, core, pit or seed removed' (http://purl.obolibrary.org/obo/FOODON_03420229) - +* liquid, low viscosity, with small particles FOODON:03430114 +* fruit, peel removed, core, pit or seed removed FOODON:03420229 orange juice @@ -4317,11 +4617,11 @@ Namely, how to characterize the threshold of ingredients that make for multi-com + A seed of a broad bean plant (Vicia faba). - http://orcid.org/0000-0002-8844-9165 - http://langual.org - SUBSET_SIREN:F1227 + http://orcid.org/0000-0002-8844-9165 + Windsor bean broad bean broadbean @@ -4331,8 +4631,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com field bean tic bean tick bean - subset_siren - broad bean (whole) + broad bean @@ -4342,13 +4641,10 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F1444 - subset_siren + SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - +* liquid FOODON:03430130 +* part of plant FOODON:03420174 vegetable juice food product @@ -4363,13 +4659,10 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Damion Dooley's note: This class is intended to provide the most generic reference to bean, as it does not imply any more information about the state of a bean - whether it is whole or in fragments, or fragments of several beans, whether it is dry, raw, or cooked etc. Damion Dooley https://en.wikipedia.org/wiki/Bean - http://langual.org - SUBSET_SIREN:F1467 - subset_siren + SIREN DB annotation: -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) - - bean substance +* seed (anatomical part) FOODON:03420155 + bean (whole or pieces) @@ -4381,8 +4674,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A liquid prepared for consumption, or a product that can be combined with water or milk to make one. Damion Dooley - http://langual.org - 2019-09-12T00:00:00 + 2019-09-12T00:00:00 beverage food product @@ -4391,14 +4683,11 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - + - http://langual.org - SUBSET_SIREN:F2001 - subset_siren + SIREN DB annotation: -* derives from 'part of animal' (http://purl.obolibrary.org/obo/FOODON_03420164) - +* part of animal FOODON:03420164 animal-derived food @@ -4418,15 +4707,12 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F2082 - subset_siren + SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'skeletal meat part, without bone or shell' (http://purl.obolibrary.org/obo/FOODON_03420125) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - +* solid FOODON:03430151 +* skeletal meat part, without bone or shell FOODON:03420125 +* water removal process FOODON:03460138 +* preservation by dehydration or drying FOODON:03470116 beef (dehydrated) @@ -4437,32 +4723,45 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F3220 + A food product served during the dessert course of a meal. + + desert preparation dessert - subset_siren SIREN DB annotation: -* has substance added 'sugar or sugar syrup added' (http://purl.obolibrary.org/obo/FOODON_03460136) - +* ingredient: sugar or sugar syrup added FOODON:03460136 dessert food + + + + + + A food product derived from a spice. + https://en.wikipedia.org/wiki/Spice + + SIREN DB annotation: +* whole, natural shape FOODON:03430150 +* not heat-treated FOODON:03440003 +* part of plant FOODON:03420174 + spice food product + + + + A cultured dairy product is a fermented dairy product in which a microbial starter was introduced to the fermentation process. - http://langual.org - SUBSET_SIREN:F3909 - subset_siren + SIREN DB annotation: -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) -* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) - +* milk (mammary secretion) UBERON:0001913 +* microbial/enzymatic modification process FOODON:03460119 cultured dairy product @@ -4473,13 +4772,10 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F4497 - subset_siren + SIREN DB annotation: -* has quality 'whole, natural shape' (http://purl.obolibrary.org/obo/FOODON_03430150) -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) - +* whole, natural shape FOODON:03430150 +* seed (anatomical part) FOODON:03420155 edible seed food product @@ -4499,15 +4795,12 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F5536 - subset_siren + SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'sugar syrup or syrup solids' (http://purl.obolibrary.org/obo/FOODON_03420271) -* has substance added 'honey added' (http://purl.obolibrary.org/obo/FOODON_03460149) - +* liquid, high viscosity, with no visible particles FOODON:03430139 +* fully heat-treated FOODON:03440014 +* sugar syrup or syrup solids FOODON:03420271 +* ingredient: honey added FOODON:03460149 honey blend table syrup @@ -4518,14 +4811,11 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F7345 - subset_siren + SIREN DB annotation: -* has quality 'crystal' (http://purl.obolibrary.org/obo/FOODON_03430143) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'white sugar' (http://purl.obolibrary.org/obo/FOODON_03420157) - +* crystal FOODON:03430143 +* fully heat-treated FOODON:03440014 +* white sugar FOODON:03420157 sugar (refined) @@ -4536,13 +4826,10 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F7539 - subset_siren + SIREN DB annotation: -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - +* water removal process FOODON:03460138 +* preservation by dehydration or drying FOODON:03470116 food (dried) @@ -4554,14 +4841,11 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F10006 - subset_siren + SIREN DB annotation: -* derives from 'seed (anatomical part)' (http://purl.obolibrary.org/obo/FOODON_03420155) -* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) - +* seed (anatomical part) FOODON:03420155 +* microbial/enzymatic modification process FOODON:03460119 +* curing or aging process FOODON:03460253 fermented bean product @@ -4572,26 +4856,40 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F10387 - subset_siren + SIREN DB annotation: -* has quality 'liquid, high viscosity, with no visible particles' (http://purl.obolibrary.org/obo/FOODON_03430139) -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - +* liquid, high viscosity, with no visible particles FOODON:03430139 +* fat or oil FOODON:03420190 oil + + + + + + + A seed of a legume plant in the family Fabaceae. + https://orcid.org/0000-0001-5275-8866 + 2020-10-21T09:28:28 + + SIREN DB annotation: +* whole, natural shape FOODON:03430150 +* not heat-treated FOODON:03440003 +* seed (anatomical part) FOODON:03420155 + legume + + + + - http://langual.org - SUBSET_SIREN:F11737 - subset_siren + processed food product @@ -4611,17 +4909,14 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F12053 - subset_siren + SIREN DB annotation: -* has quality 'divided or disintegrated' (http://purl.obolibrary.org/obo/FOODON_03430122) -* has quality 'fully heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440014) -* derives from 'skeletal meat part, without bone, without skin' (http://purl.obolibrary.org/obo/FOODON_03420268) -* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) -* formed as a result of 'water removal process' (http://purl.obolibrary.org/obo/FOODON_03460138) -* formed as a result of 'preservation by dehydration or drying' (http://purl.obolibrary.org/obo/FOODON_03470116) - +* divided or disintegrated FOODON:03430122 +* fully heat-treated FOODON:03440014 +* skeletal meat part, without bone, without skin FOODON:03420268 +* microbial/enzymatic modification process FOODON:03460119 +* water removal process FOODON:03460138 +* preservation by dehydration or drying FOODON:03470116 pork (dehydrated) @@ -4632,12 +4927,9 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F15150 - subset_siren + SIREN DB annotation: -* derives from 'milk (mammary secretion)' (http://purl.obolibrary.org/obo/UBERON_0001913) - +* milk (mammary secretion) UBERON:0001913 mammalian milk product @@ -4650,12 +4942,9 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A fish product is a home-made or commercially produced or retail or wholesale product containing substantial amounts of freshwater or saltwater fish and/or shellfish flesh. Note that this category should avoid items that mention a particular species of fish or shellfish. Damion Dooley - http://langual.org - SUBSET_SIREN:F15173 - subset_siren + SIREN DB annotation: -* derives from 'skeletal meat part' (http://purl.obolibrary.org/obo/FOODON_03420175) - +* skeletal meat part FOODON:03420175 fish product (unspecified species) https://en.wikipedia.org/wiki/Fish_products @@ -4667,14 +4956,11 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F15302 - subset_siren + SIREN DB annotation: -* derives from 'seed, skin present, germ present' (http://purl.obolibrary.org/obo/FOODON_03420133) -* formed as a result of 'microbial/enzymatic modification process' (http://purl.obolibrary.org/obo/FOODON_03460119) -* formed as a result of 'curing or aging process' (http://purl.obolibrary.org/obo/FOODON_03460253) - +* seed, skin present, germ present FOODON:03420133 +* microbial/enzymatic modification process FOODON:03460119 +* curing or aging process FOODON:03460253 cocoa food product @@ -4685,10 +4971,8 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F15552 + juice - subset_siren juice beverage @@ -4700,17 +4984,14 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A food product that is highly seasoned minced meat and is encased in a skin in the shape of a cylinder. https://en.wikipedia.org/wiki/Sausage - http://langual.org - - SUBSET_SIREN:F15904 + + sausage - subset_siren SIREN DB annotation: -* has quality 'whole, shape achieved by forming' (http://purl.obolibrary.org/obo/FOODON_03430147) -* derives from 'meat part of animal' (http://purl.obolibrary.org/obo/FOODON_03420103) -* has substance added 'flavoring, spice or herb added' (http://purl.obolibrary.org/obo/FOODON_03460227) - - sausage (whole) +* whole, shape achieved by forming FOODON:03430147 +* meat part of animal FOODON:03420103 +* ingredient: flavoring, spice or herb added FOODON:03460227 + meat sausage @@ -4721,13 +5002,10 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F15925 - subset_siren + SIREN DB annotation: -* has quality 'solid' (http://purl.obolibrary.org/obo/FOODON_03430151) -* derives from 'meat part of animal' (http://purl.obolibrary.org/obo/FOODON_03420103) - +* solid FOODON:03430151 +* meat part of animal FOODON:03420103 pate @@ -4738,15 +5016,12 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F16079 - subset_siren + SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) -* has quality 'heat-treated' (http://purl.obolibrary.org/obo/FOODON_03440022) -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) -* formed as a result of 'steeping' (http://purl.obolibrary.org/obo/FOODON_03450036) - +* liquid FOODON:03430130 +* heat-treated FOODON:03440022 +* part of plant FOODON:03420174 +* steeping FOODON:03450036 herbal infusion @@ -4757,12 +5032,9 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F16271 - subset_siren + SIREN DB annotation: -* derives from 'sugar' (http://purl.obolibrary.org/obo/FOODON_03420108) - +* sugar FOODON:03420108 sugar product @@ -4773,12 +5045,9 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F16579 - subset_siren + SIREN DB annotation: -* derives from 'part of plant' (http://purl.obolibrary.org/obo/FOODON_03420174) - +* part of plant FOODON:03420174 multi-component plant food product @@ -4790,12 +5059,9 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - SUBSET_SIREN:F16694 - subset_siren + SIREN DB annotation: -* derives from 'fat or oil' (http://purl.obolibrary.org/obo/FOODON_03420190) - +* fat or oil FOODON:03420190 vegetable fat food product @@ -4807,13 +5073,10 @@ Namely, how to characterize the threshold of ingredients that make for multi-com A meat product is a product organized by the form of - or processing done to - its meat component (a skeletal meat part of an animal or crustacean). - http://langual.org - SUBSET_SIREN:F17170 - subset_siren + SIREN DB annotation: -* derives from 'animal body or body part' (http://purl.obolibrary.org/obo/FOODON_03420127) - - meat (whole or parts) +* animal body or body part FOODON:03420127 + meat (whole or pieces) @@ -4824,8 +5087,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Natural cheese, cured or uncured, cheese product (which is further processed), or cheese product analog. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0115 + cheese or cheese product (us cfr) @@ -4838,8 +5100,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Fruit in all forms; includes fruit juices and fruit juice drinks, fruit butters, jellies, preserves, and related products. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0143 + pie filling, fruit fruit or fruit product (us cfr) @@ -4852,8 +5113,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Food product having functional characteristics similar to milk or milk products, including cream product analogs, margarine, and milk analogs. Certain alternate ingredients are substituted for those components that are responsible for specific functional properties. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0147 + milk or milk product analog (us cfr) @@ -4865,8 +5125,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Milk in all forms, milk-based beverage, cultured milk product, or milk or milk product analog. Index infant formula under *MEAL REPLACEMENT*. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0148 + milk or milk product (us cfr) @@ -4878,8 +5137,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Semisolid or jelled food prepared from fruit or fruit juice and other ingredients prescribed for the individual products (21 CFR 150). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0155 + fruit butter, jelly, preserve or related product (us cfr) @@ -4891,8 +5149,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Milk, a product derived from milk, or a dairy product analog; includes cheese and frozen dairy desserts. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0164 + dairy product (us cfr) @@ -4904,8 +5161,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Cheese made from milk or milk components, such as cream, by the following process: (1) produce curd through coagulation of milk by bacterial action and/or enzymes and/or acidification and draining of whey. (2) For cured cheese only: cure the curd. Excludes products made through further processing, such as comminuting (see *CHEESE PRODUCT*). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0187 + natural cheese (us cfr) @@ -4917,8 +5173,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Candy or other food product made with sweeteners and frequently containing nuts, fruits, starches, flavorings and other foods (21 CFR 170.3(n)(9). [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0188 + confectionery (us cfr) @@ -4930,8 +5185,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Food product prepared by heating a mixture of sweeteners and other optional ingredients according to the specific formula for each subgroup. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0204 + candy (us cfr) @@ -4943,8 +5197,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Jelled product made from one or more fruit juices and optional ingredients. Includes both fruit jelly, which may be sweetened with nutritive carbohydrate sweeteners, (21 CFR 150.140), and artificially sweetened fruit jelly (21 CFR 150.141). The finished fruit jelly must have a soluble solid content of no less than 65% and the ratio by weight of the fruit ingredient to sweetener in the starting mixture must be no less than 45:55. Artificially sweetened fruit jelly must contain no less than 55% fruit ingredient by weight. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0209 + fruit jelly (us cfr) @@ -4956,8 +5209,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Soft candy prepared by boiling milk, sugar, salt and optional ingredients to the soft-ball stage (238 degrees F.). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0213 + fudge (us cfr) @@ -4969,8 +5221,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Food product having functional characteristics similar to those of butter; it is in plastic form or liquid emulsion and contains not less than 80% fat whose origin is vegetable or rendered animal carcass fats or a mixture of these as well as other optional ingredients specified by 21 CFR 166.110. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0231 + margarine (us cfr) @@ -4982,8 +5233,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Fruits and vegetables in all forms. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0257 + fruit or vegetable product (us cfr) @@ -4995,8 +5245,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Food group having common consumption, functional or manufacturing characteristics, e.g. *FRUIT OR VEGETABLE PRODUCT*, *DAIRY PRODUCT*, *CONFECTIONARY*, *PREPARED FOOD PRODUCT*, etc. [FDA CFSAN 1995] - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0289 + LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. USA agency food product type @@ -5009,8 +5258,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Candy prepared by cooking a mixture of water, sugars and optional ingredients to a temperature of 250 degrees F. or less. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0293 + soft candy (us cfr) @@ -5022,8 +5270,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Food product having functional characteristics similar to a butter product; it may be nutritionally equivalent or inferior to the product it purports to resemble. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0294 + butter substitute butter, imitation imitation butter @@ -5038,8 +5285,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com Renamed from *PRODUCT TYPE, CODEX ALIMENTARIUS* in LanguaL 2008. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0352 + LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. international agency food product type @@ -5051,8 +5297,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0356 + LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. European Union agency food product type @@ -5066,8 +5311,7 @@ Namely, how to characterize the threshold of ingredients that make for multi-com An agency food product type is a class of food product defined by an agency or consortium. Damion Dooley - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0361 + This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible. agency food product type @@ -5086,8 +5330,7 @@ The Codex Classification of food and animal feed commodities moving in trade and The Codex Classification includes food commodities and animal feedstuffs for which Codex maximum residue limits will not necessarily be established. The Classification is intended to be as complete a listing of food commodities in trade as possible, classified into groups on the basis of the commodity's similar potential for pesticide residues. The Classification may also be appropriate for other purposes such as setting maximum levels for other types of residues or for other contaminants in food. The Codex Classification should be consulted in order to obtain a precise description of the food or animal feed commodities and, especially, in cases where Codex maximum residue limits have been set for groups of food and groups of animal feedstuffs. The Codex Classification is intended to promote harmonization of the terms used to describe commodities which are subject to maximum residue limits and of the approach to grouping commodities with similar potential for residue for which a common group maximum residue limit can be set. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0643 + LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. Codex Alimentarius classification of food and feed commodities @@ -5099,8 +5342,7 @@ The Classification may also be appropriate for other purposes such as setting ma - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0644 + LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. a. primary food commodities of plant origin (ccpr) @@ -5116,8 +5358,7 @@ The Classification may also be appropriate for other purposes such as setting ma In several countries, some of these commodities grown on large areas are distinguished as "field crops" or arable crops e.g. sugar beet. For the sake of convenience in this guide such crops are classified under Type 2 Vegetables. Exposure to pesticides is dependent on the particular part of the plant used for food and the growing practices. Vegetables may be consumed in whole or in part and in the form of fresh, dried or processed foods. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0650 + 02 vegetables (ccpr) @@ -5131,8 +5372,7 @@ Vegetables may be consumed in whole or in part and in the form of fresh, dried o Pulses are derived from the mature seeds naturally or artificially dried, of leguminous plants known as beans (dry) and peas (dry). The seeds in the pods are protected from most pesticides applied during the growing season except pesticides which show a systemic action. The dried beans and peas however are often exposed to post-harvest treatments. The dry pulses are consumed after processing or household cooking. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0680 + 015 pulses (vd) (ccpr) @@ -5143,8 +5383,7 @@ The dry pulses are consumed after processing or household cooking. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0777 + LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. eurofir food classification @@ -5157,8 +5396,7 @@ The dry pulses are consumed after processing or household cooking. The group includes marine or freshwater fish, molluscs, crustaceans, and other fauna such as reptiles, insects or frogs not in the “Meats” group. The group also includes seafood product analogs and seafood-based sausage or luncheon meat as well as such products as squid ink and clam juice. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0801 + seafood or related product (eurofir) @@ -5170,8 +5408,7 @@ The dry pulses are consumed after processing or household cooking. includes fish offal; a food product whose predominant constituent is fish (e.g. dried and salted fish, smoked fish, canned fish, pickled fish, restructured fish and fish analogues, surimi; fish paste, pâté). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0803 + seafood product (eurofir) @@ -5183,8 +5420,7 @@ The dry pulses are consumed after processing or household cooking. Alcoholic or non-alcoholic beverage; excludes milk and milk-based beverages. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0840 + beverage (non-milk) (eurofir) @@ -5196,8 +5432,7 @@ The dry pulses are consumed after processing or household cooking. Beverage containing no more than 0.5% alcohol; it may be flavoured, sweetened or carbonated; includes soft drinks and steeped beverages; excludes milk in all forms, fruit juices and vegetable juices. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0842 + non alcoholic beverage (eurofir) @@ -5209,8 +5444,7 @@ The dry pulses are consumed after processing or household cooking. Beverage prepared by extracting flavour and other components from food sources by percolation and/or immersion in water, usually at near-boiling temperature. The group includes coffee (e.g. instant coffee, coffee and chicory essence), tea, herbal tea (e.g. green tea, black tea, tisane), cocoa beverage and beverage powder. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0845 + infusion steeped beverage LanguaL curation note: Renamed from *COFFEE, TEA, COCOA (EUROFIR)* (LanguaL 2010). @@ -5225,8 +5459,7 @@ The dry pulses are consumed after processing or household cooking. EFG group 32, Eurocode-2 group 12. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0852 + LanguaL curation note: Use for foods and ingredients that could not fit into any of the above classes. miscellaneous food product (eurofir) @@ -5239,8 +5472,7 @@ The dry pulses are consumed after processing or household cooking. This subgroup includes multicomponent meals, sauces, retail salads, desserts, soups, snacks and other foods where similarity of the product type is more significant than the source of the principal ingredient(s). - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0861 + soup, sauce or miscellaneous food product prepared food product (eurofir) @@ -5253,8 +5485,7 @@ The dry pulses are consumed after processing or household cooking. A liquid food made by simmering meat, poultry, seafood or vegetables, being clear or thickened to the consistency of a thin puree or having milk or cream added, and often containing pieces of solid food such as meat, shellfish, pasta or vegetables. Soup takes precedence over other food products. Examples are egg and lemon soup, oxtail soup, fish soup, rice soup, lentil soup, minestrone, cherry soup. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0865 + soup (eurofir) @@ -5267,8 +5498,7 @@ The dry pulses are consumed after processing or household cooking. The Global System 1 (GS1) Global Product Classification (GPC) is a system that gives buyers and sellers a common language for grouping products in the same way, everywhere in the world.$br/$ The GS1 GPC classification in facet A is currently updated based on June 2017 release of GS1 GPC Standard for Food/Beverage/Tobacco, except for codes pertaining to tobacco. See the GS1 site for details [https://www.gs1.org/standards/gpc]. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0874 + GS1 Global Product Classification (GPC) @@ -5281,8 +5511,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0960 + 50220000 - cereal/grain/pulse products (gs1 gpc) @@ -5293,8 +5522,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A0969 + 50221200 - processed cereal products (gs1 gpc) @@ -5305,8 +5533,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A1061 + 50190000 - prepared/preserved foods (gs1 gpc) @@ -5317,8 +5544,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A1095 + 50192900 - pasta/noodles (gs1 gpc) @@ -5330,8 +5556,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re Food and Drugs, title 21, Code of Federal Regulations. Original food classification in LanguaL. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=A1270 + langual:A1270 LanguaL curation note: This term is for CLASSIFICATION ONLY; DO NOT USE term in indexing. Use a more precise narrower term. U.S. code of federal regulations, title 21 food product type https://www.ecfr.gov/cgi-bin/text-idx?SID=87f720ce0d0b6c4548f4bbfd1f8e4c3d&mc=true&tpl=/ecfrbrowse/Title21/21chapterI.tpl @@ -5344,8 +5569,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1009 + polysaccharide-producing plant @@ -5355,8 +5579,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1013 + plant used for producing extract or concentrate @@ -5367,8 +5590,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1016 + starch-producing plant @@ -5379,8 +5601,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B1048 + carbohydrate-producing plant @@ -5391,8 +5612,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2344 + amorphophallus konjac amorphophallus rivieri hydrosme rivieri @@ -5407,8 +5627,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=B2637 + amorphophallus rivieri var. konjac konjac plant @@ -5421,20 +5640,31 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re A broad term that includes the nutritive sweeteners dextrose, fructose, galactose, lactose, maltose and sucrose, which are simple carbohydrates with molecules composed of one or two saccharide units. Note that on a product label or in a recipe, 'sugar' means *SUCROSE* and should be so indexed. Use the broad term *SUGAR* only if the specific sugar used is not known or not listed in the vocabulary. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0108 + sugar + + + + + Anatomical or other part(s) or substances derived from plant or animal or fungal organisms. + This was renamed from "part of organism" (and from LanguaL's original "part of plant or animal") to encompass organism material that is produced by an animal or plant rather than "part of" it, such as an egg, and might not be countable per se, such as milk. Additionally the existing definition's "from which a food product or its major ingredient is derived." was removed as an unnecessary constraint. [2023/03/02] + + LanguaL curation note: "e.g. *LEAF*, *ROOT OR TUBER*, *ORGAN MEAT*, *MILK* OR *EGG*; it also includes components of parts, such as *CREAM*, and extracts, concentrates or isolates, such as *PROTEIN EXTRACT* or *SUGAR*." + organism material + + + + Extract, concentrate or isolate high in sugar, oligosaccharide or polysaccharide. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0152 + carbohydrate extract, concentrate, or isolate @@ -5447,21 +5677,35 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re Soft sugar whose crystals are covered by a film of refined dark syrup that imparts color, flavor, and moisture. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0156 + langual:C0156 brown sugar + + + + + + Material that derives from some animal. + https://orcid.org/0000-0001-5275-8866 + 2023-08-01T21:25:29Z + + Langual note: Includes eggs and milk that, although separated from the animal, are produced as integral parts and are affected by the animal's food intake and metabolism. + This branch isn't necessarily food material + animal material + + + + A physical-chemical component separated from the food source or its parts by extraction, centrifugation, filtration, heat processing, expressing or a similar process. The separated component may be converted through further processing. If this is done, the final substance is indexed. A water-extracted component may remain in aqueous dispersion. The extract, concentrate or isolate is indexed in preference to the anatomic part from which it is derived. For example, peanut oil is indexed under *PEANUT* combined wih *FAT OR OIL* rather than with *SEED OR KERNEL*. On the other hand, fruit and vegetable juices can be indexed under *FRUIT JUICE OR NECTAR* or *VEGETABLE JUICE* (A. PRODUCT TYPE); therefore the anatomic part of the plant should be indexed. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0228 + langual:C0228 Damion Dooley's note: Items in this branch will be merged into foodon food product branch. extract, concentrate or isolate of plant or animal @@ -5474,8 +5718,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re The serum or watery part of milk that is separated from the thicker or more coagulable part or curd, espcially in the process of making cheese; it contains lactose, minerals and lactalbumin. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0244 + whey mammalian milk whey @@ -5488,8 +5731,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re The oil produced by pressing or extracting lipids from plant seeds (e.g. grapeseed oil, rapeseed oil, linseed oil) /AM - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=C0307 + seed oil @@ -5501,8 +5743,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re A liquid that flows very easily at room temperature. Examples are: water, apple juice, sherry, acidophilus milk, whipping cream and some heavy liqueurs. The range of low viscosity liquid spans sucrose solutions between 0 and 45% solids (viscosity range from 1 to 10 centipoise). Prefer 'solid pieces' factor term to 'small particles' if both appear in the food. - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=E0109 + liquid, thin food (liquid, low viscosity) @@ -5515,13 +5756,11 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re A state of matter between a solid and a gas, in which a substance has the capacity to flow and conforms to the shape of the container. Liquids range from water to honey, corresponding to a range in viscosity (or apparent viscosity) from 1 to 500 centipoise (viscosity is a measure of a liquid's resistance to flow). Products that are pourable but have a higher viscosity are *SEMILIQUID*. - http://langual.org - SUBSET_SIREN:F5105 - http://www.langual.org/langual_thesaurus.asp?termid=E0130 + + fluid SIREN DB annotation: -* has quality 'liquid' (http://purl.obolibrary.org/obo/FOODON_03430130) - +* liquid FOODON:03430130 food (liquid) @@ -5530,7 +5769,6 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - http://langual.org http://purl.obolibrary.org/obo/CHEBI_83163 obsolete: molasses added true @@ -5552,8 +5790,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re This disjunction is provided for food indexers who used the LanguaL category per guidelines. Currently, by specifying the more specific nut or seed as ingredient instead, this category can be inferred. nut or seed added - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=H0177 + langual:H0177 LanguaL curation note: With the exception of peanut (see *PEANUT OR PEANUT BUTTER ADDED*), used when a nut or seed ingredient is the second ingredient in order of predominance. plant seed or nut food product @@ -5574,8 +5811,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re chocolate or cocoa added - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=H0231 + LanguaL curation note: Used when chocolate or cocoa is added at any level or when chocolate is used as a coating. chocolate or cocoa @@ -5598,8 +5834,7 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re A fat or oil derived from vegetable material Damion Dooley vegetable fat or oil added - http://langual.org - http://www.langual.org/langual_thesaurus.asp?termid=H0263 + langual:H0263 This is a convenience class inherited from LanguaL vegetable fat or oil @@ -5607,5 +5842,5 @@ The GS1 GPC classification in facet A is currently updated based on June 2017 re - + diff --git a/src/envo/imports/go_import.obo b/src/envo/imports/go_import.obo index 606a8c24..cdfa6d16 100644 --- a/src/envo/imports/go_import.obo +++ b/src/envo/imports/go_import.obo @@ -11,11 +11,6 @@ id: GO:0006091 name: generation of precursor metabolites and energy is_a: GO:0044237 ! cellular metabolic process -[Term] -id: GO:0006807 -name: nitrogen compound metabolic process -is_a: GO:0008152 ! metabolic process - [Term] id: GO:0007588 name: excretion @@ -91,7 +86,6 @@ is_a: GO:0006091 ! generation of precursor metabolites and energy [Term] id: GO:0019329 name: ammonia oxidation -is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0044281 ! small molecule metabolic process [Term] @@ -100,14 +94,12 @@ name: anaerobic respiration, using ammonium as electron donor is_a: GO:0009061 ! anaerobic respiration is_a: GO:0015975 ! energy derivation by oxidation of reduced inorganic compounds is_a: GO:0019329 ! ammonia oxidation -is_a: GO:0034641 ! cellular nitrogen compound metabolic process [Term] id: GO:0019332 name: aerobic respiration, using nitrite as electron donor is_a: GO:0009060 ! aerobic respiration is_a: GO:0015975 ! energy derivation by oxidation of reduced inorganic compounds -is_a: GO:0034641 ! cellular nitrogen compound metabolic process [Term] id: GO:0019409 @@ -115,7 +107,6 @@ name: aerobic respiration, using ammonia as electron donor is_a: GO:0009060 ! aerobic respiration is_a: GO:0015975 ! energy derivation by oxidation of reduced inorganic compounds is_a: GO:0019329 ! ammonia oxidation -is_a: GO:0034641 ! cellular nitrogen compound metabolic process [Term] id: GO:0019410 @@ -162,12 +153,6 @@ id: GO:0032501 name: multicellular organismal process is_a: GO:0008150 ! biological_process -[Term] -id: GO:0034641 -name: cellular nitrogen compound metabolic process -is_a: GO:0006807 ! nitrogen compound metabolic process -is_a: GO:0044237 ! cellular metabolic process - [Term] id: GO:0042755 name: eating behavior @@ -214,25 +199,14 @@ id: GO:0045333 name: cellular respiration is_a: GO:0015980 ! energy derivation by oxidation of organic compounds -[Term] -id: GO:0071704 -name: organic substance metabolic process -is_a: GO:0008152 ! metabolic process - [Term] id: GO:0120251 name: hydrocarbon biosynthetic process +is_a: GO:0009058 ! biosynthetic process is_a: GO:0120252 ! hydrocarbon metabolic process -is_a: GO:1901576 ! organic substance biosynthetic process [Term] id: GO:0120252 name: hydrocarbon metabolic process -is_a: GO:0071704 ! organic substance metabolic process - -[Term] -id: GO:1901576 -name: organic substance biosynthetic process -is_a: GO:0009058 ! biosynthetic process -is_a: GO:0071704 ! organic substance metabolic process +is_a: GO:0008152 ! metabolic process diff --git a/src/envo/imports/go_import.owl b/src/envo/imports/go_import.owl index a3886898..de67dc34 100644 --- a/src/envo/imports/go_import.owl +++ b/src/envo/imports/go_import.owl @@ -88,15 +88,6 @@ - - - - - nitrogen compound metabolic process - - - - @@ -228,7 +219,6 @@ - ammonia oxidation @@ -241,7 +231,6 @@ - anaerobic respiration, using ammonium as electron donor @@ -252,7 +241,6 @@ - aerobic respiration, using nitrite as electron donor @@ -264,7 +252,6 @@ - aerobic respiration, using ammonia as electron donor @@ -347,16 +334,6 @@ - - - - - - cellular nitrogen compound metabolic process - - - - @@ -435,20 +412,11 @@ - - - - - organic substance metabolic process - - - - + - hydrocarbon biosynthetic process @@ -457,22 +425,12 @@ - + hydrocarbon metabolic process - - - - - - - - - organic substance biosynthetic process - - + diff --git a/src/envo/imports/iao_import.owl b/src/envo/imports/iao_import.owl index 1e8e0571..070c96ac 100644 --- a/src/envo/imports/iao_import.owl +++ b/src/envo/imports/iao_import.owl @@ -489,5 +489,5 @@ - + diff --git a/src/envo/imports/ncbitaxon_import.obo b/src/envo/imports/ncbitaxon_import.obo index c89a2768..a3c7057d 100644 --- a/src/envo/imports/ncbitaxon_import.obo +++ b/src/envo/imports/ncbitaxon_import.obo @@ -6,11 +6,6 @@ id: NCBITaxon:1 name: root synonym: "all" RELATED [] -[Term] -id: NCBITaxon:104431 -name: Obtectomera -is_a: NCBITaxon:37567 ! Ditrysia - [Term] id: NCBITaxon:106220 name: Mytiloidea @@ -18,18 +13,17 @@ is_a: NCBITaxon:6546 ! Mytilida [Term] id: NCBITaxon:1117 -name: Cyanobacteria +name: Cyanobacteriota synonym: "blue-green algae" EXACT [] synonym: "blue-green bacteria" EXACT [] +synonym: "Cyanobacteria" RELATED [] synonym: "cyanobacteria" RELATED [] -synonym: "Cyanobacteriota" RELATED [] -synonym: "Cyanophyceae" RELATED [] synonym: "Cyanophycota" RELATED [] synonym: "Cyanophyta" RELATED [] synonym: "cyanophytes" EXACT [] synonym: "Oxygenic photosynthetic bacteria" RELATED [] synonym: "Oxyphotobacteria" RELATED [] -is_a: NCBITaxon:1798711 ! Cyanobacteria/Melainabacteria group +is_a: NCBITaxon:1798711 ! Cyanobacteriota/Melainabacteria group [Term] id: NCBITaxon:1118 @@ -67,7 +61,7 @@ is_a: NCBITaxon:1892254 ! Oscillatoriaceae [Term] id: NCBITaxon:1161 name: Nostocales -is_a: NCBITaxon:1117 ! Cyanobacteria +is_a: NCBITaxon:3028117 ! Cyanophyceae [Term] id: NCBITaxon:1162 @@ -79,21 +73,11 @@ id: NCBITaxon:1163 name: Anabaena is_a: NCBITaxon:1162 ! Nostocaceae -[Term] -id: NCBITaxon:1164880 -name: Oedaleus senegalensis -is_a: NCBITaxon:227570 ! Oedaleus - [Term] id: NCBITaxon:1175 name: Aphanizomenon is_a: NCBITaxon:1892259 ! Aphanizomenonaceae -[Term] -id: NCBITaxon:117558 -name: Bathymodiolinae -is_a: NCBITaxon:6547 ! Mytilidae - [Term] id: NCBITaxon:117570 name: Teleostomi @@ -131,15 +115,10 @@ id: NCBITaxon:1206795 name: Lophotrochozoa is_a: NCBITaxon:2697495 ! Spiralia -[Term] -id: NCBITaxon:12965 -name: Bathymodiolus -is_a: NCBITaxon:117558 ! Bathymodiolinae - [Term] id: NCBITaxon:1301283 name: Oscillatoriophycideae -is_a: NCBITaxon:1117 ! Cyanobacteria +is_a: NCBITaxon:3028117 ! Cyanophyceae [Term] id: NCBITaxon:13100 @@ -160,11 +139,6 @@ name: cellular organisms synonym: "biota" RELATED [] is_a: NCBITaxon:1 ! root -[Term] -id: NCBITaxon:1316646 -name: Salicornioideae -is_a: NCBITaxon:1804623 ! Chenopodiaceae - [Term] id: NCBITaxon:1329799 name: Archelosauria @@ -219,17 +193,6 @@ id: NCBITaxon:1446379 name: Cupressales is_a: NCBITaxon:2821351 ! Conifers II -[Term] -id: NCBITaxon:1583079 -name: Erebinae -is_a: NCBITaxon:695564 ! Erebidae - -[Term] -id: NCBITaxon:162985 -name: Hapalosiphon -synonym: "Cyanothrix" RELATED [] -is_a: NCBITaxon:1892263 ! Hapalosiphonaceae - [Term] id: NCBITaxon:169697 name: Arecoideae @@ -253,19 +216,9 @@ is_a: NCBITaxon:2 ! Bacteria [Term] id: NCBITaxon:1798711 -name: Cyanobacteria/Melainabacteria group +name: Cyanobacteriota/Melainabacteria group is_a: NCBITaxon:1783272 ! Terrabacteria group -[Term] -id: NCBITaxon:1804623 -name: Chenopodiaceae -is_a: NCBITaxon:3524 ! Caryophyllales - -[Term] -id: NCBITaxon:1890440 -name: Schizotrichaceae -is_a: NCBITaxon:2881377 ! Pseudanabaenales - [Term] id: NCBITaxon:1890449 name: Microcystaceae @@ -285,6 +238,7 @@ is_a: NCBITaxon:1150 ! Oscillatoriales [Term] id: NCBITaxon:1892254 name: Oscillatoriaceae +synonym: "Phormidiaceae" RELATED [] is_a: NCBITaxon:1150 ! Oscillatoriales [Term] @@ -292,26 +246,6 @@ id: NCBITaxon:1892259 name: Aphanizomenonaceae is_a: NCBITaxon:1161 ! Nostocales -[Term] -id: NCBITaxon:1892263 -name: Hapalosiphonaceae -is_a: NCBITaxon:1161 ! Nostocales - -[Term] -id: NCBITaxon:1892265 -name: Gloeotrichiaceae -is_a: NCBITaxon:1161 ! Nostocales - -[Term] -id: NCBITaxon:190523 -name: Laguncularia -is_a: NCBITaxon:3954 ! Combretaceae - -[Term] -id: NCBITaxon:190524 -name: Laguncularia racemosa -is_a: NCBITaxon:190523 ! Laguncularia - [Term] id: NCBITaxon:1955150 name: Acrididea @@ -328,15 +262,13 @@ name: Mandibulata synonym: "mandibulates" EXACT [] is_a: NCBITaxon:6656 ! Arthropoda -[Term] -id: NCBITaxon:198592 -name: Umezakia -is_a: NCBITaxon:1892259 ! Aphanizomenonaceae - [Term] id: NCBITaxon:2 name: Bacteria synonym: "bacteria" RELATED [] +synonym: "Bacteria (ex Cavalier-Smith 1987)" RELATED [] +synonym: "Bacteria Woese et al. 2024" RELATED [] +synonym: "Bacteriobiota" RELATED [] synonym: "eubacteria" EXACT [] synonym: "Monera" RELATED [] synonym: "Procaryotae" RELATED [] @@ -352,33 +284,6 @@ name: Homininae synonym: "Homo/Pan/Gorilla group" RELATED [] is_a: NCBITaxon:9604 ! Hominidae -[Term] -id: NCBITaxon:2116530 -name: Salicornia subgen. Amerocornia -is_a: NCBITaxon:46104 ! Salicornia - -[Term] -id: NCBITaxon:227566 -name: Hieroglyphus -is_a: NCBITaxon:227572 ! Oxyinae - -[Term] -id: NCBITaxon:227570 -name: Oedaleus -synonym: "Oedalus" RELATED [] -is_a: NCBITaxon:27549 ! Oedipodinae - -[Term] -id: NCBITaxon:227572 -name: Oxyinae -is_a: NCBITaxon:7002 ! Acrididae - -[Term] -id: NCBITaxon:240294 -name: Schizothrix -synonym: "Dictyothrix" RELATED [] -is_a: NCBITaxon:1890440 ! Schizotrichaceae - [Term] id: NCBITaxon:2696291 name: Ochrophyta @@ -419,11 +324,6 @@ id: NCBITaxon:2785011 name: Autobranchia is_a: NCBITaxon:6544 ! Bivalvia -[Term] -id: NCBITaxon:28073 -name: Lyngbya -is_a: NCBITaxon:1892254 ! Oscillatoriaceae - [Term] id: NCBITaxon:2821351 name: Conifers II @@ -456,26 +356,22 @@ synonym: "Pyrrhophyta" RELATED [] synonym: "Pyrrophyta" RELATED [] is_a: NCBITaxon:33630 ! Alveolata -[Term] -id: NCBITaxon:2881377 -name: Pseudanabaenales -is_a: NCBITaxon:1117 ! Cyanobacteria - [Term] id: NCBITaxon:2910 name: Peridiniales is_a: NCBITaxon:2864 ! Dinophyceae -[Term] -id: NCBITaxon:301957 -name: Modiolinae -is_a: NCBITaxon:6547 ! Mytilidae - [Term] id: NCBITaxon:301959 name: Mytilinae is_a: NCBITaxon:6547 ! Mytilidae +[Term] +id: NCBITaxon:3028117 +name: Cyanophyceae +synonym: "Gloeobacteria" RELATED [] +is_a: NCBITaxon:1117 ! Cyanobacteriota + [Term] id: NCBITaxon:314146 name: Euarchontoglires @@ -582,12 +478,6 @@ name: Polyneoptera synonym: "Orthopteroidea" RELATED [] is_a: NCBITaxon:33340 ! Neoptera -[Term] -id: NCBITaxon:33392 -name: Endopterygota -synonym: "Holometabola" RELATED [] -is_a: NCBITaxon:33340 ! Neoptera - [Term] id: NCBITaxon:33511 name: Deuterostomia @@ -626,23 +516,11 @@ synonym: "flowering plants" RELATED [] synonym: "Magnoliophyta" RELATED [] is_a: NCBITaxon:58024 ! Spermatophyta -[Term] -id: NCBITaxon:3524 -name: Caryophyllales -synonym: "Centrospermae" RELATED [] -is_a: NCBITaxon:1437201 ! Pentapetalae - [Term] id: NCBITaxon:35493 name: Streptophyta is_a: NCBITaxon:33090 ! Viridiplantae -[Term] -id: NCBITaxon:365482 -name: Salicornia pacifica -synonym: "Sarcocornia pacifica" RELATED [] -is_a: NCBITaxon:2116530 ! Salicornia subgen. Amerocornia - [Term] id: NCBITaxon:3699 name: Brassicales @@ -657,33 +535,11 @@ synonym: "spur-throated grasshoppers" EXACT [] synonym: "spur-throated locusts" EXACT [] is_a: NCBITaxon:7002 ! Acrididae -[Term] -id: NCBITaxon:37567 -name: Ditrysia -is_a: NCBITaxon:41197 ! Heteroneura - -[Term] -id: NCBITaxon:37570 -name: Noctuoidea -is_a: NCBITaxon:104431 ! Obtectomera - [Term] id: NCBITaxon:376913 name: Haplorrhini is_a: NCBITaxon:9443 ! Primates -[Term] -id: NCBITaxon:3954 -name: Combretaceae -synonym: "Indian almond family" EXACT [] -is_a: NCBITaxon:41944 ! Myrtales - -[Term] -id: NCBITaxon:40255 -name: Modiolus -synonym: "horsemussels" EXACT [] -is_a: NCBITaxon:301957 ! Modiolinae - [Term] id: NCBITaxon:403651 name: Pfiesteriaceae @@ -702,21 +558,6 @@ synonym: "mammals" EXACT [] synonym: "mammals" RELATED [] is_a: NCBITaxon:32524 ! Amniota -[Term] -id: NCBITaxon:41191 -name: Glossata -is_a: NCBITaxon:7088 ! Lepidoptera - -[Term] -id: NCBITaxon:41196 -name: Neolepidoptera -is_a: NCBITaxon:41191 ! Glossata - -[Term] -id: NCBITaxon:41197 -name: Heteroneura -is_a: NCBITaxon:41196 ! Neolepidoptera - [Term] id: NCBITaxon:41377 name: Avicennia @@ -740,12 +581,6 @@ id: NCBITaxon:4185 name: Acanthaceae is_a: NCBITaxon:4143 ! Lamiales -[Term] -id: NCBITaxon:41944 -name: Myrtales -synonym: "Myrtanae" RELATED [] -is_a: NCBITaxon:91836 ! malvids - [Term] id: NCBITaxon:436486 name: Dinosauria @@ -768,11 +603,6 @@ id: NCBITaxon:436492 name: Coelurosauria is_a: NCBITaxon:436491 ! Theropoda -[Term] -id: NCBITaxon:436880 -name: Chortoicetes -is_a: NCBITaxon:27549 ! Oedipodinae - [Term] id: NCBITaxon:4434 name: Bataceae @@ -804,18 +634,6 @@ name: Microcystis viridis synonym: "Polycystis viridis" RELATED [] is_a: NCBITaxon:1125 ! Microcystis -[Term] -id: NCBITaxon:46104 -name: Salicornia -synonym: "Arthrocnemum" RELATED [] -synonym: "Sarcocornia" RELATED [] -is_a: NCBITaxon:1316646 ! Salicornioideae - -[Term] -id: NCBITaxon:465832 -name: Calyptra -is_a: NCBITaxon:1583079 ! Erebinae - [Term] id: NCBITaxon:4710 name: Arecaceae @@ -841,17 +659,11 @@ is_a: NCBITaxon:33154 ! Opisthokonta [Term] id: NCBITaxon:50557 name: Insecta +synonym: "insects" EXACT [] synonym: "insects" RELATED [] synonym: "true insects" EXACT [] is_a: NCBITaxon:6960 ! Hexapoda -[Term] -id: NCBITaxon:519494 -name: Chortoicetes terminifera -synonym: "Australian plague locust" EXACT [] -synonym: "Epacromia terminifera" RELATED [] -is_a: NCBITaxon:436880 ! Chortoicetes - [Term] id: NCBITaxon:51952 name: Elaeis @@ -962,17 +774,12 @@ synonym: "arthropods" EXACT [] synonym: "arthropods" RELATED [] is_a: NCBITaxon:88770 ! Panarthropoda -[Term] -id: NCBITaxon:695564 -name: Erebidae -is_a: NCBITaxon:37570 ! Noctuoidea - [Term] id: NCBITaxon:6960 name: Hexapoda synonym: "Atelocerata" RELATED [] +synonym: "hexapods" EXACT [] synonym: "hexapods" RELATED [] -synonym: "insects" EXACT [] synonym: "Tracheata" RELATED [] synonym: "Uniramia" RELATED [] is_a: NCBITaxon:197562 ! Pancrustacea @@ -980,7 +787,7 @@ is_a: NCBITaxon:197562 ! Pancrustacea [Term] id: NCBITaxon:6993 name: Orthoptera -synonym: "grasshoppers, crickets, and katydids" RELATED [] +synonym: "grasshoppers, crickets, & katydids" RELATED [] synonym: "Saltatoria" RELATED [] is_a: NCBITaxon:33341 ! Polyneoptera @@ -1020,14 +827,6 @@ synonym: "desert locust" EXACT [] synonym: "Locusta gregaria" RELATED [] is_a: NCBITaxon:7008 ! Schistocerca -[Term] -id: NCBITaxon:7088 -name: Lepidoptera -synonym: "butterflies and moths" EXACT [] -synonym: "moths" EXACT [] -synonym: "moths" RELATED [] -is_a: NCBITaxon:85604 ! Amphiesmenoptera - [Term] id: NCBITaxon:70910 name: Acridomorpha @@ -1078,11 +877,6 @@ id: NCBITaxon:7624 name: Echinozoa is_a: NCBITaxon:133551 ! Eleutherozoa -[Term] -id: NCBITaxon:77021 -name: Cylindrospermopsis -is_a: NCBITaxon:1892259 ! Aphanizomenonaceae - [Term] id: NCBITaxon:7705 name: Holothuroidea @@ -1141,11 +935,6 @@ id: NCBITaxon:85512 name: Dicondylia is_a: NCBITaxon:50557 ! Insecta -[Term] -id: NCBITaxon:85604 -name: Amphiesmenoptera -is_a: NCBITaxon:33392 ! Endopterygota - [Term] id: NCBITaxon:8782 name: Aves @@ -1188,11 +977,6 @@ id: NCBITaxon:92621 name: Acridoidea is_a: NCBITaxon:70910 ! Acridomorpha -[Term] -id: NCBITaxon:92939 -name: Gloeotrichia -is_a: NCBITaxon:1892265 ! Gloeotrichiaceae - [Term] id: NCBITaxon:9347 name: Eutheria diff --git a/src/envo/imports/ncbitaxon_import.owl b/src/envo/imports/ncbitaxon_import.owl index 0f8e3255..a40cc791 100644 --- a/src/envo/imports/ncbitaxon_import.owl +++ b/src/envo/imports/ncbitaxon_import.owl @@ -7,7 +7,8 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" + xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> @@ -29,27 +30,93 @@ + + + + + + - + + synonym_type_property + + + + + + + + has_alternative_id + - + + has_broad_synonym + + + + + + + + database_cross_reference + - + + has_exact_synonym + + + + + + + + has_obo_format_version + + + + + + + + has_obo_namespace + - + + has_related_synonym + + + + + + + + has_synonym_type + + + + + + + + + + + + + @@ -73,9 +140,20 @@ + GC_ID:1 + PMID:30365038 + PMID:32761142 + ncbi_taxonomy all + NCBITaxon:1 root + + + + all + + @@ -83,6 +161,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:104431 Obtectomera @@ -92,6 +174,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:106220 Mytiloidea @@ -101,18 +187,83 @@ + + GC_ID:11 + PMID:11542017 + PMID:15388760 + PMID:20190018 + PMID:24408952 + PMID:24709563 + PMID:25505344 + PMID:31618454 + PMID:9382701 blue-green algae blue-green bacteria cyanophytes - Cyanobacteriota - Cyanophyceae + ncbi_taxonomy + Cyanobacteria Cyanophycota Cyanophyta Oxygenic photosynthetic bacteria Oxyphotobacteria cyanobacteria - Cyanobacteria - + NCBITaxon:1117 + Cyanobacteriota + + + + + cyanobacteria + + + + + + blue-green algae + + + + + + blue-green bacteria + + + + + + cyanophytes + + + + + + Cyanobacteria + + + + + + Cyanophycota + + + + + + Cyanophyta + + + + + + Oxygenic photosynthetic bacteria + + + + + + Oxyphotobacteria + + @@ -120,6 +271,10 @@ + + GC_ID:11 + ncbi_taxonomy + NCBITaxon:1118 Chroococcales @@ -129,9 +284,19 @@ + + GC_ID:11 + ncbi_taxonomy Coccochloris + NCBITaxon:1121 Aphanothece + + + + Coccochloris + + @@ -139,6 +304,16 @@ + + GC_ID:11 + PMID:10758887 + PMID:11321098 + PMID:11411709 + PMID:12483602 + PMID:8240966 + PMID:9226902 + ncbi_taxonomy + NCBITaxon:1125 Microcystis @@ -148,9 +323,21 @@ + + GC_ID:11 + PMID:10758887 + PMID:11411709 + ncbi_taxonomy Micraloa aeruginosa + NCBITaxon:1126 Microcystis aeruginosa + + + + Micraloa aeruginosa + + @@ -158,6 +345,10 @@ + + GC_ID:11 + ncbi_taxonomy + NCBITaxon:1150 Oscillatoriales @@ -167,16 +358,30 @@ + + GC_ID:11 + ncbi_taxonomy Plaxonema + NCBITaxon:1158 Oscillatoria + + + + Plaxonema + + - + + + GC_ID:11 + ncbi_taxonomy + NCBITaxon:1161 Nostocales @@ -186,6 +391,10 @@ + + GC_ID:11 + ncbi_taxonomy + NCBITaxon:1162 Nostocaceae @@ -195,24 +404,26 @@ + + GC_ID:11 + PMID:11321098 + PMID:1581185 + ncbi_taxonomy + NCBITaxon:1163 Anabaena - - - - - Oedaleus senegalensis - - - - + + GC_ID:11 + PMID:11321098 + ncbi_taxonomy + NCBITaxon:1175 Aphanizomenon @@ -222,6 +433,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:117558 Bathymodiolinae @@ -231,6 +446,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:117570 Teleostomi @@ -240,9 +459,20 @@ + + NCBITaxon:40673 + GC_ID:1 bony vertebrates + ncbi_taxonomy + NCBITaxon:117571 Euteleostomi + + + + bony vertebrates + + @@ -250,9 +480,20 @@ + + GC_ID:11 + PMID:1581185 + ncbi_taxonomy Amorphonostoc + NCBITaxon:1177 Nostoc + + + + Amorphonostoc + + @@ -260,6 +501,10 @@ + + GC_ID:11 + ncbi_taxonomy + NCBITaxon:1198 Phormidium @@ -269,6 +514,10 @@ + + GC_ID:11 + ncbi_taxonomy + NCBITaxon:1205 Trichodesmium @@ -278,6 +527,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1206794 Ecdysozoa @@ -287,6 +540,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1206795 Lophotrochozoa @@ -296,6 +553,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:12965 Bathymodiolus @@ -304,7 +565,11 @@ - + + + GC_ID:11 + ncbi_taxonomy + NCBITaxon:1301283 Oscillatoriophycideae @@ -314,9 +579,19 @@ + + GC_ID:1 junipers + ncbi_taxonomy + NCBITaxon:13100 Juniperus + + + + junipers + + @@ -324,10 +599,26 @@ + + GC_ID:1 charophyte/embryophyte group + ncbi_taxonomy Charophyta/Embryophyta group + NCBITaxon:131221 Streptophytina + + + + charophyte/embryophyte group + + + + + + Charophyta/Embryophyta group + + @@ -335,9 +626,18 @@ + GC_ID:1 + ncbi_taxonomy biota + NCBITaxon:131567 cellular organisms + + + + biota + + @@ -345,6 +645,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1316646 Salicornioideae @@ -354,10 +658,28 @@ + + GC_ID:1 + PMID:22839753 + PMID:25450099 + ncbi_taxonomy Archosauria-Testudines Testudines + Archosauria group + NCBITaxon:1329799 Archelosauria + + + + Archosauria-Testudines + + + + + + Testudines + Archosauria group + + @@ -365,6 +687,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:133551 Eleutherozoa @@ -374,6 +700,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1338369 Dipnotetrapodomorpha @@ -383,9 +713,19 @@ + + GC_ID:1 cypress + ncbi_taxonomy + NCBITaxon:13468 Cupressus + + + + cypress + + @@ -393,9 +733,21 @@ + + GC_ID:1 + PMID:11743200 + PMID:11791233 + ncbi_taxonomy Boreotheria + NCBITaxon:1437010 Boreoeutheria + + + + Boreotheria + + @@ -403,6 +755,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1437180 Acrogymnospermae @@ -412,6 +768,11 @@ + + GC_ID:1 + PMID:25249442 + ncbi_taxonomy + NCBITaxon:1437183 Mesangiospermae @@ -421,6 +782,11 @@ + + GC_ID:1 + PMID:26350789 + ncbi_taxonomy + NCBITaxon:1437197 Petrosaviidae @@ -430,6 +796,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1437201 Pentapetalae @@ -439,6 +809,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1446379 Cupressales @@ -448,25 +822,23 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1583079 Erebinae - - - - - Cyanothrix - Hapalosiphon - - - - + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:169697 Arecoideae @@ -476,9 +848,19 @@ + + GC_ID:1 + ncbi_taxonomy Cocoeae + NCBITaxon:169705 Cocoseae + + + + Cocoeae + + @@ -486,6 +868,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:169729 Elaeidinae @@ -495,6 +881,12 @@ + + GC_ID:11 + PMID:18988685 + PMID:23851394 + ncbi_taxonomy + NCBITaxon:1783272 Terrabacteria group @@ -504,7 +896,12 @@ - Cyanobacteria/Melainabacteria group + + GC_ID:11 + PMID:24709563 + ncbi_taxonomy + NCBITaxon:1798711 + Cyanobacteriota/Melainabacteria group @@ -513,24 +910,23 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1804623 Chenopodiaceae - - - - - Schizotrichaceae - - - - + + GC_ID:11 + ncbi_taxonomy + NCBITaxon:1890449 Microcystaceae @@ -540,6 +936,10 @@ + + GC_ID:11 + ncbi_taxonomy + NCBITaxon:1890450 Aphanothecaceae @@ -549,9 +949,20 @@ + + GC_ID:11 + PMID:27007635 + ncbi_taxonomy Microcoleae + NCBITaxon:1892252 Microcoleaceae + + + + Microcoleae + + @@ -559,8 +970,19 @@ + + GC_ID:11 + ncbi_taxonomy + Phormidiaceae + NCBITaxon:1892254 Oscillatoriaceae + + + + Phormidiaceae + + @@ -568,33 +990,23 @@ + + GC_ID:11 + ncbi_taxonomy + NCBITaxon:1892259 Aphanizomenonaceae - - - - - Hapalosiphonaceae - - - - - - - - - Gloeotrichiaceae - - - - + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:190523 Laguncularia @@ -604,8 +1016,19 @@ + + GC_ID:1 + ncbi_taxonomy + Conocarpus racemosus + NCBITaxon:190524 Laguncularia racemosa + + + + Conocarpus racemosus + + @@ -613,6 +1036,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:1955150 Acrididea @@ -622,6 +1049,12 @@ + + GC_ID:1 + PMID:10874751 + PMID:11557979 + ncbi_taxonomy + NCBITaxon:197562 Pancrustacea @@ -631,18 +1064,21 @@ + + GC_ID:1 + PMID:11557979 + PMID:9727836 mandibulates + ncbi_taxonomy + NCBITaxon:197563 Mandibulata - - - - - - - - Umezakia - + + + + mandibulates + + @@ -650,7 +1086,39 @@ + + GC_ID:11 + PMID:10425795 + PMID:10425796 + PMID:10425797 + PMID:10490293 + PMID:10843050 + PMID:10939651 + PMID:10939673 + PMID:10939677 + PMID:11211268 + PMID:11321083 + PMID:11321113 + PMID:11411719 + PMID:11540071 + PMID:11542017 + PMID:11542087 + PMID:11760965 + PMID:12054223 + PMID:270744 + PMID:32628106 + PMID:36748408 + PMID:7520741 + PMID:8123559 + PMID:8186100 + PMID:8590690 + PMID:9103655 + PMID:9336922 eubacteria + ncbi_taxonomy + Bacteria (ex Cavalier-Smith 1987) + Bacteria Woese et al. 2024 + Bacteriobiota Monera Procaryotae Prokaryota @@ -658,8 +1126,75 @@ bacteria prokaryote prokaryotes + NCBITaxon:2 Bacteria + + + + eubacteria + + + + + + Bacteria (ex Cavalier-Smith 1987) + + + + + + Bacteria Woese et al. 2024 + + + + + + Bacteriobiota + + + + + + Monera + + + + + + Procaryotae + + + + + + Prokaryota + + + + + + Prokaryotae + + + + + + bacteria + + + + + + prokaryote + + + + + + prokaryotes + + @@ -667,9 +1202,19 @@ + + GC_ID:1 + ncbi_taxonomy Homo/Pan/Gorilla group + NCBITaxon:207598 Homininae + + + + Homo/Pan/Gorilla group + + @@ -677,53 +1222,23 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:2116530 Salicornia subgen. Amerocornia - - - - - Hieroglyphus - - - - - - - - - Oedalus - Oedaleus - - - - - - - - - Oxyinae - - - - - - - - - Dictyothrix - Schizothrix - - - - + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:2696291 Ochrophyta @@ -733,6 +1248,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:2697495 Spiralia @@ -742,9 +1261,19 @@ + + GC_ID:1 + ncbi_taxonomy SAR supergroup + NCBITaxon:2698737 Sar + + + + SAR supergroup + + @@ -752,10 +1281,27 @@ + + NCBITaxon:7015 + GC_ID:1 band-winged grasshoppers + ncbi_taxonomy Locustinae + NCBITaxon:27549 Oedipodinae + + + + band-winged grasshoppers + + + + + + Locustinae + + @@ -763,15 +1309,63 @@ + + GC_ID:1 + PMID:23020233 + PMID:30257078 eucaryotes eukaryotes + ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes + NCBITaxon:2759 Eukaryota + + + + eucaryotes + + + + + + eukaryotes + + + + + + Eucarya + + + + + + Eucaryotae + + + + + + Eukarya + + + + + + Eukaryotae + + + + + + eukaryotes + + @@ -779,24 +1373,24 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:2785011 Autobranchia - - - - - Lyngbya - - - - + + GC_ID:1 + PMID:19761858 + ncbi_taxonomy + NCBITaxon:2821351 Conifers II @@ -806,15 +1400,61 @@ + + GC_ID:1 bacillariophytes diatoms + ncbi_taxonomy Diatomea Diatomeae Diatomophyceae algae diatoms + NCBITaxon:2836 Bacillariophyta + + + + bacillariophytes + + + + + + diatoms + + + + + + Diatomea + + + + + + Diatomeae + + + + + + Diatomophyceae + + + + + + algae + + + + + + diatoms + + @@ -822,8 +1462,11 @@ + + GC_ID:1 dinoflagellates dinophytes + ncbi_taxonomy Chromophyta Dinoflagellata Dinophycidae @@ -832,17 +1475,69 @@ Pyrrophyta algae dinoflagellates + NCBITaxon:2864 Dinophyceae - - - - - - - - Pseudanabaenales - + + + + dinoflagellates + + + + + + dinophytes + + + + + + Chromophyta + + + + + + Dinoflagellata + + + + + + Dinophycidae + + + + + + Dinophyta + + + + + + Pyrrhophyta + + + + + + Pyrrophyta + + + + + + algae + + + + + + dinoflagellates + + @@ -850,6 +1545,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:2910 Peridiniales @@ -859,6 +1558,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:301957 Modiolinae @@ -868,15 +1571,49 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:301959 Mytilinae + + + + + + NCBITaxon:307596 + GC_ID:11 + PMID:11837318 + ncbi_taxonomy + Gloeobacteria + NCBITaxon:3028117 + Cyanophyceae + + + + + Gloeobacteria + + + + + + + GC_ID:1 + PMID:11214319 + PMID:12082125 + PMID:12878460 + PMID:15522813 + ncbi_taxonomy + NCBITaxon:314146 Euarchontoglires @@ -886,9 +1623,19 @@ + + GC_ID:1 + ncbi_taxonomy Anthropoidea + NCBITaxon:314293 Simiiformes + + + + Anthropoidea + + @@ -896,10 +1643,26 @@ + + GC_ID:1 ape apes + ncbi_taxonomy + NCBITaxon:314295 Hominoidea + + + + ape + + + + + + apes + + @@ -907,12 +1670,40 @@ + + GC_ID:1 higher plants land plants plants + ncbi_taxonomy land plants + NCBITaxon:3193 Embryophyta + + + + higher plants + + + + + + land plants + + + + + + plants + + + + + + land plants + + @@ -920,9 +1711,19 @@ + + GC_ID:1 tetrapods + ncbi_taxonomy + NCBITaxon:32523 Tetrapoda + + + + tetrapods + + @@ -930,9 +1731,19 @@ + + GC_ID:1 amniotes + ncbi_taxonomy + NCBITaxon:32524 Amniota + + + + amniotes + + @@ -940,9 +1751,19 @@ + + GC_ID:1 Theria + ncbi_taxonomy + NCBITaxon:32525 Theria <mammals> + + + + Theria + + @@ -950,10 +1771,26 @@ + + GC_ID:1 diapsids + ncbi_taxonomy Diapsida + NCBITaxon:32561 Sauria + + + + diapsids + + + + + + Diapsida + + @@ -961,14 +1798,56 @@ + + GC_ID:1 + PMID:16248873 + PMID:30257078 Chlorophyta/Embryophyta group chlorophyte/embryophyte group green plants + ncbi_taxonomy Chlorobionta Chloroplastida green plants + NCBITaxon:33090 Viridiplantae + + + + Chlorophyta/Embryophyta group + + + + + + chlorophyte/embryophyte group + + + + + + green plants + + + + + + Chlorobionta + + + + + + Chloroplastida + + + + + + green plants + + @@ -976,9 +1855,20 @@ + + NCBITaxon:1445965 + GC_ID:1 + ncbi_taxonomy Coniferales + NCBITaxon:3313 Pinidae + + + + Coniferales + + @@ -986,10 +1876,26 @@ + + GC_ID:1 + ncbi_taxonomy Fungi/Metazoa group opisthokonts + NCBITaxon:33154 Opisthokonta + + + + Fungi/Metazoa group + + + + + + opisthokonts + + @@ -997,12 +1903,40 @@ + + GC_ID:1 metazoans multicellular animals + ncbi_taxonomy Animalia animals + NCBITaxon:33208 Metazoa + + + + metazoans + + + + + + multicellular animals + + + + + + Animalia + + + + + + animals + + @@ -1010,6 +1944,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33213 Bilateria @@ -1019,6 +1957,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33317 Protostomia @@ -1028,6 +1970,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:33340 Neoptera @@ -1037,9 +1983,20 @@ + + NCBITaxon:1955245 + GC_ID:1 + ncbi_taxonomy Orthopteroidea + NCBITaxon:33341 Polyneoptera + + + + Orthopteroidea + + @@ -1047,9 +2004,19 @@ + + GC_ID:1 + ncbi_taxonomy Holometabola + NCBITaxon:33392 Endopterygota + + + + Holometabola + + @@ -1057,9 +2024,19 @@ + + GC_ID:1 deuterostomes + ncbi_taxonomy + NCBITaxon:33511 Deuterostomia + + + + deuterostomes + + @@ -1067,9 +2044,19 @@ + + GC_ID:1 alveolates + ncbi_taxonomy + NCBITaxon:33630 Alveolata + + + + alveolates + + @@ -1077,12 +2064,40 @@ + + GC_ID:1 heterokonts + ncbi_taxonomy Chromophyta Heterokonta Straminipila + NCBITaxon:33634 Stramenopiles + + + + Heterokonta + + + + + + Straminipila + + + + + + heterokonts + + + + + + Chromophyta + + @@ -1090,10 +2105,27 @@ + + NCBITaxon:3314 + GC_ID:1 cypress family + ncbi_taxonomy Taxodiaceae + NCBITaxon:3367 Cupressaceae + + + + cypress family + + + + + + Taxodiaceae + + @@ -1101,13 +2133,48 @@ + + GC_ID:1 + PMID:25249442 angiosperms flowering plants + ncbi_taxonomy Angiospermae Magnoliophyta flowering plants + NCBITaxon:3398 Magnoliopsida + + + + angiosperms + + + + + + flowering plants + + + + + + Angiospermae + + + + + + Magnoliophyta + + + + + + flowering plants + + @@ -1115,9 +2182,22 @@ + + NCBITaxon:3614 + NCBITaxon:4352 + NCBITaxon:63764 + GC_ID:1 + ncbi_taxonomy Centrospermae + NCBITaxon:3524 Caryophyllales + + + + Centrospermae + + @@ -1125,6 +2205,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:35493 Streptophyta @@ -1134,9 +2218,19 @@ + + GC_ID:1 + ncbi_taxonomy Sarcocornia pacifica + NCBITaxon:365482 Salicornia pacifica + + + + Sarcocornia pacifica + + @@ -1144,9 +2238,19 @@ + + GC_ID:1 + ncbi_taxonomy Capparales + NCBITaxon:3699 Brassicales + + + + Capparales + + @@ -1154,11 +2258,33 @@ + + GC_ID:1 migratory bird locusts spur-throated grasshoppers spur-throated locusts + ncbi_taxonomy + NCBITaxon:37267 Cyrtacanthacridinae + + + + migratory bird locusts + + + + + + spur-throated grasshoppers + + + + + + spur-throated locusts + + @@ -1166,6 +2292,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:37567 Ditrysia @@ -1175,6 +2305,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:37570 Noctuoidea @@ -1184,6 +2318,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:376913 Haplorrhini @@ -1193,9 +2331,19 @@ + + GC_ID:1 Indian almond family + ncbi_taxonomy + NCBITaxon:3954 Combretaceae + + + + Indian almond family + + @@ -1203,9 +2351,19 @@ + + GC_ID:1 horsemussels + ncbi_taxonomy + NCBITaxon:40255 Modiolus + + + + horsemussels + + @@ -1213,6 +2371,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:403651 Pfiesteriaceae @@ -1222,9 +2384,21 @@ + + NCBITaxon:4709 + GC_ID:1 + PMID:26350789 + ncbi_taxonomy Areciflorae + NCBITaxon:40551 Arecales + + + + Areciflorae + + @@ -1232,10 +2406,26 @@ + + GC_ID:1 mammals + ncbi_taxonomy mammals + NCBITaxon:40674 Mammalia + + + + mammals + + + + + + mammals + + @@ -1243,6 +2433,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:41191 Glossata @@ -1252,6 +2446,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:41196 Neolepidoptera @@ -1261,6 +2459,11 @@ + + NCBITaxon:37583 + GC_ID:1 + ncbi_taxonomy + NCBITaxon:41197 Heteroneura @@ -1270,6 +2473,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:41377 Avicennia @@ -1279,11 +2486,33 @@ + + GC_ID:1 black mangrove + ncbi_taxonomy Avicennia nitida Bontia germinans + NCBITaxon:41378 Avicennia germinans + + + + black mangrove + + + + + + Avicennia nitida + + + + + + Bontia germinans + + @@ -1291,6 +2520,11 @@ + + GC_ID:1 + PMID:12144762 + ncbi_taxonomy + NCBITaxon:4143 Lamiales @@ -1300,6 +2534,11 @@ + + NCBITaxon:41376 + GC_ID:1 + ncbi_taxonomy + NCBITaxon:4185 Acanthaceae @@ -1309,9 +2548,20 @@ + + NCBITaxon:3927 + GC_ID:1 + ncbi_taxonomy Myrtanae + NCBITaxon:41944 Myrtales + + + + Myrtanae + + @@ -1319,10 +2569,26 @@ + + GC_ID:1 dinosaur dinosaurs + ncbi_taxonomy + NCBITaxon:436486 Dinosauria + + + + dinosaur + + + + + + dinosaurs + + @@ -1330,6 +2596,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:436489 Saurischia @@ -1339,6 +2609,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:436491 Theropoda @@ -1348,24 +2622,23 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:436492 Coelurosauria - - - - - Chortoicetes - - - - + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:4434 Bataceae @@ -1375,9 +2648,19 @@ + + GC_ID:1 Batis + ncbi_taxonomy + NCBITaxon:4435 Batis <eudicots> + + + + Batis + + @@ -1385,6 +2668,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:4436 Batis maritima @@ -1394,12 +2681,41 @@ + + GC_ID:1 + PMID:25249442 monocots monocotyledons + ncbi_taxonomy Monocotyledoneae monocots + NCBITaxon:4447 Liliopsida + + + + monocots + + + + + + monocotyledons + + + + + + Monocotyledoneae + + + + + + monocots + + @@ -1407,9 +2723,21 @@ + + GC_ID:11 + PMID:10758887 + PMID:11411709 + ncbi_taxonomy Polycystis viridis + NCBITaxon:44822 Microcystis viridis + + + + Polycystis viridis + + @@ -1417,10 +2745,28 @@ + + NCBITaxon:239180 + NCBITaxon:239182 + GC_ID:1 + ncbi_taxonomy Arthrocnemum Sarcocornia + NCBITaxon:46104 Salicornia + + + + Arthrocnemum + + + + + + Sarcocornia + + @@ -1428,6 +2774,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:465832 Calyptra @@ -1437,11 +2787,34 @@ + + GC_ID:1 + PMID:26350789 Palmae palm family palms + ncbi_taxonomy + NCBITaxon:4710 Arecaceae + + + + Palmae + + + + + + palm family + + + + + + palms + + @@ -1449,10 +2822,27 @@ + + GC_ID:1 + PMID:26350789 + ncbi_taxonomy Commelinidae Commeliniflorae + NCBITaxon:4734 commelinids + + + + Commelinidae + + + + + + Commeliniflorae + + @@ -1460,10 +2850,28 @@ + + GC_ID:1 + PMID:11062127 + PMID:12684019 + ncbi_taxonomy Mycota fungi + NCBITaxon:4751 Fungi + + + + Mycota + + + + + + fungi + + @@ -1471,21 +2879,33 @@ + + GC_ID:1 + insects true insects + ncbi_taxonomy insects + NCBITaxon:50557 Insecta - - - - - - - - Australian plague locust - Epacromia terminifera - Chortoicetes terminifera - + + + + insects + + + + + + true insects + + + + + + insects + + @@ -1493,6 +2913,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:51952 Elaeis @@ -1502,9 +2926,19 @@ + + GC_ID:1 African oil palm + ncbi_taxonomy + NCBITaxon:51953 Elaeis guineensis + + + + African oil palm + + @@ -1512,9 +2946,22 @@ + + GC_ID:11 + PMID:11321098 + PMID:12361260 + PMID:25757799 + ncbi_taxonomy Oscillatoria sect. Prolificae + NCBITaxon:54304 Planktothrix + + + + Oscillatoria sect. Prolificae + + @@ -1522,9 +2969,19 @@ + + GC_ID:1 + ncbi_taxonomy Coniferopsida + NCBITaxon:58019 Pinopsida + + + + Coniferopsida + + @@ -1532,10 +2989,26 @@ + + GC_ID:1 vascular plants + ncbi_taxonomy vascular plants + NCBITaxon:58023 Tracheophyta + + + + vascular plants + + + + + + vascular plants + + @@ -1543,10 +3016,26 @@ + + GC_ID:1 seed plants + ncbi_taxonomy seed plants + NCBITaxon:58024 Spermatophyta + + + + seed plants + + + + + + seed plants + + @@ -1554,6 +3043,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:6072 Eumetazoa @@ -1563,12 +3056,40 @@ + + GC_ID:1 cnidarians coelenterates + ncbi_taxonomy Coelenterata cnidarians + NCBITaxon:6073 Cnidaria + + + + cnidarians + + + + + + coelenterates + + + + + + Coelenterata + + + + + + cnidarians + + @@ -1576,10 +3097,26 @@ + + GC_ID:1 anthozoans + ncbi_taxonomy anthozoans + NCBITaxon:6101 Anthozoa + + + + anthozoans + + + + + + anthozoans + + @@ -1587,9 +3124,20 @@ + + NCBITaxon:423301 + GC_ID:1 + ncbi_taxonomy Avicenniaceae + NCBITaxon:624272 Avicennioideae + + + + Avicenniaceae + + @@ -1597,11 +3145,33 @@ + + GC_ID:1 molluscs mollusks + ncbi_taxonomy molluscs + NCBITaxon:6447 Mollusca + + + + molluscs + + + + + + mollusks + + + + + + molluscs + + @@ -1609,12 +3179,40 @@ + + GC_ID:1 bivalves + ncbi_taxonomy Lamellibranchiata Pelecypoda bivalves + NCBITaxon:6544 Bivalvia + + + + bivalves + + + + + + Lamellibranchiata + + + + + + Pelecypoda + + + + + + bivalves + + @@ -1622,9 +3220,19 @@ + + GC_ID:1 + ncbi_taxonomy Pteriomorpha + NCBITaxon:6545 Pteriomorphia + + + + Pteriomorpha + + @@ -1632,9 +3240,19 @@ + + GC_ID:1 + ncbi_taxonomy Mytiloida + NCBITaxon:6546 Mytilida + + + + Mytiloida + + @@ -1642,6 +3260,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:6547 Mytilidae @@ -1651,6 +3273,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:6548 Mytilus @@ -1660,10 +3286,26 @@ + + GC_ID:1 arthropods + ncbi_taxonomy arthropods + NCBITaxon:6656 Arthropoda + + + + arthropods + + + + + + arthropods + + @@ -1671,6 +3313,11 @@ + + NCBITaxon:1089105 + GC_ID:1 + ncbi_taxonomy + NCBITaxon:695564 Erebidae @@ -1680,13 +3327,47 @@ - insects + + GC_ID:1 + hexapods + ncbi_taxonomy Atelocerata Tracheata Uniramia hexapods + NCBITaxon:6960 Hexapoda + + + + hexapods + + + + + + Atelocerata + + + + + + Tracheata + + + + + + Uniramia + + + + + + hexapods + + @@ -1694,10 +3375,26 @@ + + GC_ID:1 + ncbi_taxonomy Saltatoria - grasshoppers, crickets, and katydids + grasshoppers, crickets, & katydids + NCBITaxon:6993 Orthoptera + + + + Saltatoria + + + + + + grasshoppers, crickets, & katydids + + @@ -1705,10 +3402,26 @@ + + GC_ID:1 grasshoppers and locusts + ncbi_taxonomy grasshoppers + NCBITaxon:7001 Caelifera + + + + grasshoppers and locusts + + + + + + grasshoppers + + @@ -1716,9 +3429,19 @@ + + GC_ID:1 short-horned grasshoppers + ncbi_taxonomy + NCBITaxon:7002 Acrididae + + + + short-horned grasshoppers + + @@ -1726,6 +3449,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:7003 Locusta @@ -1735,9 +3462,19 @@ + + GC_ID:1 migratory locust + ncbi_taxonomy + NCBITaxon:7004 Locusta migratoria + + + + migratory locust + + @@ -1745,6 +3482,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:7008 Schistocerca @@ -1754,10 +3495,26 @@ + + GC_ID:1 desert locust + ncbi_taxonomy Locusta gregaria + NCBITaxon:7010 Schistocerca gregaria + + + + desert locust + + + + + + Locusta gregaria + + @@ -1765,11 +3522,33 @@ + + GC_ID:1 butterflies and moths moths + ncbi_taxonomy moths + NCBITaxon:7088 Lepidoptera + + + + butterflies and moths + + + + + + moths + + + + + + moths + + @@ -1777,6 +3556,9 @@ + GC_ID:1 + ncbi_taxonomy + NCBITaxon:70910 Acridomorpha @@ -1786,6 +3568,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:71000 Pfiesteria @@ -1795,12 +3581,43 @@ + + NCBITaxon:3399 + GC_ID:1 + PMID:25249442 + PMID:26724406 + ncbi_taxonomy Dicotyledoneae dicots dicotyledons eudicots + NCBITaxon:71240 eudicotyledons + + + + Dicotyledoneae + + + + + + dicots + + + + + + dicotyledons + + + + + + eudicots + + @@ -1808,9 +3625,20 @@ + + GC_ID:1 + PMID:12144762 Asteridae + ncbi_taxonomy + NCBITaxon:71274 asterids + + + + Asteridae + + @@ -1818,9 +3646,19 @@ + + GC_ID:1 + ncbi_taxonomy Rosidae + NCBITaxon:71275 rosids + + + + Rosidae + + @@ -1828,10 +3666,26 @@ + + GC_ID:1 Pterygota winged insects + ncbi_taxonomy + NCBITaxon:7496 Pterygota <insects> + + + + Pterygota + + + + + + winged insects + + @@ -1839,10 +3693,26 @@ + + GC_ID:1 echinoderms + ncbi_taxonomy echinoderms + NCBITaxon:7586 Echinodermata + + + + echinoderms + + + + + + echinoderms + + @@ -1850,30 +3720,53 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:7624 Echinozoa - - - - - Cylindrospermopsis - - - - + + GC_ID:1 holothurians sea cucumbers + ncbi_taxonomy Holothurioidea sea cucumbers + NCBITaxon:7705 Holothuroidea + + + + holothurians + + + + + + sea cucumbers + + + + + + Holothurioidea + + + + + + sea cucumbers + + @@ -1881,10 +3774,26 @@ + + GC_ID:1 chordates + ncbi_taxonomy chordates + NCBITaxon:7711 Chordata + + + + chordates + + + + + + chordates + + @@ -1892,11 +3801,33 @@ + + GC_ID:1 Vertebrata vertebrates + ncbi_taxonomy vertebrates + NCBITaxon:7742 Vertebrata <vertebrates> + + + + Vertebrata + + + + + + vertebrates + + + + + + vertebrates + + @@ -1904,10 +3835,26 @@ + + GC_ID:1 Gnathostomata jawed vertebrates + ncbi_taxonomy + NCBITaxon:7776 Gnathostomata <vertebrates> + + + + Gnathostomata + + + + + + jawed vertebrates + + @@ -1915,9 +3862,19 @@ + + GC_ID:1 euphyllophytes + ncbi_taxonomy + NCBITaxon:78536 Euphyllophyta + + + + euphyllophytes + + @@ -1925,6 +3882,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:8287 Sarcopterygii @@ -1934,9 +3895,19 @@ + + GC_ID:1 sauropsids + ncbi_taxonomy + NCBITaxon:8457 Sauropsida + + + + sauropsids + + @@ -1944,6 +3915,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:8492 Archosauria @@ -1953,6 +3928,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:85512 Dicondylia @@ -1962,6 +3941,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:85604 Amphiesmenoptera @@ -1971,11 +3954,33 @@ + + GC_ID:1 birds + ncbi_taxonomy avian birds + NCBITaxon:8782 Aves + + + + birds + + + + + + avian + + + + + + birds + + @@ -1983,6 +3988,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:88770 Panarthropoda @@ -1992,9 +4001,19 @@ + + GC_ID:1 Craniata + ncbi_taxonomy + NCBITaxon:89593 Craniata <chordates> + + + + Craniata + + @@ -2002,10 +4021,27 @@ + + NCBITaxon:1437200 + GC_ID:1 core eudicots core eudicotyledons + ncbi_taxonomy + NCBITaxon:91827 Gunneridae + + + + core eudicots + + + + + + core eudicotyledons + + @@ -2013,6 +4049,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:91836 malvids @@ -2022,9 +4062,21 @@ + + NCBITaxon:41935 + GC_ID:1 + PMID:12144762 + ncbi_taxonomy euasterids I + NCBITaxon:91888 lamiids + + + + euasterids I + + @@ -2032,31 +4084,60 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:92621 Acridoidea - - - - - Gloeotrichia - - - - + + GC_ID:1 eutherian mammals placental mammals placentals + ncbi_taxonomy Placentalia placentals + NCBITaxon:9347 Eutheria + + + + eutherian mammals + + + + + + placental mammals + + + + + + placentals + + + + + + Placentalia + + + + + + placentals + + @@ -2064,11 +4145,33 @@ + + GC_ID:1 primate + ncbi_taxonomy Primata primates + NCBITaxon:9443 Primates + + + + primate + + + + + + Primata + + + + + + primates + + @@ -2076,6 +4179,10 @@ + + GC_ID:1 + ncbi_taxonomy + NCBITaxon:9526 Catarrhini @@ -2085,10 +4192,26 @@ + + GC_ID:1 great apes + ncbi_taxonomy Pongidae + NCBITaxon:9604 Hominidae + + + + great apes + + + + + + Pongidae + + @@ -2096,9 +4219,19 @@ + + GC_ID:1 humans + ncbi_taxonomy + NCBITaxon:9605 Homo + + + + humans + + @@ -2106,12 +4239,22 @@ + + GC_ID:1 human + ncbi_taxonomy + NCBITaxon:9606 Homo sapiens + + + + human + + - + diff --git a/src/envo/imports/obi_import.obo b/src/envo/imports/obi_import.obo index 1cf4c102..d567e418 100644 --- a/src/envo/imports/obi_import.obo +++ b/src/envo/imports/obi_import.obo @@ -26,25 +26,18 @@ def: "A continuant that is a bearer of quality and realizable entity entities, i def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000031 ! generically dependent continuant [Term] id: BFO:0000006 name: spatial region is_a: BFO:0000141 ! immaterial entity disjoint_from: BFO:0000029 ! site -disjoint_from: BFO:0000029 ! site -disjoint_from: BFO:0000140 ! continuant fiat boundary [Term] id: BFO:0000008 name: temporal region is_a: BFO:0000003 ! occurrent disjoint_from: BFO:0000011 ! spatiotemporal region -disjoint_from: BFO:0000011 ! spatiotemporal region -disjoint_from: BFO:0000015 ! process -disjoint_from: BFO:0000035 ! process boundary [Term] id: BFO:0000011 @@ -83,7 +76,6 @@ def: "A continuant that inheres in or is borne by other entities. Every instance def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000031 ! generically dependent continuant [Term] id: BFO:0000023 @@ -94,7 +86,6 @@ is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000024 name: fiat object -name: fiat object part is_a: BFO:0000040 ! material entity [Term] @@ -179,7 +170,7 @@ is_a: IAO:0000308 ! figure [Term] id: IAO:0000104 name: plan specification -def: "A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." [] +def: "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified." [] is_a: IAO:0000033 ! directive information entity [Term] @@ -376,12 +367,6 @@ name: physical object quality def: "A quality which inheres in a continuant." [] is_a: BFO:0000019 ! quality -[Term] -id: PATO:0001291 -name: electromagnetic (EM) radiation quality -def: "A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation." [] -is_a: PATO:0001739 ! radiation quality - [Term] id: PATO:0001296 name: luminous flux @@ -392,7 +377,7 @@ is_a: PATO:0001300 ! optical quality id: PATO:0001300 name: optical quality def: "An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light." [] -is_a: PATO:0001291 ! electromagnetic (EM) radiation quality +is_a: PATO:0070060 ! quality of interaction of a substance with electromagnetic radiation [Term] id: PATO:0001422 @@ -424,17 +409,11 @@ name: 3-D extent def: "A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions." [] is_a: PATO:0000117 ! size -[Term] -id: PATO:0001739 -name: radiation quality -def: "A quality that inheres in an bearer by virtue of how that bearer interacts with radiation." [] -is_a: PATO:0001018 ! physical quality - [Term] id: PATO:0001740 name: activity (of a radionuclide) def: "A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate." [] -is_a: PATO:0001739 ! radiation quality +is_a: PATO:0002198 ! quality of a substance [Term] id: PATO:0001741 @@ -466,3 +445,9 @@ name: quality of a substance def: "A quality inhering in a bearer by virtue of its constitution." [] is_a: PATO:0001018 ! physical quality +[Term] +id: PATO:0070060 +name: quality of interaction of a substance with electromagnetic radiation +def: "A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength." [] +is_a: PATO:0002198 ! quality of a substance + diff --git a/src/envo/imports/obi_import.owl b/src/envo/imports/obi_import.owl index cb0057e5..de7d47b2 100644 --- a/src/envo/imports/obi_import.owl +++ b/src/envo/imports/obi_import.owl @@ -6,7 +6,8 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> @@ -40,6 +41,42 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -90,8 +127,6 @@ - - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) independent continuant @@ -103,8 +138,6 @@ - - spatial region @@ -114,9 +147,6 @@ - - - temporal region @@ -176,7 +206,6 @@ - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) @@ -200,7 +229,6 @@ fiat object - fiat object part @@ -277,7 +305,6 @@ An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity material entity @@ -345,7 +372,7 @@ - A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. + A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. plan specification @@ -687,16 +714,6 @@ - - - - - A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. - electromagnetic (EM) radiation quality - - - - @@ -710,7 +727,7 @@ - + An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. optical quality @@ -767,20 +784,10 @@ - - - - - A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. - radiation quality - - - - - + A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate. activity (of a radionuclide) @@ -837,6 +844,16 @@ + + + + + A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength. + quality of interaction of a substance with electromagnetic radiation + + + + + diff --git a/src/envo/imports/pato_import.obo b/src/envo/imports/pato_import.obo index 2d9cacf1..083f5a2e 100644 --- a/src/envo/imports/pato_import.obo +++ b/src/envo/imports/pato_import.obo @@ -15,7 +15,7 @@ def: "An entity that has temporal parts and that happens, unfolds or develops th [Term] id: BFO:0000004 name: independent continuant -def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant @@ -27,7 +27,7 @@ is_a: BFO:0000141 ! immaterial entity [Term] id: BFO:0000015 name: process -def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] is_a: BFO:0000003 ! occurrent [Term] @@ -45,15 +45,14 @@ is_a: BFO:0000020 ! specifically dependent continuant [Term] id: BFO:0000020 name: specifically dependent continuant -def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] is_a: BFO:0000002 ! continuant [Term] id: BFO:0000023 name: role def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] -is_a: CHEBI:50906 ! role -equivalent_to: CHEBI:50906 ! role +is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000034 @@ -185,21 +184,6 @@ is_a: CHEBI:16646 ! carbohydrate is_a: CHEBI:167559 ! glycan is_a: CHEBI:33694 ! biomacromolecule -[Term] -id: CHEBI:18248 -name: iron atom -def: "An iron group element atom that has atomic number 26." [] -synonym: "26Fe" RELATED [] -synonym: "Eisen" RELATED [] -synonym: "Fe" RELATED [] -synonym: "fer" RELATED [] -synonym: "ferrum" RELATED [] -synonym: "hierro" RELATED [] -synonym: "Iron" RELATED [] -synonym: "iron" EXACT [] -synonym: "iron" RELATED [] -is_a: CHEBI:33356 ! iron group element atom - [Term] id: CHEBI:22563 name: anion @@ -235,7 +219,6 @@ id: CHEBI:24432 name: biological role def: "A role played by the molecular entity or part thereof within a biological context." [] synonym: "biological function" RELATED [] -is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] @@ -284,22 +267,6 @@ synonym: "inorganic oxides" RELATED [] is_a: CHEBI:24835 ! inorganic molecular entity is_a: CHEBI:25741 ! oxide -[Term] -id: CHEBI:24866 -name: salt -def: "A salt is an assembly of cations and anions." [] -synonym: "ionic compound" RELATED [] -synonym: "ionic compounds" RELATED [] -synonym: "sal" RELATED [] -synonym: "sales" RELATED [] -synonym: "salt" EXACT [] -synonym: "salts" RELATED [] -synonym: "Salz" RELATED [] -synonym: "Salze" RELATED [] -synonym: "sel" RELATED [] -synonym: "sels" RELATED [] -is_a: CHEBI:37577 ! heteroatomic molecular entity - [Term] id: CHEBI:24870 name: ion @@ -311,14 +278,6 @@ synonym: "iones" RELATED [] synonym: "ions" RELATED [] is_a: CHEBI:23367 ! molecular entity -[Term] -id: CHEBI:24873 -name: iron molecular entity -synonym: "iron compounds" RELATED [] -synonym: "iron molecular entities" RELATED [] -synonym: "iron molecular entity" EXACT [] -is_a: CHEBI:33744 ! iron group molecular entity - [Term] id: CHEBI:25362 name: elemental molecule @@ -401,13 +360,6 @@ name: phosphorus molecular entity synonym: "phosphorus molecular entities" RELATED [] is_a: CHEBI:33302 ! pnictogen molecular entity -[Term] -id: CHEBI:26712 -name: sodium molecular entity -synonym: "sodium compounds" RELATED [] -synonym: "sodium molecular entities" RELATED [] -is_a: CHEBI:33296 ! alkali metal molecular entity - [Term] id: CHEBI:26833 name: sulfur atom @@ -452,23 +404,6 @@ synonym: "sulphuric acid" RELATED [] synonym: "tetraoxosulfuric acid" EXACT [] is_a: CHEBI:33402 ! sulfur oxoacid -[Term] -id: CHEBI:27081 -name: transition element atom -def: "An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell." [] -synonym: "metal de transicion" RELATED [] -synonym: "metal de transition" RELATED [] -synonym: "metales de transicion" RELATED [] -synonym: "metaux de transition" RELATED [] -synonym: "transition element" EXACT [] -synonym: "transition element" RELATED [] -synonym: "transition elements" RELATED [] -synonym: "transition metal" RELATED [] -synonym: "transition metals" RELATED [] -synonym: "Uebergangselement" RELATED [] -synonym: "Uebergangsmetalle" RELATED [] -is_a: CHEBI:33521 ! metal atom - [Term] id: CHEBI:27594 name: carbon atom @@ -518,7 +453,6 @@ is_a: CHEBI:60242 ! monovalent inorganic cation id: CHEBI:33232 name: application def: "Intended use of the molecular entity or part thereof by humans." [] -is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] @@ -609,13 +543,6 @@ synonym: "fertiliser" RELATED [] synonym: "fertilizers" RELATED [] is_a: CHEBI:33286 ! agrochemical -[Term] -id: CHEBI:33296 -name: alkali metal molecular entity -def: "A molecular entity containing one or more atoms of an alkali metal." [] -synonym: "alkali metal molecular entities" RELATED [] -is_a: CHEBI:33674 ! s-block molecular entity - [Term] id: CHEBI:33300 name: pnictogen @@ -686,14 +613,6 @@ synonym: "main group element" RELATED [] synonym: "main group elements" EXACT [] is_a: CHEBI:33250 ! atom -[Term] -id: CHEBI:33356 -name: iron group element atom -synonym: "group 8 elements" EXACT [] -synonym: "iron group element" RELATED [] -synonym: "iron group elements" RELATED [] -is_a: CHEBI:33561 ! d-block element atom - [Term] id: CHEBI:33402 name: sulfur oxoacid @@ -725,25 +644,6 @@ synonym: "chalcogen oxoanion" EXACT [] synonym: "chalcogen oxoanions" RELATED [] is_a: CHEBI:35406 ! oxoanion -[Term] -id: CHEBI:33497 -name: transition element molecular entity -def: "A molecular entity containing one or more atoms of a transition element." [] -synonym: "transition element molecular entities" RELATED [] -synonym: "transition metal molecular entity" RELATED [] -is_a: CHEBI:23367 ! molecular entity - -[Term] -id: CHEBI:33521 -name: metal atom -def: "An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity." [] -synonym: "elemental metal" RELATED [] -synonym: "elemental metals" RELATED [] -synonym: "metal element" RELATED [] -synonym: "metal elements" RELATED [] -synonym: "metals" RELATED [] -is_a: CHEBI:33250 ! atom - [Term] id: CHEBI:33560 name: p-block element atom @@ -752,13 +652,6 @@ synonym: "p-block element" RELATED [] synonym: "p-block elements" RELATED [] is_a: CHEBI:33318 ! main group element atom -[Term] -id: CHEBI:33561 -name: d-block element atom -synonym: "d-block element" RELATED [] -synonym: "d-block elements" RELATED [] -is_a: CHEBI:27081 ! transition element atom - [Term] id: CHEBI:33579 name: main group molecular entity @@ -816,15 +709,6 @@ synonym: "p-block molecular entities" RELATED [] synonym: "p-block molecular entitiy" RELATED [] is_a: CHEBI:33579 ! main group molecular entity -[Term] -id: CHEBI:33676 -name: d-block molecular entity -def: "A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element." [] -synonym: "d-block compounds" RELATED [] -synonym: "d-block molecular entities" RELATED [] -synonym: "d-block molecular entity" EXACT [] -is_a: CHEBI:33497 ! transition element molecular entity - [Term] id: CHEBI:33692 name: hydrides @@ -843,13 +727,6 @@ synonym: "biopolymers" RELATED [] is_a: CHEBI:33839 ! macromolecule is_a: CHEBI:50860 ! organic molecular entity -[Term] -id: CHEBI:33744 -name: iron group molecular entity -synonym: "iron group molecular entities" RELATED [] -synonym: "iron group molecular entity" EXACT [] -is_a: CHEBI:33676 ! d-block molecular entity - [Term] id: CHEBI:33839 name: macromolecule @@ -1051,13 +928,12 @@ is_a: CHEBI:33582 ! carbon group molecular entity id: CHEBI:50906 name: role def: "A role is particular behaviour which a material entity may exhibit." [] -is_a: BFO:0000023 ! role +is_a: PATO:0000001 ! quality [Term] id: CHEBI:51086 name: chemical role def: "A role played by the molecular entity or part thereof within a chemical context." [] -is_a: BFO:0000023 ! role is_a: CHEBI:50906 ! role [Term] @@ -1174,37 +1050,16 @@ def: "Any inorganic anion with a valency of two." [] synonym: "divalent inorganic anions" RELATED [] is_a: CHEBI:24834 ! inorganic anion -[Term] -id: GO:0003008 -name: system process -def: "A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective." [] -synonym: "organ system process" EXACT [] -is_a: GO:0032501 ! multicellular organismal process - -[Term] -id: GO:0007588 -name: excretion -def: "The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds." [] -is_a: GO:0003008 ! system process - [Term] id: GO:0008150 name: biological_process -def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [] +def: "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [] synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] is_a: BFO:0000015 ! process -[Term] -id: GO:0032501 -name: multicellular organismal process -def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [] -synonym: "organismal physiological process" EXACT [] -synonym: "single-multicellular organism process" RELATED [] -is_a: GO:0008150 ! biological_process - [Term] id: NCBITaxon:1 name: root @@ -4242,6 +4097,16 @@ name: organismal entity def: "A material entity that is one or more organisms, viruses or viroids." [] is_a: BFO:0000040 ! material entity +[Term] +id: PR:000050567 +name: protein-containing material entity +def: "A material entity that minimally consists of a protein." [] +synonym: "protein" NARROW [] +synonym: "protein aggregate" NARROW [] +synonym: "protein complex" NARROW [] +synonym: "protein-containing complex" NARROW [] +is_a: BFO:0000040 ! material entity + [Term] id: RO:0002577 name: system @@ -4257,6 +4122,8 @@ synonym: "region of skin" EXACT [] synonym: "skin" EXACT [] synonym: "skin region" EXACT [] synonym: "skin zone" EXACT [] +is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 ! zone of organ [Term] @@ -4292,14 +4159,6 @@ synonym: "cardinal organ part" EXACT [] synonym: "regional part of organ" RELATED [] is_a: UBERON:0010000 ! multicellular anatomical structure -[Term] -id: UBERON:0000160 -name: intestine -def: "Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine." [] -synonym: "bowel" EXACT [] -synonym: "intestinal tract" RELATED [] -is_a: UBERON:0004921 ! subdivision of digestive tract - [Term] id: UBERON:0000165 name: mouth @@ -4320,16 +4179,6 @@ synonym: "vestibule of mouth" RELATED [] synonym: "vestibulum oris" RELATED [] is_a: UBERON:0004921 ! subdivision of digestive tract -[Term] -id: UBERON:0000174 -name: excreta -def: "A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity." [] -synonym: "excreted substance" EXACT [] -synonym: "excretion" RELATED [] -synonym: "portion of excreted substance" EXACT [] -synonym: "waste substance" EXACT [] -is_a: UBERON:0000463 ! organism substance - [Term] id: UBERON:0000178 name: blood @@ -4337,6 +4186,7 @@ def: "A fluid that is composed of blood plasma and erythrocytes." [] synonym: "portion of blood" EXACT [] synonym: "vertebrate blood" EXACT [] synonym: "whole blood" RELATED [] +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid [Term] @@ -4399,13 +4249,6 @@ synonym: "simple tissue" NARROW [] synonym: "tissue portion" EXACT [] is_a: UBERON:0010000 ! multicellular anatomical structure -[Term] -id: UBERON:0000912 -name: mucus -def: "Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water." [] -is_a: UBERON:0000456 ! secretion of exocrine gland -is_a: UBERON:0006314 ! bodily fluid - [Term] id: UBERON:0001062 name: anatomical entity @@ -4470,50 +4313,9 @@ synonym: "blood plasm" EXACT [] synonym: "plasma" BROAD [] synonym: "portion of blood plasma" EXACT [] synonym: "portion of plasma" BROAD [] +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid -[Term] -id: UBERON:0001970 -name: bile -def: "Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium." [] -synonym: "fel" RELATED [] -synonym: "gall" RELATED [] -is_a: UBERON:0000456 ! secretion of exocrine gland -is_a: UBERON:0006314 ! bodily fluid - -[Term] -id: UBERON:0001988 -name: feces -def: "Portion of semisolid bodily waste discharged through the anus[MW,modified]." [] -synonym: "cow dung" NARROW [] -synonym: "cow pat" NARROW [] -synonym: "droppings" RELATED [] -synonym: "dung" NARROW [] -synonym: "excrement" RELATED [] -synonym: "excreta" BROAD [] -synonym: "faeces" EXACT [] -synonym: "fecal material" EXACT [] -synonym: "fecal matter" EXACT [] -synonym: "fewmet" NARROW [] -synonym: "frass" NARROW [] -synonym: "guano" NARROW [] -synonym: "ordure" RELATED [] -synonym: "piece of shit" EXACT [] -synonym: "portion of dung" NARROW [] -synonym: "portion of excrement" EXACT [] -synonym: "portion of faeces" EXACT [] -synonym: "portion of fecal material" EXACT [] -synonym: "portion of fecal matter" EXACT [] -synonym: "portion of feces" EXACT [] -synonym: "portion of guano" NARROW [] -synonym: "portion of scat" NARROW [] -synonym: "portionem cacas" EXACT [] -synonym: "scat" NARROW [] -synonym: "spoor" RELATED [] -synonym: "spraint" NARROW [] -synonym: "stool" EXACT [] -is_a: UBERON:0000174 ! excreta - [Term] id: UBERON:0002416 name: integumental system @@ -4525,6 +4327,7 @@ synonym: "integumentary system" EXACT [] synonym: "integumentum commune" RELATED [] synonym: "organism surface" RELATED [] synonym: "surface" RELATED [] +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system [Term] @@ -4538,6 +4341,13 @@ synonym: "ostia" RELATED [] synonym: "ostium" RELATED [] is_a: UBERON:0010000 ! multicellular anatomical structure +[Term] +id: UBERON:0004121 +name: ectoderm-derived structure +def: "An anatomical structure that develops (entirely or partially) from the ectoderm." [] +synonym: "ectodermal deriviative" EXACT [] +is_a: UBERON:0000061 ! anatomical structure + [Term] id: UBERON:0004765 name: skeletal element @@ -4549,6 +4359,7 @@ id: UBERON:0004921 name: subdivision of digestive tract def: "A proximal-distal subdivision of the digestive tract." [] synonym: "alimentary system subdivision" RELATED [] +synonym: "gut section" RELATED [] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [] diff --git a/src/envo/imports/pato_import.owl b/src/envo/imports/pato_import.owl index 7c05483b..7ef93f46 100644 --- a/src/envo/imports/pato_import.owl +++ b/src/envo/imports/pato_import.owl @@ -35,6 +35,12 @@ + + + + + + @@ -124,7 +130,7 @@ - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) independent continuant @@ -143,7 +149,7 @@ - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) process @@ -173,7 +179,7 @@ - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) specifically dependent continuant @@ -182,8 +188,7 @@ - - + A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role @@ -360,25 +365,6 @@ - - - - - An iron group element atom that has atomic number 26. - iron - 26Fe - Eisen - Fe - Iron - fer - ferrum - hierro - iron - iron atom - - - - @@ -424,7 +410,6 @@ - A role played by the molecular entity or part thereof within a biological context. biological function @@ -499,26 +484,6 @@ - - - - - A salt is an assembly of cations and anions. - salt - Salz - Salze - ionic compound - ionic compounds - sal - sales - salts - sel - sels - salt - - - - @@ -534,18 +499,6 @@ - - - - - iron molecular entity - iron compounds - iron molecular entities - iron molecular entity - - - - @@ -664,17 +617,6 @@ - - - - - sodium compounds - sodium molecular entities - sodium molecular entity - - - - @@ -731,27 +673,6 @@ - - - - - An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell. - transition element - Uebergangselement - Uebergangsmetalle - metal de transicion - metal de transition - metales de transicion - metaux de transition - transition element - transition elements - transition metal - transition metals - transition element atom - - - - @@ -812,7 +733,6 @@ - Intended use of the molecular entity or part thereof by humans. application @@ -952,17 +872,6 @@ - - - - - A molecular entity containing one or more atoms of an alkali metal. - alkali metal molecular entities - alkali metal molecular entity - - - - @@ -1057,18 +966,6 @@ - - - - - group 8 elements - iron group element - iron group elements - iron group element atom - - - - @@ -1116,33 +1013,6 @@ - - - - - A molecular entity containing one or more atoms of a transition element. - transition element molecular entities - transition metal molecular entity - transition element molecular entity - - - - - - - - - An atom of an element that exhibits typical metallic properties, being typically shiny, with high electrical and thermal conductivity. - elemental metal - elemental metals - metal element - metal elements - metals - metal atom - - - - @@ -1155,17 +1025,6 @@ - - - - - d-block element - d-block elements - d-block element atom - - - - @@ -1251,19 +1110,6 @@ - - - - - A d-block molecular entity is a molecular entity containing one or more atoms of a d-block element. - d-block molecular entity - d-block compounds - d-block molecular entities - d-block molecular entity - - - - @@ -1290,17 +1136,6 @@ - - - - - iron group molecular entity - iron group molecular entities - iron group molecular entity - - - - @@ -1597,7 +1432,7 @@ - + A role is particular behaviour which a material entity may exhibit. role @@ -1607,7 +1442,6 @@ - A role played by the molecular entity or part thereof within a chemical context. chemical role @@ -1781,32 +1615,11 @@ - - - - - A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective. - organ system process - system process - - - - - - - - - The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds. - excretion - - - - - A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. + A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. biological process physiological process single organism process @@ -1816,18 +1629,6 @@ - - - - - Any biological process, occurring at the level of a multicellular organism, pertinent to its function. - organismal physiological process - single-multicellular organism process - multicellular organismal process - - - - @@ -4787,6 +4588,16 @@ + + + + + A quality of radiation that reflects the fluence spectrum of charged and neutral particles within the material or medium where dose is being deposited. + radiation quality + + + + @@ -6637,6 +6448,20 @@ + + + + + A material entity that minimally consists of a protein. + protein + protein aggregate + protein complex + protein-containing complex + protein-containing material entity + + + + @@ -6650,6 +6475,8 @@ + + Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. portion of skin @@ -6711,18 +6538,6 @@ - - - - - Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. - bowel - intestinal tract - intestine - - - - @@ -6747,23 +6562,10 @@ - - - - - A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity. - excreted substance - portion of excreted substance - waste substance - excretion - excreta - - - - + A fluid that is composed of blood plasma and erythrocytes. portion of blood @@ -6858,17 +6660,6 @@ - - - - - - Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. - mucus - - - - @@ -6952,6 +6743,7 @@ + The liquid component of blood, in which erythrocytes are suspended. plasma @@ -6963,59 +6755,10 @@ - - - - - - Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. - fel - gall - bile - - - - - - - - - Portion of semisolid bodily waste discharged through the anus[MW,modified]. - excreta - faeces - fecal material - fecal matter - piece of shit - portion of excrement - portion of faeces - portion of fecal material - portion of fecal matter - portion of feces - portionem cacas - stool - cow dung - cow pat - dung - fewmet - frass - guano - portion of dung - portion of guano - portion of scat - scat - spraint - droppings - excrement - ordure - spoor - feces - - - - + Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. integumentary system @@ -7045,6 +6788,17 @@ + + + + + An anatomical structure that develops (entirely or partially) from the ectoderm. + ectodermal deriviative + ectoderm-derived structure + + + + @@ -7061,6 +6815,7 @@ A proximal-distal subdivision of the digestive tract. alimentary system subdivision + gut section intestinal tract segment of intestinal tract subdivision of alimentary system @@ -7182,5 +6937,5 @@ - + diff --git a/src/envo/imports/pco_import.owl b/src/envo/imports/pco_import.owl index 7162c759..7d9ea8a4 100644 --- a/src/envo/imports/pco_import.owl +++ b/src/envo/imports/pco_import.owl @@ -247,5 +247,5 @@ Classes for population already exist in IDO ('organism population', I - + diff --git a/src/envo/imports/po_import.obo b/src/envo/imports/po_import.obo index 3c1e8ab9..ebf48c91 100644 --- a/src/envo/imports/po_import.obo +++ b/src/envo/imports/po_import.obo @@ -13,25 +13,31 @@ synonym: "bush (narrow)" NARROW [] synonym: "clonal colony (related)" RELATED [] synonym: "colony (related)" RELATED [] synonym: "frutex (narrow)" NARROW [FNA:e4dde193-57f7-4ab9-9d25-96b4ca0088ba] -synonym: "frutices (narrow)" NARROW Plural [FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b] +synonym: "frutices (narrow, plural)" NARROW OMO:0003004 [FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b] synonym: "gametophyte (narrow)" NARROW [] synonym: "genet (broad)" BROAD [] synonym: "herb (narrow)" NARROW [] synonym: "liana (narrow)" NARROW [] synonym: "planta entera (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] -synonym: "prothalli (narrow)" NARROW Plural [FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0] +synonym: "prothalli (narrow, plural)" NARROW OMO:0003004 [FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0] synonym: "prothallium (narrow)" NARROW [] synonym: "prothallus (narrow)" NARROW [FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8] synonym: "ramet (broad)" BROAD [] -synonym: "seedling (narrow)" NARROW [] synonym: "shrub (narrow)" NARROW [] synonym: "sporophyte (narrow)" NARROW [] synonym: "suffrutex (narrow)" NARROW [FNA:99508f62-7116-4e2b-90c0-19ff55ebd967] -synonym: "suffrutices (narrow)" NARROW Plural [FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2] +synonym: "suffrutices (narrow, plural)" NARROW OMO:0003004 [FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2] synonym: "tree (narrow)" NARROW [] synonym: "vine (narrow)" NARROW [] synonym: "woody clump (narrow)" NARROW [FNA:c1ccca7d-2a98-4a9d-8603-c34b551935e0] synonym: "植物体全体 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0 +xref: FNA:99508f62-7116-4e2b-90c0-19ff55ebd967 +xref: FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2 +xref: FNA:c1ccca7d-2a98-4a9d-8603-c34b551935e0 +xref: FNA:e4dde193-57f7-4ab9-9d25-96b4ca0088ba +xref: FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b +xref: FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8 xref: PO_GIT:538 xref: PO_GIT:69 is_a: PO:0009011 ! plant structure @@ -47,7 +53,7 @@ synonym: "cuticle (broad)" BROAD [] synonym: "植物クチクラ (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:416 is_a: PO:0025161 ! portion of plant substance -relationship: RO:0002220 PO:0005679 ! epidermis +relationship: RO:0002220 PO:0005679 ! plant epidermis [Term] id: PO:0000037 @@ -106,7 +112,7 @@ def: "A primordium (PO:0025127) that develops from a root anlagen (PO:0025433) a comment: A root primordium may arise from cells of a pericycle (PO:0006203) in a root in most seed plant (pericyclic lateral root primordium; PO:0025492), from cells of an endodermis (PO:0000252) in ferns and some seed plants (non-pericyclic lateral root primordium: PO:0025493), or from cells of a shoot axis (PO:0025029), in the case of a basal root primordium (PO:0025479) or shoot-borne root primordium (PO:0025480). Transition from root primordium to root occurs with the formation of a root cap (PO:0020123), shortly after the development of a root apical meristem (PO:0020147). synonym: "portion of root primordium tissue (exact)" EXACT [] synonym: "primordio de raíz (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] -synonym: "root primordia (exact, plural)" EXACT [] +synonym: "root primordia (exact, plural)" EXACT OMO:0003004 [] synonym: "根原基（可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:467 is_a: PO:0025127 ! primordium @@ -114,16 +120,16 @@ relationship: RO:0002202 PO:0025433 ! root anlagen [Term] id: PO:0005679 -name: epidermis +name: plant epidermis namespace: plant_anatomy -def: "A portion of plant tissue (PO:0009007) composed of epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011)." [POC:curators] +def: "A portion of plant tissue (PO:0009007) composed of plant epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011)." [POC:curators] comment: The epidermis can be composed of one or more layers of cells. In some species of vascular plants, the epidermis, which is a primary tissue, is replaced by periderm, which is secondary tissue, later in development. The epidermis can also include trichomes, stomatal pores, root hairs, and rhizoids. subset: TraitNet synonym: "dermal tissue (exact)" EXACT [] synonym: "epidermal layer (exact)" EXACT [] -synonym: "epidermides (exact, plural)" EXACT [FNA:35df04e5-fde5-465e-b79e-ae7d5e1537bb] +synonym: "epidermides (exact, plural)" EXACT OMO:0003004 [FNA:35df04e5-fde5-465e-b79e-ae7d5e1537bb] synonym: "epidermis (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] -synonym: "epidermises (exact, plural)" EXACT [FNA:0d1bd0e6-c039-4de3-a162-68299a2f342a] +synonym: "epidermises (exact, plural)" EXACT OMO:0003004 [FNA:0d1bd0e6-c039-4de3-a162-68299a2f342a] synonym: "multiseriate epidermis (related)" RELATED [] synonym: "portion of epidermal tissue (exact)" EXACT [] synonym: "表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] @@ -163,13 +169,13 @@ relationship: BFO:0000050 PO:0025034 ! leaf id: PO:0006035 name: shoot system epidermis namespace: plant_anatomy -def: "A portion of epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020)." [ISBN:0471245208, POC:curators, POC:Laurel_Cooper] +def: "A portion of plant epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020)." [ISBN:0471245208, POC:curators, POC:Laurel_Cooper] comment: Often interrupted by stomatal complexes (PO:0002000) and other structures. The shoot system epidermis is different from the root epidermis (PO:0006036) in its origin, function and structure. synonym: "epidermis del epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "シュート表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:111 -is_a: PO:0005679 ! epidermis -intersection_of: PO:0005679 ! epidermis +is_a: PO:0005679 ! plant epidermis +intersection_of: PO:0005679 ! plant epidermis intersection_of: BFO:0000050 PO:0009006 ! shoot system relationship: BFO:0000050 PO:0009006 ! shoot system relationship: RO:0002202 PO:0009020 ! meristem L1 layer @@ -179,15 +185,15 @@ id: PO:0006036 name: root epidermis namespace: plant_anatomy alt_id: PO:0006037 -def: "A portion of epidermis (PO:0005679) that is part of a root (PO:0009005)." [ISBN:0080374913] +def: "A portion of plant epidermis (PO:0005679) that is part of a root (PO:0009005)." [ISBN:0080374913] comment: The root epidermis is different from the shoot epidermis in its origin, function and structure. synonym: "epiblem (related)" RELATED [] synonym: "epidermis de la raíz (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "rhizodermis (related)" RELATED [] synonym: "根表皮 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:111 -is_a: PO:0005679 ! epidermis -intersection_of: PO:0005679 ! epidermis +is_a: PO:0005679 ! plant epidermis +intersection_of: PO:0005679 ! plant epidermis intersection_of: BFO:0000050 PO:0009005 ! root relationship: BFO:0000050 PO:0009005 ! root @@ -238,7 +244,7 @@ relationship: RO:0000057 PO:0000003 ! whole plant id: PO:0009002 name: plant cell namespace: plant_anatomy -def: "A cell which is a plant structure (PO:0009011)." [GO:0005623, POC:curators] +def: "A cell which is a plant structure (PO:0009011)." [CL:0000000, POC:curators] comment: Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. subset: CL subset: reference @@ -272,9 +278,10 @@ subset: TraitNet synonym: "aerial root (narrow)" NARROW [] synonym: "climbing root (narrow)" NARROW [FNA:bf0ce902-e91c-401a-92a8-26b20142ce5f] synonym: "raíz (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] -synonym: "radices (exact, plural)" EXACT [FNA:3c46e84c-23e4-416b-91cd-2f7c42e4b13d] +synonym: "radices (exact, plural)" EXACT OMO:0003004 [FNA:3c46e84c-23e4-416b-91cd-2f7c42e4b13d] synonym: "radix (exact)" EXACT [FNA:e6315684-fc99-4976-b39d-b356c4b7e7fd] synonym: "根 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: FNA:bf0ce902-e91c-401a-92a8-26b20142ce5f xref: PO_GIT:578 is_a: PO:0025004 ! plant axis relationship: BFO:0000050 PO:0025025 ! root system @@ -291,10 +298,12 @@ subset: TraitNet synonym: "Poaceae crown (related)" RELATED [] synonym: "shoot (related)" RELATED [] synonym: "sistema de epiblasto (epiblastema) (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] -synonym: "thalli (related)" RELATED Plural [FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85] +synonym: "thalli (related, plural)" RELATED OMO:0003004 [FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85] synonym: "thallus (related)" RELATED [FNA:02756ad4-a09c-48d7-8754-903254e557a9] synonym: "tree crown (narrow)" NARROW [] synonym: "シュート系、苗条系 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: FNA:02756ad4-a09c-48d7-8754-903254e557a9 +xref: FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85 xref: PO_GIT:135 is_a: PO:0025007 ! collective plant organ structure disjoint_from: PO:0025025 ! root system @@ -329,6 +338,7 @@ synonym: "compound plant organ (related)" RELATED [] synonym: "organ (broad)" BROAD [] synonym: "simple plant organ (related)" RELATED [PATO:01503] synonym: "植物 器官 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: PATO:01503 xref: PO_GIT:55 is_a: PO:0025496 ! multi-tissue plant structure @@ -336,8 +346,8 @@ is_a: PO:0025496 ! multi-tissue plant structure id: PO:0009011 name: plant structure namespace: plant_anatomy -def: "A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant." [CARO:0000003, POC:curators] -comment: 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. {xref="PO:cooperl"} +def: "A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant." [CARO:0000003, PO:cooperl, POC:curators] +comment: 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. subset: TraitNet synonym: "estructura vegetal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "植物 構造 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] @@ -356,6 +366,7 @@ synonym: "Arabidopsis growth (related)" RELATED [TAIR:0000205] synonym: "etapa de desarrollo de estructura vegetal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "plant growth and development stage (exact)" EXACT [] xref: PO_GIT:185 +xref: TAIR:0000205 is_a: BFO:0000015 [Term] @@ -425,7 +436,7 @@ def: "An axial plant organ (PO:0009008)." [POC:curators] comment: Includes roots and shoots. subset: TraitNet synonym: "eje de la planta (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] -synonym: "plant axes (exact, plural)" EXACT [FNA:2355281f-ab10-4ae2-a3d8-672cace068a8] +synonym: "plant axes (exact, plural)" EXACT OMO:0003004 [FNA:2355281f-ab10-4ae2-a3d8-672cace068a8] synonym: "植物軸（軸柱） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] is_a: PO:0009008 ! plant organ created_by: rwalls @@ -456,6 +467,7 @@ subset: TraitNet synonym: "root (broad)" BROAD [FNA:b7ce680b-c6ed-4d2e-81e6-66970f7deff9] synonym: "sistema de raíz (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "根系 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] +xref: FNA:b7ce680b-c6ed-4d2e-81e6-66970f7deff9 xref: PO_GIT:136 is_a: PO:0025007 ! collective plant organ structure relationship: RO:0000056 PO:0028002 ! sporophyte development stage @@ -505,7 +517,7 @@ def: "A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO: comment: A primordium appears as a protrusion and is the first distinct form of a plant organ (PO:0009008), cardinal organ part (PO:0025001), or collective plant organ structure (PO:0025007). The transition from a primordium to the plant structure it develops into is marked by the development of non-meristematic cells, although meristematic cells may be present after the transition. synonym: "portion of primordial tissue (exact)" EXACT [] synonym: "portion of primordium tissue (exact)" EXACT [] -synonym: "primordia (exact, plural)" EXACT [] +synonym: "primordia (exact, plural)" EXACT OMO:0003004 [] synonym: "primordio (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "原基（可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:186 @@ -519,7 +531,7 @@ name: phyllome primordium namespace: plant_anatomy def: "A primordium (PO:0025127) that develops from a phyllome anlagen (PO:0025430) and is part of a shoot apex (PO:0000037) and is committed to the development of a phyllome (PO:0006001)." [PMID:11572953, POC:curators] comment: The transition from phyllome primordium to phyllome occurs when the first non-meristematic tissue develops begins to develop. -synonym: "phyllome primordia (exact, plural)" EXACT [] +synonym: "phyllome primordia (exact, plural)" EXACT OMO:0003004 [] synonym: "portion of phyllome primordium tissue (exact)" EXACT [] synonym: "primordio del filoma (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "フィロム原基（可視的） (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] @@ -534,8 +546,8 @@ creation_date: 2010-11-15T09:27:11Z id: PO:0025131 name: plant anatomical entity namespace: plant_anatomy -def: "An anatomical entity that is or was part of a plant." [BFO:0000004, CARO:0000000, POC:curators] -comment: Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. {xref="CAROC:Brownsville2014"} +def: "An anatomical entity that is or was part of a plant." [BFO:0000004, CARO:0000000, CAROC:Brownsville2014, POC:curators] +comment: Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. synonym: "entidad anatómica vegetal (Spanish, exact)" EXACT Spanish [POC:Maria_Alejandra_Gandolfo] synonym: "植物 解剖学（形態）的実体 (Japanese, exact)" EXACT Japanese [NIG:Yukiko_Yamazaki] xref: PO_GIT:224 diff --git a/src/envo/imports/po_import.owl b/src/envo/imports/po_import.owl index 565dfcea..205a1fa2 100644 --- a/src/envo/imports/po_import.owl +++ b/src/envo/imports/po_import.owl @@ -1,12 +1,14 @@ @@ -35,6 +37,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -137,6 +163,12 @@ + + + + + + @@ -250,24 +282,30 @@ A plant structure (PO:0005679) which is a whole organism. genet (broad) ramet (broad) + FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0 + FNA:99508f62-7116-4e2b-90c0-19ff55ebd967 + FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2 + FNA:c1ccca7d-2a98-4a9d-8603-c34b551935e0 + FNA:e4dde193-57f7-4ab9-9d25-96b4ca0088ba + FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b + FNA:f8f31520-e4bc-4430-9274-8dd3cee7ffd8 PO_GIT:538 PO_GIT:69 planta entera (Spanish, exact) 植物体全体 (Japanese, exact) bush (narrow) frutex (narrow) - frutices (narrow) + frutices (narrow, plural) gametophyte (narrow) herb (narrow) liana (narrow) - prothalli (narrow) + prothalli (narrow, plural) prothallium (narrow) prothallus (narrow) - seedling (narrow) shrub (narrow) sporophyte (narrow) suffrutex (narrow) - suffrutices (narrow) + suffrutices (narrow, plural) tree (narrow) vine (narrow) woody clump (narrow) @@ -315,16 +353,16 @@ - frutices (narrow) + frutices (narrow, plural) FNA:ec8c2064-2a67-43d7-8e14-aecfef5cf33b - + - prothalli (narrow) + prothalli (narrow, plural) FNA:4b610104-1bb0-4c6b-9bb9-e3cc61d11ac0 - + @@ -341,9 +379,9 @@ - suffrutices (narrow) + suffrutices (narrow, plural) FNA:ba1b1bd5-75bd-4195-b11c-3aba08da08c2 - + @@ -598,6 +636,12 @@ POC:Maria_Alejandra_Gandolfo + + + + root primordia (exact, plural) + + @@ -618,7 +662,7 @@ - A portion of plant tissue (PO:0009007) composed of epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011). + A portion of plant tissue (PO:0009007) composed of plant epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011). PO_GIT:109 dermal tissue (exact) epidermal layer (exact) @@ -632,12 +676,12 @@ PO:0005679 The epidermis can be composed of one or more layers of cells. In some species of vascular plants, the epidermis, which is a primary tissue, is replaced by periderm, which is secondary tissue, later in development. The epidermis can also include trichomes, stomatal pores, root hairs, and rhizoids. - epidermis + plant epidermis - A portion of plant tissue (PO:0009007) composed of epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011). + A portion of plant tissue (PO:0009007) composed of plant epidermal cells (PO:0004013) that develops from the protoderm (PO:0006210) and covers the surface of a plant structure (PO:0009011). POC:curators @@ -645,6 +689,7 @@ epidermides (exact, plural) FNA:35df04e5-fde5-465e-b79e-ae7d5e1537bb + @@ -658,6 +703,7 @@ epidermises (exact, plural) FNA:0d1bd0e6-c039-4de3-a162-68299a2f342a + @@ -798,7 +844,7 @@ - A portion of epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020). + A portion of plant epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020). PO_GIT:111 epidermis del epiblasto (epiblastema) (Spanish, exact) シュート表皮 (Japanese, exact) @@ -810,7 +856,7 @@ - A portion of epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020). + A portion of plant epidermis (PO:0005679) that is part of a shoot system (PO:0009006) and arises from the meristem L1 layer (PO:0009020). ISBN:0471245208 POC:Laurel_Cooper POC:curators @@ -853,7 +899,7 @@ - A portion of epidermis (PO:0005679) that is part of a root (PO:0009005). + A portion of plant epidermis (PO:0005679) that is part of a root (PO:0009005). PO:0006037 PO_GIT:111 epidermis de la ra&#237z (Spanish, exact) @@ -868,7 +914,7 @@ - A portion of epidermis (PO:0005679) that is part of a root (PO:0009005). + A portion of plant epidermis (PO:0005679) that is part of a root (PO:0009005). ISBN:0080374913 @@ -1029,7 +1075,7 @@ A cell which is a plant structure (PO:0009011). - GO:0005623 + CL:0000000 POC:curators @@ -1067,6 +1113,7 @@ A plant axis (PO:0025004) that lacks shoot axis nodes (PO:0005004) and usually grows indeterminately. PO:0003006 + FNA:bf0ce902-e91c-401a-92a8-26b20142ce5f PO_GIT:578 ra&#237z (Spanish, exact) radices (exact, plural) @@ -1111,6 +1158,7 @@ radices (exact, plural) FNA:3c46e84c-23e4-416b-91cd-2f7c42e4b13d + @@ -1140,6 +1188,8 @@ A collective plant organ structure (PO:0025007) that produces shoot-borne portions of meristem tissue (PO:0009013) and the plant structures (PO:0009011) that arise from them. + FNA:02756ad4-a09c-48d7-8754-903254e557a9 + FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85 PO_GIT:135 sistema de epiblasto (epiblastema) (Spanish, exact) シュート系、苗条系 (Japanese, exact) @@ -1147,7 +1197,7 @@ plant_anatomy Poaceae crown (related) shoot (related) - thalli (related) + thalli (related, plural) thallus (related) PO:0009006 @@ -1179,9 +1229,9 @@ - thalli (related) + thalli (related, plural) FNA:d1431b5c-7b86-46a0-8d3c-bd426fe12c85 - + @@ -1212,6 +1262,13 @@ A portion of plant tissue may contain one or several types of cells that are organized in a specific spatial arrangement into a structural unit (which includes a mass of callus) and may include an intercellular matrix. May include other types of isolated cells, such as idioblasts. portion of plant tissue + + + + porci&#243n de un tejido vegetal (Spanish, exact) + POC:Maria_Alejandra_Gandolfo + + @@ -1226,13 +1283,6 @@ POC:curators TAIR_curator:Leonore_Reiser - - - - porci&#243n de un tejido vegetal (Spanish, exact) - POC:Maria_Alejandra_Gandolfo - - @@ -1242,6 +1292,7 @@ A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path. organ (broad) + PATO:01503 PO_GIT:55 &#243rgano vegetal (Spanish, exact) 植物 器官 (Japanese, exact) @@ -1301,6 +1352,7 @@ A plant anatomical entity (PO:0025131) that is, or was, part of a plant, or was derived from a part of a plant. CARO:0000003 + PO:cooperl POC:curators @@ -1317,12 +1369,6 @@ NIG:Yukiko_Yamazaki - - - - 'Part' includes both proper parts and the whole plant. CARO:0000003 'connected anatomical structure' is defined as: Material anatomical entity that is a single connected structure with inherent 3D shape, generated by coordinated expression of the organism's own genome. - PO:cooperl - @@ -1333,6 +1379,7 @@ A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. PO:0007021 PO_GIT:185 + TAIR:0000205 etapa de desarrollo de estructura vegetal (Spanish, exact) plant growth and development stage (exact) plant_structure_development_stage @@ -1586,6 +1633,7 @@ plant axes (exact, plural) FNA:2355281f-ab10-4ae2-a3d8-672cace068a8 + @@ -1656,6 +1704,7 @@ rwalls 2010-07-01T02:11:26Z root (broad) + FNA:b7ce680b-c6ed-4d2e-81e6-66970f7deff9 PO_GIT:136 sistema de ra&#237z (Spanish, exact) 根系 (Japanese, exact) @@ -1809,6 +1858,12 @@ A portion of meristem tissue (PO:0009013) that has as parts protoderm (PO:0006210) and sub-epidermal meristematic tissue and is committed to the development of a particular plant structure (PO:0009011). POC:curators + + + + primordia (exact, plural) + + @@ -1862,6 +1917,12 @@ PMID:11572953 POC:curators + + + + phyllome primordia (exact, plural) + + @@ -1883,7 +1944,7 @@ - + An anatomical entity that is or was part of a plant. rwalls 2010-11-15T11:41:38Z @@ -1895,14 +1956,14 @@ Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. plant anatomical entity - + - + cjm @@ -1911,6 +1972,7 @@ An anatomical entity that is or was part of a plant. BFO:0000004 CARO:0000000 + CAROC:Brownsville2014 POC:curators @@ -1927,12 +1989,6 @@ NIG:Yukiko_Yamazaki - - - - Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'. - CAROC:Brownsville2014 - @@ -2485,9 +2541,15 @@ NIG:Yukiko_Yamazaki + + + + + + - + diff --git a/src/envo/imports/ro_import.obo b/src/envo/imports/ro_import.obo index df05bf2e..fa821f0f 100644 --- a/src/envo/imports/ro_import.obo +++ b/src/envo/imports/ro_import.obo @@ -1,112 +1,14 @@ format-version: 1.2 ontology: envo/imports/ro_import -owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n############################\n# Object Properties\n############################\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectUnionOf( ))\n\n# Object Property: ()\n\nIrreflexiveObjectProperty()\n\n# Object Property: ()\n\nIrreflexiveObjectProperty()\n\n\n\n############################\n# Classes\n############################\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\") Annotation(rdfs:label \"infer input from direct reg\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),\ne.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'\") Annotation(rdfs:label \"enabling an MF enables its parts\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'\") Annotation(rdfs:label \"involved in BP\") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.\") Annotation(rdfs:label \"inferring direct reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct neg reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"inferring direct positive reg edge from input to regulatory subfunction\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"effector input is compound function input\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"Input of effector is input of its parent MF\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly regulates X, its parent MF directly regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:comment \"if effector directly positively regulates X, its parent MF directly positively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"if effector directly negatively regulates X, its parent MF directly negatively regulates X\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) - -[Term] -id: BFO:0000002 -name: continuant -def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] -disjoint_from: BFO:0000003 ! occurrent -relationship: BFO:0000050 BFO:0000002 ! part of continuant - -[Term] -id: BFO:0000003 -name: occurrent -def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] -relationship: BFO:0000050 BFO:0000003 ! part of occurrent - -[Term] -id: BFO:0000004 -name: independent continuant -def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] -is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000004 ! part of independent continuant - -[Term] -id: BFO:0000006 -name: spatial region -is_a: BFO:0000141 ! immaterial entity - -[Term] -id: BFO:0000015 -name: process -def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] -is_a: BFO:0000003 ! occurrent - -[Term] -id: BFO:0000016 -name: disposition -is_a: BFO:0000017 ! realizable entity -disjoint_from: BFO:0000023 ! role - -[Term] -id: BFO:0000017 -name: realizable entity -def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] -is_a: BFO:0000020 ! specifically dependent continuant -disjoint_from: BFO:0000019 ! quality -relationship: BFO:0000050 BFO:0000017 ! part of realizable entity - -[Term] -id: BFO:0000019 -name: quality -is_a: BFO:0000020 ! specifically dependent continuant -relationship: BFO:0000050 BFO:0000019 ! part of quality - -[Term] -id: BFO:0000020 -name: specifically dependent continuant -def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] -is_a: BFO:0000002 ! continuant -disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: BFO:0000050 BFO:0000020 ! part of specifically dependent continuant - -[Term] -id: BFO:0000023 -name: role -def: "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts." [] -is_a: BFO:0000017 ! realizable entity - -[Term] -id: BFO:0000031 -name: generically dependent continuant -def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] -is_a: BFO:0000002 ! continuant -relationship: BFO:0000050 BFO:0000031 ! part of generically dependent continuant - -[Term] -id: BFO:0000034 -name: function -is_a: BFO:0000016 ! disposition - -[Term] -id: BFO:0000040 -name: material entity -def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] -is_a: BFO:0000004 ! independent continuant -disjoint_from: BFO:0000141 ! immaterial entity - -[Term] -id: BFO:0000141 -name: immaterial entity -is_a: BFO:0000004 ! independent continuant - -[Term] -id: CHEBI:50906 -is_a: PATO:0000001 - -[Term] -id: GO:0016301 +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\n############################\n# Object Properties\n############################\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf()))\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectIntersectionOf( ObjectSomeValuesFrom( )))\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n# Object Property: ()\n\nObjectPropertyRange( ObjectSomeValuesFrom( ))\n\n\n############################\n# Classes\n############################\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n# Class: ()\n\nDisjointClasses( ObjectSomeValuesFrom( ))\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ObjectInverseOf()) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\nSubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) )\n) [Term] id: RO:0002577 name: system def: "A material entity consisting of multiple components that are causally integrated." [] -is_a: BFO:0000040 ! material entity +is_a: BFO:0000040 property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.jbiomedsem.com/content/4/1/43 xsd:string [Typedef] @@ -136,6 +38,7 @@ property_value: RO:0040042 BFO:0000031 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +property_value: seeAlso https://wiki.geneontology.org/Part_of xsd:anyURI is_transitive: true is_a: RO:0002131 ! overlaps inverse_of: BFO:0000051 ! has part @@ -171,8 +74,8 @@ property_value: IAO:0000118 "is realized by" xsd:string property_value: IAO:0000118 "realized_in" xsd:string property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000017 ! realizable entity -range: BFO:0000015 ! process +domain: BFO:0000017 +range: BFO:0000015 inverse_of: BFO:0000055 ! realizes [Typedef] @@ -185,21 +88,21 @@ property_value: IAO:0000112 "this investigation realizes this investigator role" property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl -domain: BFO:0000015 ! process -range: BFO:0000017 ! realizable entity +domain: BFO:0000015 +range: BFO:0000017 [Typedef] id: BFO:0000062 name: preceded by def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: http://purl.org/dc/terms/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string property_value: IAO:0000118 "preceded_by" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 holds_over_chain: BFO:0000050 BFO:0000062 holds_over_chain: RO:0002091 BFO:0000062 holds_over_chain: RO:0002092 BFO:0000062 @@ -213,8 +116,8 @@ name: precedes def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco property_value: IAO:0000111 "precedes" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 holds_over_chain: BFO:0000050 BFO:0000063 holds_over_chain: RO:0002092 BFO:0000063 is_transitive: true @@ -233,8 +136,9 @@ property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant +property_value: seeAlso https://wiki.geneontology.org/Occurs_in xsd:anyURI +domain: BFO:0000003 +range: BFO:0000004 holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process transitive_over: BFO:0000050 ! part of @@ -272,7 +176,7 @@ property_value: IAO:0000116 "A bearer can have many dependents, and its dependen property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 -range: BFO:0000020 ! specifically dependent continuant +range: BFO:0000020 is_inverse_functional: true [Typedef] @@ -284,23 +188,23 @@ property_value: IAO:0000112 "this blood clot participates in this blood coagulat property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string property_value: IAO:0000118 "participates_in" xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000003 ! occurrent +domain: BFO:0000002 +range: BFO:0000003 inverse_of: RO:0000057 ! has participant [Typedef] id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: http://purl.org/dc/terms/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant +domain: BFO:0000003 +range: BFO:0000002 holds_over_chain: BFO:0000051 RO:0000057 [Typedef] @@ -309,8 +213,8 @@ name: is concretized as def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string -domain: BFO:0000031 ! generically dependent continuant -range: BFO:0000020 ! specifically dependent continuant +domain: BFO:0000031 +range: BFO:0000020 inverse_of: RO:0000059 ! concretizes [Typedef] @@ -319,8 +223,8 @@ name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string -domain: BFO:0000020 ! specifically dependent continuant -range: BFO:0000031 ! generically dependent continuant +domain: BFO:0000020 +range: BFO:0000031 [Typedef] id: RO:0000079 @@ -331,7 +235,7 @@ property_value: IAO:0000112 "this catalysis function is a function of this enzym property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string -domain: BFO:0000034 ! function +domain: BFO:0000034 is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -366,8 +270,8 @@ def: "a relation between an independent continuant (the bearer) and a function, property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "has_function" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000034 ! function +domain: BFO:0000004 +range: BFO:0000034 is_a: RO:0000053 ! has characteristic [Typedef] @@ -377,7 +281,7 @@ def: "a relation between an independent continuant (the bearer) and a quality, i property_value: IAO:0000112 "this apple has quality this red color" xsd:string property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string property_value: IAO:0000118 "has_quality" xsd:string -range: BFO:0000019 ! quality +range: BFO:0000019 is_a: RO:0000053 ! has characteristic [Typedef] @@ -387,16 +291,16 @@ def: "a relation between an independent continuant (the bearer) and a role, in w property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "has_role" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000023 ! role +domain: BFO:0000004 +range: BFO:0000023 is_a: RO:0000053 ! has characteristic [Typedef] id: RO:0000091 name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] -domain: BFO:0000004 ! independent continuant -range: BFO:0000016 ! disposition +domain: BFO:0000004 +range: BFO:0000016 is_a: RO:0000053 ! has characteristic inverse_of: RO:0000092 ! disposition of @@ -447,32 +351,27 @@ inverse_of: RO:0001025 ! located in [Typedef] id: RO:0001018 -name: contained in -subset: ro-eco +name: obsolete contained in property_value: IAO:0000111 "contained in" xsd:string property_value: IAO:0000116 "Containment is location not involving parthood, and arises only where some immaterial continuant is involved." xsd:string property_value: IAO:0000116 "Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):" xsd:string -property_value: IAO:0000116 "Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n " xsd:string property_value: IAO:0000118 "contained_in" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000004 ! independent continuant -holds_over_chain: RO:0001025 BFO:0000050 -inverse_of: RO:0001019 ! contains +property_value: seeAlso https://github.com/oborel/obo-relations/issues/693 +is_obsolete: true [Typedef] id: RO:0001019 -name: contains -subset: ro-eco +name: obsolete contains property_value: IAO:0000111 "contains" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: seeAlso https://github.com/oborel/obo-relations/issues/693 +is_obsolete: true [Typedef] id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string +property_value: http://purl.org/dc/terms/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string @@ -480,8 +379,9 @@ property_value: IAO:0000116 "Location as a relation between instances: The primi property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +property_value: seeAlso https://wiki.geneontology.org/Located_in xsd:anyURI +domain: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} +range: BFO:0000004 {http://purl.obolibrary.org/obo/IAO_0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} is_transitive: true transitive_over: BFO:0000050 ! part of @@ -491,8 +391,8 @@ name: bounding layer of def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -range: BFO:0000040 ! material entity +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +range: BFO:0000040 is_a: BFO:0000050 ! part of [Typedef] @@ -502,93 +402,9 @@ def: "A relation that holds between two linear structures that are approximately comment: Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. subset: ro-eco property_value: IAO:0000116 "Note from NCEAS meeting: consider changing primary label" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: RO:0002323 ! mereotopologically related to -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by -created_by: dos -creation_date: 2017-05-24T09:30:46Z - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] -comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:01Z - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] -comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:17Z - -[Typedef] -id: RO:0002017 -name: has component activity -comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. -is_a: RO:0002018 ! has component process -created_by: dos -creation_date: 2017-05-24T09:44:33Z - -[Typedef] -id: RO:0002018 -name: has component process -def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_a: RO:0002180 ! has component -created_by: dos -creation_date: 2017-05-24T09:49:21Z - -[Typedef] -id: RO:0002022 -name: directly regulated by -comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} -is_a: RO:0002334 ! regulated by -inverse_of: RO:0002578 ! directly regulates -created_by: dos -creation_date: 2017-09-17T13:52:24Z - -[Typedef] -id: RO:0002023 -name: directly negatively regulated by -def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002630 ! directly negatively regulates -created_by: dos -creation_date: 2017-09-17T13:52:38Z - -[Typedef] -id: RO:0002024 -name: directly positively regulated by -def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] -is_a: RO:0002022 ! directly regulated by -inverse_of: RO:0002629 ! directly positively regulates -created_by: dos -creation_date: 2017-09-17T13:52:47Z - -[Typedef] -id: RO:0002025 -name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] -comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. -is_functional: true -is_a: RO:0002017 ! has component activity -created_by: dos -creation_date: 2017-09-22T14:14:36Z - [Typedef] id: RO:0002084 name: during which ends @@ -602,7 +418,7 @@ inverse_of: RO:0002093 ! ends during id: RO:0002085 name: encompasses comment: Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "di" xsd:string is_transitive: true is_a: RO:0002088 ! during which starts @@ -643,6 +459,7 @@ name: immediately precedes comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "ends_at_start_of" xsd:string property_value: IAO:0000118 "meets" xsd:string property_value: RO:0002575 BFO:0000063 @@ -656,8 +473,8 @@ comment: X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "io" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 is_a: RO:0002222 ! temporally related to [Typedef] @@ -671,6 +488,7 @@ subset: ro-eco property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "d" xsd:string property_value: IAO:0000118 "during" xsd:string +property_value: seeAlso https://wiki.geneontology.org/Happens_during xsd:anyURI is_transitive: true is_a: RO:0002091 ! starts during is_a: RO:0002093 ! ends during @@ -707,13 +525,13 @@ id: RO:0002150 name: continuous with def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000118 "connected to" xsd:string property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso FMA:85972 xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant +domain: BFO:0000004 +range: BFO:0000004 is_symmetric: true is_a: RO:0002323 ! mereotopologically related to @@ -736,12 +554,12 @@ def: "x is in taxon y if an only if y is an organism, and the relationship betwe comment: Connects a biological entity to its taxon of origin. subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Jennifer Deegan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -range: CARO:0001010 +range: OBI:0100026 holds_over_chain: BFO:0000050 RO:0002162 holds_over_chain: BFO:0000051 RO:0002162 holds_over_chain: RO:0002202 RO:0002162 @@ -758,7 +576,7 @@ def: "A is spatially_disjoint_from B if and only if they have no parts in common subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string property_value: RO:0001900 RO:0001901 @@ -785,7 +603,7 @@ property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern xsd:anyURI property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern xsd:anyURI -domain: BFO:0000004 ! independent continuant +domain: BFO:0000004 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -793,8 +611,8 @@ id: RO:0002177 name: attached to part of def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 holds_over_chain: RO:0002371 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002323 ! mereotopologically related to is_a: RO:0002567 ! biomechanically related to @@ -825,13 +643,14 @@ name: develops from def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] comment: This is the transitive form of the develops from relation property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Melissa Haendel" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 +domain: BFO:0000004 +range: BFO:0000004 is_transitive: true +is_a: RO:0002254 ! has developmental contribution from is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002203 ! develops into @@ -841,9 +660,9 @@ name: develops into def: "inverse of develops from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "Terry Meehan" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 +property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 is_transitive: true is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002387 ! has potential to develop into @@ -854,10 +673,10 @@ id: RO:0002207 name: directly develops from def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 "has developmental precursor" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 property_value: IAO:0000119 "FBbt" xsd:string property_value: RO:0002575 RO:0002202 is_a: RO:0002202 ! develops from @@ -879,22 +698,20 @@ def: "p regulates q iff p is causally upstream of q, the execution of p is not c subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "David Hill" xsd:string -property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 +property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "GO" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string property_value: IAO:0000589 "regulates (processual)" xsd:string property_value: IAO:0000600 "false" xsd:boolean -domain: BFO:0000015 ! process -range: BFO:0000015 ! process +domain: BFO:0000015 +range: BFO:0000015 holds_over_chain: RO:0002230 RO:0002211 -holds_over_chain: RO:0002578 RO:0002578 is_transitive: true is_a: RO:0002411 ! causally upstream of inverse_of: RO:0002334 ! regulated by -transitive_over: RO:0002025 ! has effector activity [Typedef] id: RO:0002212 @@ -903,7 +720,7 @@ def: "p negatively regulates q iff p regulates q, and p decreases the rate or ma subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 @@ -919,7 +736,7 @@ def: "p positively regulates q iff p regulates q, and p increases the rate or ma subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string property_value: RO:0004049 RO:0002211 @@ -937,20 +754,20 @@ def: "A relation between a material entity (such as a cell) and a process, in wh subset: ro-eco property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function realized in" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000015 ! process +domain: BFO:0000004 +range: BFO:0000015 is_a: RO:0002216 ! capable of part of [Typedef] id: RO:0002216 name: capable of part of def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ holds_over_chain: RO:0002215 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} @@ -962,7 +779,7 @@ id: RO:0002217 name: obsolete actively participates in def: "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" [] comment: Obsoleted as the inverse property was obsoleted. -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "agent in" xsd:string is_obsolete: true replaced_by: RO:0002608 @@ -971,7 +788,7 @@ replaced_by: RO:0002608 id: RO:0002218 name: obsolete has active participant def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has agent" xsd:string is_obsolete: true replaced_by: RO:0002500 @@ -981,7 +798,7 @@ id: RO:0002219 name: surrounded by def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to inverse_of: RO:0002221 ! surrounds @@ -999,10 +816,10 @@ property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cy property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant +domain: BFO:0000004 +range: BFO:0000004 is_a: RO:0002163 ! spatially disjoint from [Typedef] @@ -1011,7 +828,7 @@ name: surrounds def: "inverse of surrounded by" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0001900 RO:0001901 is_a: RO:0002220 ! adjacent to @@ -1022,11 +839,11 @@ comment: A relation that holds between two occurrents. This is a grouping relati subset: ro-eco property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 [Typedef] id: RO:0002223 @@ -1035,6 +852,7 @@ def: "inverse of starts with" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "Allen" xsd:string is_a: BFO:0000050 ! part of is_a: RO:0002222 ! temporally related to @@ -1048,6 +866,7 @@ subset: ro-eco property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: BFO:0000051 ! has part @@ -1058,7 +877,7 @@ id: RO:0002225 name: develops from part of def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002207 BFO:0000050 is_a: RO:0002202 ! develops from @@ -1067,10 +886,10 @@ id: RO:0002226 name: develops in def: "x develops_in y if x is located in y whilst x is developing" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 "EHDAA2" xsd:string property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: CARO:0000000 +domain: UBERON:0001062 holds_over_chain: RO:0002207 RO:0001025 is_a: RO:0002258 ! developmentally preceded by @@ -1081,6 +900,7 @@ def: "inverse of ends with" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000050 ! part of is_a: RO:0002222 ! temporally related to inverse_of: RO:0002230 ! ends with @@ -1092,6 +912,7 @@ def: "x ends with y if and only if x has part y and the time point at which x en subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: BFO:0000051 ! has part @@ -1103,10 +924,10 @@ name: has start location def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "starts with process that occurs in" xsd:string -domain: BFO:0000015 ! process -range: BFO:0000004 ! independent continuant +domain: BFO:0000015 +range: BFO:0000004 holds_over_chain: RO:0002224 BFO:0000066 is_a: RO:0002479 ! has part that occurs in @@ -1116,10 +937,10 @@ name: has end location def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "ends with process that occurs in" xsd:string -domain: BFO:0000015 ! process -range: BFO:0000004 ! independent continuant +domain: BFO:0000015 +range: BFO:0000004 holds_over_chain: RO:0002230 BFO:0000066 is_a: RO:0002479 ! has part that occurs in @@ -1132,9 +953,10 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "consumes" xsd:string -domain: BFO:0000015 ! process +property_value: seeAlso https://wiki.geneontology.org/Has_input xsd:anyURI +domain: BFO:0000015 holds_over_chain: RO:0002224 RO:0002233 is_a: RO:0000057 ! has participant inverse_of: RO:0002352 ! input of @@ -1148,8 +970,9 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "produces" xsd:string +property_value: seeAlso https://wiki.geneontology.org/Has_output xsd:anyURI holds_over_chain: RO:0002230 RO:0002234 is_a: RO:0000057 ! has participant inverse_of: RO:0002353 ! output of @@ -1160,9 +983,9 @@ name: has developmental contribution from def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000000 -range: CARO:0000000 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: UBERON:0001062 +range: UBERON:0001062 holds_over_chain: BFO:0000051 RO:0002202 is_a: RO:0002258 ! developmentally preceded by inverse_of: RO:0002255 ! developmentally contributes to @@ -1173,7 +996,7 @@ name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002203 BFO:0000050 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002385 ! has potential to developmentally contribute to @@ -1185,10 +1008,10 @@ def: "Candidate definition: x developmentally related to y if and only if there comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "false" xsd:boolean -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant +domain: BFO:0000002 +range: BFO:0000002 is_a: RO:0002324 ! developmentally related to inverse_of: RO:0002286 ! developmentally succeeded by @@ -1199,7 +1022,6 @@ def: "c acts upstream of p if and only if c enables some f that is involved in p subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of -holds_over_chain: RO:0002327 RO:0002411 is_a: RO:0002264 ! acts upstream of or within [Typedef] @@ -1209,8 +1031,7 @@ def: "c acts upstream of or within p if c is enables f, and f is causally upstre subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within -holds_over_chain: RO:0002327 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Acts_upstream_of_or_within xsd:anyURI is_a: RO:0002500 ! causal agent in process [Typedef] @@ -1218,7 +1039,7 @@ id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -1226,7 +1047,7 @@ id: RO:0002287 name: part of developmental precursor of property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000050 RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -1236,22 +1057,22 @@ name: results in developmental progression of def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso Ontology:extensions domain: GO:0008150 -range: CARO:0000000 +range: UBERON:0001062 is_a: RO:0002324 ! developmentally related to [Typedef] id: RO:0002297 -name: results in formation of +name: results in formation of anatomical entity subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 GOC:mtg_berkeley_2013 xsd:string is_a: RO:0002234 ! has output is_a: RO:0002295 ! results in developmental progression of @@ -1265,9 +1086,9 @@ comment: A population of xs will possess adaptations (either evolved naturally o subset: ro-eco property_value: IAO:0000112 "Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat'\nwhere\n'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Pier Buttigieg" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-4366-3088 property_value: IAO:0000118 "adapted for living in" xsd:string -domain: CARO:0001010 +domain: OBI:0100026 range: ENVO:01000254 is_a: RO:0002321 ! ecologically related to @@ -1278,8 +1099,9 @@ def: "p is causally upstream of, positive effect q iff p is casually upstream of comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -1289,8 +1111,9 @@ name: causally upstream of, negative effect def: "p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: RO:0002411 ! causally upstream of is_a: RO:0004046 ! causally upstream of or within, negative effect @@ -1299,7 +1122,7 @@ id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "inheres in part of" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 property_value: RO:0001900 RO:0001901 @@ -1312,7 +1135,7 @@ transitive_over: BFO:0000050 ! part of id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] @@ -1321,14 +1144,14 @@ name: ecologically related to def: "A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297)" [] subset: ro-eco property_value: IAO:0000116 "Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions" xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string property_value: RO:0001900 RO:0001901 @@ -1336,7 +1159,7 @@ property_value: RO:0001900 RO:0001901 id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] @@ -1347,41 +1170,24 @@ property_value: IAO:0000112 "ATP citrate lyase (ACL) in Arabidopsis: it is a het property_value: IAO:0000112 "eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to \"ribosome binding\". And all three are part_of an eIF2 complex" xsd:string property_value: IAO:0000112 "Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity." xsd:string property_value: IAO:0000116 "We would like to say\n\nif and only if\n exists c', p'\n c part_of c' and c' capable_of p\n and\n c capable_of p' and p' part_of p\nthen\n c contributes_to p\n\nHowever, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. " xsd:string +property_value: seeAlso https://wiki.geneontology.org/Contributes_to xsd:anyURI is_a: RO:0002216 ! capable of part of is_a: RO:0002329 ! part of structure that is capable of -[Typedef] -id: RO:0002327 -name: enables -def: "c enables p iff c is capable of p and c acts to execute p." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string -is_a: RO:0002215 ! capable of -inverse_of: RO:0002333 ! enabled by -transitive_over: BFO:0000051 ! has part -transitive_over: RO:0002017 ! has component activity - [Typedef] id: RO:0002328 name: functionally related to def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "false" xsd:boolean holds_over_chain: BFO:0000050 RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002328 ! functionally related to @@ -1390,33 +1196,23 @@ is_a: RO:0002328 ! functionally related to id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string -property_value: seeAlso Involved:in -holds_over_chain: RO:0002327 BFO:0000050 +property_value: seeAlso https://wiki.geneontology.org/Involved_in xsd:anyURI is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of transitive_over: BFO:0000050 ! part of -[Typedef] -id: RO:0002333 -name: enabled by -def: "inverse of enables" [] -subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0000057 ! has participant -is_a: RO:0002328 ! functionally related to - [Typedef] id: RO:0002334 name: regulated by def: "inverse of regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "regulated by (processual)" xsd:string -domain: BFO:0000015 ! process -range: BFO:0000015 ! process +domain: BFO:0000015 +range: BFO:0000015 is_transitive: true is_a: RO:0002427 ! causally downstream of or within @@ -1425,7 +1221,7 @@ id: RO:0002335 name: negatively regulated by def: "inverse of negatively regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] @@ -1433,7 +1229,7 @@ id: RO:0002336 name: positively regulated by def: "inverse of positively regulates" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002334 ! regulated by [Typedef] @@ -1462,7 +1258,7 @@ name: input of def: "inverse of has input" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to @@ -1472,14 +1268,14 @@ name: output of def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0000056 ! participates in is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002353 ! output of [Typedef] @@ -1487,7 +1283,7 @@ id: RO:0002371 name: attached to def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string is_symmetric: true is_a: RO:0002170 ! connected to @@ -1498,14 +1294,14 @@ id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png property_value: seeAlso https://github.com/obophenotype/uberon/issues/170 xsd:anyURI -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: RO:0002323 ! mereotopologically related to [Typedef] @@ -1516,7 +1312,7 @@ subset: ro-eco property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "drains into" xsd:string property_value: IAO:0000118 "drains to" xsd:string property_value: IAO:0000118 "tributary channel of" xsd:string @@ -1536,7 +1332,7 @@ comment: This is both a mereotopological relationship and a relationship defined subset: ro-eco property_value: IAO:0000112 "Deschutes River distributary_of Little Lava Lake" xsd:string property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "branch of" xsd:string property_value: IAO:0000118 "distributary channel of" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Distributary xsd:string @@ -1548,7 +1344,7 @@ id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: RO:0002131 ! overlaps @@ -1557,9 +1353,9 @@ id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: CARO:0000000 -range: CARO:0000000 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: UBERON:0001062 +range: UBERON:0001062 is_a: RO:0002324 ! developmentally related to [Typedef] @@ -1567,7 +1363,7 @@ id: RO:0002385 name: has potential to developmentally contribute to def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -1575,7 +1371,7 @@ id: RO:0002387 name: has potential to develop into def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] @@ -1583,7 +1379,7 @@ id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002387 ! has potential to develop into [Typedef] @@ -1591,55 +1387,17 @@ id: RO:0002404 name: causally downstream of def: "inverse of upstream of" [] property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: BFO:0000062 ! preceded by is_a: RO:0002427 ! causally downstream of or within inverse_of: RO:0002411 ! causally upstream of -[Typedef] -id: RO:0002405 -name: immediately causally downstream of -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0002087 ! immediately preceded by -is_a: RO:0002404 ! causally downstream of -inverse_of: RO:0002412 ! immediately causally upstream of - -[Typedef] -id: RO:0002407 -name: indirectly positively regulates -def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly activates" xsd:string -property_value: RO:0002579 RO:0002213 -holds_over_chain: RO:0002409 RO:0002409 -holds_over_chain: RO:0002629 RO:0002407 -holds_over_chain: RO:0002629 RO:0002629 -is_transitive: true -is_a: RO:0002213 ! positively regulates -is_a: RO:0012012 ! indirectly regulates -transitive_over: RO:0002629 ! directly positively regulates - -[Typedef] -id: RO:0002409 -name: indirectly negatively regulates -def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "indirectly inhibits" xsd:string -property_value: RO:0002579 RO:0002212 -holds_over_chain: RO:0002630 RO:0002409 -holds_over_chain: RO:0002630 RO:0002630 -is_transitive: true -is_a: RO:0002212 ! negatively regulates -is_a: RO:0012012 ! indirectly regulates -transitive_over: RO:0002630 ! directly negatively regulates - [Typedef] id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string [Typedef] @@ -1648,27 +1406,18 @@ name: causally upstream of def: "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: BFO:0000063 ! precedes is_a: RO:0002418 ! causally upstream of or within -[Typedef] -id: RO:0002412 -name: immediately causally upstream of -def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: RO:0002575 RO:0002411 -is_a: RO:0002090 ! immediately precedes -is_a: RO:0002411 ! causally upstream of - [Typedef] id: RO:0002418 name: causally upstream of or within def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "influences (processual)" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -1679,7 +1428,7 @@ id: RO:0002427 name: causally downstream of or within def: "inverse of causally upstream of or within" [] subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -1688,8 +1437,7 @@ is_a: RO:0002501 ! causal relation between processes id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -holds_over_chain: RO:0002327 RO:0002211 +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002331 RO:0002211 is_a: RO:0002263 ! acts upstream of is_a: RO:0002431 ! involved in or involved in regulation of @@ -1698,9 +1446,8 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004049 RO:0002428 -holds_over_chain: RO:0002327 RO:0002213 holds_over_chain: RO:0002331 RO:0002213 is_a: RO:0002428 ! involved in regulation of @@ -1708,9 +1455,8 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 -holds_over_chain: RO:0002327 RO:0002212 holds_over_chain: RO:0002331 RO:0002212 is_a: RO:0002428 ! involved in regulation of @@ -1719,24 +1465,12 @@ id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "involved in or reguates" xsd:string is_a: RO:0002264 ! acts upstream of or within is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process -[Typedef] -id: RO:0002432 -name: is active in -def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] -synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "executes activity in" xsd:string -holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -is_a: RO:0002131 ! overlaps -is_a: RO:0002328 ! functionally related to - [Typedef] id: RO:0002434 name: interacts with @@ -1746,114 +1480,45 @@ synonym: "in pairwise interaction with" EXACT [] property_value: closeMatch http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_symmetric: true -[Typedef] -id: RO:0002436 -name: molecularly interacts with -def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string -property_value: seeAlso ECO:0000353 -is_symmetric: true -is_a: RO:0002434 ! interacts with - [Typedef] id: RO:0002437 name: biotically interacts with def: "An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "interacts with on organism level" xsd:string property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 property_value: seeAlso http://eol.org/schema/terms/interactsWith xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_symmetric: true is_a: RO:0002321 ! ecologically related to is_a: RO:0002434 ! interacts with -[Typedef] -id: RO:0002438 -name: trophically interacts with -def: "An interaction relationship in which the partners are related via a feeding relationship." [] -subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -is_a: RO:0002574 ! participates in a biotic-biotic interaction with - -[Typedef] -id: RO:0002447 -name: phosphorylates -property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string -is_a: RO:0002436 ! molecularly interacts with - -[Typedef] -id: RO:0002448 -name: directly regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] -synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002436 ! molecularly interacts with -is_a: RO:0011002 ! regulates activity of - -[Typedef] -id: RO:0002449 -name: directly negatively regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] -synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string -property_value: IAO:0000118 "directly inhibits" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002448 ! directly regulates activity of - -[Typedef] -id: RO:0002450 -name: directly positively regulates activity of -def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] -synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string -property_value: IAO:0000118 "directly activates" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002448 ! directly regulates activity of - [Typedef] id: RO:0002457 name: acquires nutrients from +def: "Inverse of provides nutrients for" [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion." xsd:string -is_a: RO:0002438 ! trophically interacts with +is_a: RO:0002437 ! biotically interacts with inverse_of: RO:0002469 ! provides nutrients for -[Typedef] -id: RO:0002464 -name: helper property (not for use in curation) -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string - [Typedef] id: RO:0002469 name: provides nutrients for +def: "A biotic interaction where a material entity provides nutrition for an organism." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0002438 ! trophically interacts with +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002437 ! biotically interacts with [Typedef] id: RO:0002473 @@ -1861,11 +1526,11 @@ name: composed primarily of def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] subset: ro-eco property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +domain: BFO:0000040 +range: BFO:0000040 is_a: BFO:0000051 ! has part [Typedef] @@ -1873,22 +1538,16 @@ id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000004 ! independent continuant +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +domain: BFO:0000003 +range: BFO:0000004 holds_over_chain: BFO:0000051 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} -[Typedef] -id: RO:0002481 -name: is kinase activity -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0002564 ! molecular interaction relation helper property - [Typedef] id: RO:0002494 name: transformation of def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: RO:0002202 ! develops from @@ -1896,7 +1555,7 @@ is_a: RO:0002202 ! develops from id: RO:0002495 name: immediate transformation of def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0002575 RO:0002494 is_a: RO:0002207 ! directly develops from is_a: RO:0002494 ! transformation of @@ -1913,17 +1572,17 @@ inverse_of: RO:0002608 ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000003 ! occurrent +domain: BFO:0000003 +range: BFO:0000003 is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] @@ -1931,7 +1590,7 @@ id: RO:0002503 name: towards def: "q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2" [] property_value: IAO:0000116 "This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 is_a: RO:0002502 ! depends on @@ -1939,11 +1598,11 @@ is_a: RO:0002502 ! depends on id: RO:0002506 name: causal relation between entities property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant +domain: BFO:0000002 +range: BFO:0000002 is_a: RO:0002410 ! causally related to [Typedef] @@ -1951,15 +1610,15 @@ id: RO:0002507 name: determined by def: "s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s." [] subset: ro-eco -property_value: http://purl.org/dc/terms/creator "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/creator "Pier Buttigieg" xsd:string +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000112 "A coral reef environment is determined by a particular coral reef" xsd:string property_value: IAO:0000116 "The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/24330602 property_value: IAO:0000589 "determined by (system to material entity)" xsd:string domain: RO:0002577 ! system -range: BFO:0000040 ! material entity +range: BFO:0000040 is_a: BFO:0000050 ! part of is_a: RO:0002509 ! determined by part of is_a: RO:0002559 ! causally influenced by @@ -1971,7 +1630,7 @@ name: determines def: "inverse of determined by" [] subset: ro-eco subset: RO:0002259 -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000589 "determines (material entity to system)" xsd:string is_a: RO:0002566 ! causally influences @@ -1980,9 +1639,9 @@ id: RO:0002509 name: determined by part of def: "s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w." [] subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: RO:0002577 ! system -range: BFO:0000040 ! material entity +range: BFO:0000040 holds_over_chain: RO:0002507 BFO:0000050 {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002131 ! overlaps is_a: RO:0002506 ! causal relation between entities @@ -1990,78 +1649,40 @@ is_a: RO:0002506 ! causal relation between entities [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences -[Typedef] -id: RO:0002563 -name: interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ xsd:anyURI -is_a: RO:0002464 ! helper property (not for use in curation) - -[Typedef] -id: RO:0002564 -name: molecular interaction relation helper property -property_value: IAO:0000117 "Chris Mungall" xsd:string -is_a: RO:0002563 ! interaction relation helper property - [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string -domain: BFO:0000002 ! continuant -range: BFO:0000002 ! continuant +domain: BFO:0000002 +range: BFO:0000002 is_a: RO:0002506 ! causal relation between entities [Typedef] id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string -domain: CARO:0000003 -range: CARO:0000003 +domain: UBERON:0000061 +range: UBERON:0000061 is_a: RO:0002328 ! functionally related to -[Typedef] -id: RO:0002574 -name: participates in a biotic-biotic interaction with -subset: ro-eco -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: seeAlso http://dx.doi.org/10.1016/j.ecoinf.2014.08.005 -domain: CARO:0001010 -range: CARO:0001010 -is_a: RO:0002437 ! biotically interacts with - -[Typedef] -id: RO:0002578 -name: directly regulates -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: RO:0002575 RO:0002211 -is_a: RO:0002211 ! regulates -is_a: RO:0002412 ! immediately causally upstream of - [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: BFO:0000051 RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process @@ -2071,10 +1692,10 @@ id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -domain: BFO:0000040 ! material entity -range: BFO:0000015 ! process +domain: BFO:0000040 +range: BFO:0000015 is_a: RO:0002410 ! causally related to [Typedef] @@ -2110,32 +1731,6 @@ def: "Inverse of 'causal agent in process'" [] property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to -[Typedef] -id: RO:0002629 -name: directly positively regulates -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002578 -is_a: RO:0002213 ! positively regulates -is_a: RO:0002578 ! directly regulates - -[Typedef] -id: RO:0002630 -name: directly negatively regulates -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string -property_value: RO:0004050 RO:0002578 -is_a: RO:0002212 ! negatively regulates -is_a: RO:0002578 ! directly regulates - [Typedef] id: RO:0003000 name: produces @@ -2143,9 +1738,9 @@ def: "a produces b if some process that occurs_in a has_output b, where a and b comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +domain: BFO:0000040 +range: BFO:0000040 inverse_of: RO:0003001 ! produced by [Typedef] @@ -2154,91 +1749,37 @@ name: produced by def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Melissa Haendel" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 +domain: BFO:0000040 +range: BFO:0000040 [Typedef] id: RO:0004028 name: realized in response to stimulus def: "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." [] -domain: BFO:0000017 ! realizable entity -range: BFO:0000040 ! material entity +domain: BFO:0000017 +range: BFO:0000040 holds_over_chain: RO:0009501 RO:0002233 is_a: RO:0002410 ! causally related to -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2017-12-26T19:45:49Z -[Typedef] -id: RO:0004031 -name: enables subfunction -def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] -holds_over_chain: RO:0002327 BFO:0000051 -is_a: RO:0002328 ! functionally related to -created_by: cjm -creation_date: 2018-01-25T23:20:13Z - -[Typedef] -id: RO:0004032 -name: acts upstream of or within, positive effect -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002264 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect -holds_over_chain: RO:0002327 RO:0004047 -is_a: RO:0002264 ! acts upstream of or within -created_by: cjm -creation_date: 2018-01-26T23:49:30Z - -[Typedef] -id: RO:0004033 -name: acts upstream of or within, negative effect -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004050 RO:0002264 -holds_over_chain: RO:0002327 RO:0004046 -is_a: RO:0002264 ! acts upstream of or within -created_by: cjm -creation_date: 2018-01-26T23:49:51Z - -[Typedef] -id: RO:0004034 -name: acts upstream of, positive effect -def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect -holds_over_chain: RO:0002327 RO:0002304 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004032 ! acts upstream of or within, positive effect -created_by: cjm -creation_date: 2018-01-26T23:53:14Z - -[Typedef] -id: RO:0004035 -name: acts upstream of, negative effect -def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004050 RO:0002263 -property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect -holds_over_chain: RO:0002327 RO:0002305 -is_a: RO:0002263 ! acts upstream of -is_a: RO:0004033 ! acts upstream of or within, negative effect -created_by: cjm -creation_date: 2018-01-26T23:53:22Z - [Typedef] id: RO:0004046 name: causally upstream of or within, negative effect property_value: RO:0004050 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect xsd:anyURI is_a: RO:0002418 ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect property_value: RO:0004049 RO:0002418 +property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: RO:0002418 ! causally upstream of or within -created_by: cjm +created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-03-13T23:55:19Z [Typedef] @@ -2248,25 +1789,25 @@ def: "\"has substance added\" is a relation existing between a (physical) entity property_value: IAO:0000112 "muffin 'has substance added' some 'baking soda'" xsd:string property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000116 "The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients." xsd:string -property_value: IAO:0000117 "Damion Dooley" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity +property_value: IAO:0000117 https://orcid.org/0000-0002-8844-9165 +domain: BFO:0000040 +range: BFO:0000040 [Typedef] id: RO:0009501 name: realized in response to def: "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." [] -synonym: "triggered by process" EXACT [RO:cjm] -property_value: http://purl.org/dc/terms/contributor "Austin Meier" xsd:string -property_value: http://purl.org/dc/terms/contributor "Chris Mungall" xsd:string -property_value: http://purl.org/dc/terms/contributor "David Osumi-Sutherland" xsd:string -property_value: http://purl.org/dc/terms/contributor "Marie Angelique Laporte" xsd:string +synonym: "triggered by process" EXACT [https://orcid.org/0000-0002-6601-2165] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6996-0040 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8461-9745 property_value: IAO:0000112 "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." xsd:string property_value: IAO:0000112 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" xsd:string property_value: IAO:0000112 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." xsd:string property_value: seeAlso https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit xsd:anyURI -domain: BFO:0000017 ! realizable entity -range: BFO:0000015 ! process +domain: BFO:0000017 +range: BFO:0000015 holds_over_chain: BFO:0000054 RO:0002404 is_a: RO:0002410 ! causally related to @@ -2281,8 +1822,8 @@ property_value: IAO:0000112 "The pattern shared by chess boards generically depe property_value: IAO:0000112 "The score of a symphony g-depends on a copy of the score." xsd:string property_value: IAO:0000112 "This pdf file generically depends on this server." xsd:string property_value: IAO:0000119 "[072-ISO]" xsd:string -domain: BFO:0000031 ! generically dependent continuant -range: BFO:0000004 ! independent continuant +domain: BFO:0000031 +range: BFO:0000004 holds_over_chain: RO:0000052 RO:0000058 inverse_of: RO:0010002 ! is carrier of @@ -2294,73 +1835,20 @@ property_value: IAO:0000112 "Molecules of DNA are carriers of genetic informatio property_value: IAO:0000112 "This copy of *War and Peace* is carrier of the novel written by Tolstoy." xsd:string property_value: IAO:0000112 "This hard drive is carrier of these data items." xsd:string property_value: IAO:0000119 "[072-ISO]" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000031 ! generically dependent continuant +domain: BFO:0000004 +range: BFO:0000031 holds_over_chain: RO:0000059 RO:0000053 -[Typedef] -id: RO:0011002 -name: regulates activity of -def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 "Vasundra Touré" xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002566 ! causally influences - -[Typedef] -id: RO:0012011 -name: indirectly causally upstream of -def: "p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q." [] -is_a: RO:0002411 ! causally upstream of -created_by: pg -creation_date: 2022-09-26T06:07:17Z - -[Typedef] -id: RO:0012012 -name: indirectly regulates -def: "p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q." [] -is_a: RO:0002211 ! regulates -is_a: RO:0012011 ! indirectly causally upstream of -created_by: pg -creation_date: 2022-09-26T06:08:01Z - [Typedef] id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345 property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 xsd:string property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: RO:0002215 RO:0002233 creation_date: 2021-11-08T12:00:00Z -[Typedef] -id: RO:0019000 -name: regulates characteristic -def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 -domain: BFO:0000015 ! process -range: PATO:0000001 -holds_over_chain: RO:0002211 RO:0019000 -is_a: RO:0002410 ! causally related to - -[Typedef] -id: RO:0019001 -name: positively regulates characteristic -def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 -holds_over_chain: RO:0002213 RO:0019001 -is_a: RO:0019000 ! regulates characteristic - -[Typedef] -id: RO:0019002 -name: negatively regulates characteristic -def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] -property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 -holds_over_chain: RO:0002212 RO:0019001 -holds_over_chain: RO:0002213 RO:0019002 -is_a: RO:0019000 ! regulates characteristic - diff --git a/src/envo/imports/ro_import.owl b/src/envo/imports/ro_import.owl index 9636a039..b2e18d15 100644 --- a/src/envo/imports/ro_import.owl +++ b/src/envo/imports/ro_import.owl @@ -1,7 +1,6 @@ @@ -50,9 +46,7 @@ - - definition - + @@ -126,6 +120,7 @@ An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. + temporal interpretation @@ -137,12 +132,6 @@ - - - - - - @@ -185,42 +174,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -251,20 +204,6 @@ - - - - - - - - - - subset_property - - - - @@ -279,75 +218,37 @@ - - has_broad_synonym - + - - database_cross_reference - + - - has_exact_synonym - + - - has_narrow_synonym - - - - - - - - has_obo_format_version - + - - has_related_synonym - - - - - - - + - - in_subset - - - - - - - - - - - - - + @@ -407,6 +308,7 @@ A continuant cannot be part of an occurrent: use 'participates in'. An http://www.obofoundry.org/ro/#OBO_REL:part_of + https://wiki.geneontology.org/Part_of @@ -498,7 +400,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by + http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by @@ -553,6 +455,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in + https://wiki.geneontology.org/Occurs_in @@ -643,7 +546,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant + http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant @@ -846,24 +749,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - contained in Containment is location not involving parthood, and arises only where some immaterial continuant is involved. Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): - Intended meaning: -domain: material entity -range: spatial region or site (immaterial continuant) - contained_in - - - contained in + obsolete contained in + + true @@ -872,9 +764,9 @@ range: spatial region or site (immaterial continuant) contains - - - contains + obsolete contains + + true @@ -917,9 +809,10 @@ range: spatial region or site (immaterial continuant) Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in - http://www.obofoundry.org/ro/#OBO_REL:located_in + http://www.obofoundry.org/ro/#OBO_REL:located_in located in + https://wiki.geneontology.org/Located_in @@ -961,7 +854,7 @@ range: spatial region or site (immaterial continuant) has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of @@ -997,7 +890,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other. Note from NCEAS meeting: consider changing primary label - David Osumi-Sutherland + Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence. coincident with @@ -1005,150 +898,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos - 2017-05-24T09:30:46Z - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - has positive regulatory component activity - - - - - - - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - has component activity - - - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - has component process - - - - - - - - - - dos - 2017-09-17T13:52:24Z - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - directly regulated by - - - - - Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. - GOC:dos - - - - - - - - - - Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - dos - 2017-09-17T13:52:38Z - directly negatively regulated by - - - - - Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. - GOC:dos - - - - - - - - - - Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - dos - 2017-09-17T13:52:47Z - directly positively regulated by - - - - - Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. - GOC:dos - - - - - - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - has effector activity - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos - - - - @@ -1168,7 +917,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland + di Previously had ID http://purl.obolibrary.org/obo/RO_0002124 in test files in sandpit - but this seems to have been dropped from ro-edit.owl at some point. No re-use under this ID AFAIK, but leaving note here in case we run in to clashes down the line. Official ID now chosen from DOS ID range. encompasses @@ -1231,6 +980,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + David Osumi-Sutherland ends_at_start_of meets @@ -1272,6 +1022,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during + https://wiki.geneontology.org/Happens_during @@ -1341,7 +1092,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 X continuous_with Y if and only if X and Y share a fiat boundary. - David Osumi-Sutherland + connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) @@ -1377,7 +1128,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + @@ -1408,8 +1159,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - Chris Mungall - Jennifer Deegan + + @@ -1427,7 +1178,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - Chris Mungall + Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) @@ -1498,8 +1249,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - + + @@ -1551,6 +1302,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 + @@ -1558,10 +1310,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - Chris Mungall - David Osumi-Sutherland - Melissa Haendel - Terry Meehan + + + + This is the transitive form of the develops from relation develops from @@ -1577,9 +1329,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 inverse of develops from - Chris Mungall - David Osumi-Sutherland - Terry Meehan + + + develops into @@ -1591,29 +1343,13 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - - - - - - - - - - - - - - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - Chris Mungall - David Osumi-Sutherland - has developmental precursor + + FBbt + has developmental precursor TODO - add child relations from DOS directly develops from @@ -1641,22 +1377,14 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - - - - - - p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - Chris Mungall - David Hill - Tanya Berardini + + + GO Regulation precludes parthood; the regulatory process may not be within the regulated process. @@ -1681,7 +1409,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - Chris Mungall + negatively regulates (process to process) @@ -1709,7 +1437,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - Chris Mungall + positively regulates (process to process) @@ -1730,7 +1458,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - Chris Mungall + has function realized in @@ -1751,7 +1479,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - Chris Mungall + has function in capable of part of @@ -1772,7 +1500,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role - Chris Mungall + agent in Obsoleted as the inverse property was obsoleted. @@ -1786,7 +1514,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 OBSOLETE x has participant y if and only if x realizes some active role that inheres in y - Chris Mungall + has agent obsolete has active participant @@ -1802,7 +1530,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - Chris Mungall + surrounded by @@ -1822,7 +1550,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - Chris Mungall + @@ -1844,7 +1572,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 inverse of surrounded by - Chris Mungall + surrounds @@ -1858,7 +1586,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Chris Mungall + Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 @@ -1877,6 +1605,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 inverse of starts with + Chris Mungall Allen @@ -1894,6 +1623,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall started by @@ -1912,7 +1642,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - Chris Mungall + develops from part of @@ -1922,14 +1652,14 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + x develops_in y if x is located in y whilst x is developing - Chris Mungall + EHDAA2 Jonathan Bard, EHDAA2 develops in @@ -1945,6 +1675,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 inverse of ends with + Chris Mungall ends @@ -1960,6 +1691,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. + Chris Mungall finished by @@ -1980,7 +1712,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - Chris Mungall + starts with process that occurs in has start location @@ -2000,7 +1732,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - Chris Mungall + ends with process that occurs in has end location @@ -2020,13 +1752,14 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - Chris Mungall + consumes has input + https://wiki.geneontology.org/Has_input @@ -2042,13 +1775,14 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - Chris Mungall + produces has output + https://wiki.geneontology.org/Has_output @@ -2058,8 +1792,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - + + @@ -2067,7 +1801,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y - Chris Mungall + has developmental contribution from @@ -2084,7 +1818,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 inverse of has developmental contribution from - Chris Mungall + developmentally contributes to @@ -2101,7 +1835,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - Chris Mungall + In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -2113,10 +1847,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. @@ -2130,16 +1860,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - - - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within - + https://wiki.geneontology.org/Acts_upstream_of_or_within @@ -2150,7 +1876,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 Inverse of developmentally preceded by - Chris Mungall + developmentally succeeded by @@ -2166,7 +1892,7 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - Chris Mungall + part of developmental precursor of @@ -2177,11 +1903,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - Chris Mungall + results in developmental progression of @@ -2197,12 +1923,12 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - Chris Mungall + GOC:mtg_berkeley_2013 - results in formation of + results in formation of anatomical entity @@ -2211,14 +1937,14 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - + Hydrozoa (NCBITaxon_6074) SubClassOf 'has habitat' some 'Hydrozoa habitat' where 'Hydrozoa habitat' SubClassOf overlaps some ('marine environment' (ENVO_00000569) and 'freshwater environment' (ENVO_01000306) and 'wetland' (ENVO_00000043)) and 'has part' some (freshwater (ENVO_00002011) or 'sea water' (ENVO_00002149)) -- http://eol.org/pages/1795/overview x 'has habitat' y if and only if: x is an organism, y is a habitat, and y can sustain and allow the growth of a population of xs. - Pier Buttigieg + adapted for living in A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to exist and grow in y. @@ -2234,11 +1960,12 @@ where p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - cjm + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect + @@ -2250,10 +1977,11 @@ where p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - cjm + causally upstream of, negative effect + @@ -2272,7 +2000,7 @@ where q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - Chris Mungall + inheres in part of @@ -2295,7 +2023,7 @@ where A relationship that holds via some environmental process - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -2307,7 +2035,7 @@ where A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) Awaiting class for domain/range constraint, see: https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving ecological interactions ecologically related to @@ -2319,7 +2047,7 @@ where A mereological relationship or a topological relationship - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to @@ -2331,7 +2059,7 @@ where A relationship that holds between entities participating in some developmental process (GO:0032502) - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -2357,38 +2085,11 @@ then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction. - Chris Mungall + In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology. contributes to - - - - - - - - - - - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity - c enables p iff c is capable of p and c acts to execute p. - Chris Mungall - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. - - enables + https://wiki.geneontology.org/Contributes_to @@ -2397,7 +2098,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - Chris Mungall + This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to @@ -2413,7 +2114,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati this relation holds between c and p when c is part of some c', and c' is capable of p. - Chris Mungall + false part of structure that is capable of @@ -2434,33 +2135,16 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - - - c involved_in p if and only if c enables some process p', and p' is part of p - Chris Mungall + actively involved in enables part of involved in - - - - - - - - - - - inverse of enables - Chris Mungall - - enabled by + https://wiki.geneontology.org/Involved_in @@ -2473,7 +2157,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of regulates - Chris Mungall + regulated by (processual) regulated by @@ -2486,7 +2170,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of negatively regulates - Chris Mungall + negatively regulated by @@ -2498,7 +2182,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of positively regulates - Chris Mungall + positively regulated by @@ -2525,7 +2209,6 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - has member is a mereological relation between a collection and an item. SIO @@ -2540,7 +2223,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has input - Chris Mungall + input of @@ -2554,7 +2237,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of has output - Chris Mungall + output of @@ -2566,7 +2249,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - Chris Mungall + formed as result of @@ -2579,7 +2262,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - Chris Mungall + attached to (anatomical structure to anatomical structure) attached to @@ -2595,7 +2278,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) @@ -2615,7 +2298,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - Chris Mungall + drains into drains to tributary channel of @@ -2638,7 +2321,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati Deschutes River distributary_of Little Lava Lake x distributary_of y if and only if x is capable of channeling the flow of a substance to y, where y channels less of the substance than x - Chris Mungall + branch of distributary channel of http://en.wikipedia.org/wiki/Distributary @@ -2661,7 +2344,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - Chris Mungall + This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -2672,11 +2355,11 @@ However, this is not possible in OWL. We instead make this relation a sub-relati - - + + x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - Chris Mungall + has developmental potential involving @@ -2688,7 +2371,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - Chris Mungall + has potential to developmentally contribute to @@ -2700,7 +2383,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has the potential to develop into y iff x develops into y or if x is capable of developing into y - Chris Mungall + has potential to develop into @@ -2712,7 +2395,7 @@ However, this is not possible in OWL. We instead make this relation a sub-relati x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - Chris Mungall + has potential to directly develop into @@ -2726,94 +2409,23 @@ However, this is not possible in OWL. We instead make this relation a sub-relati inverse of upstream of - Chris Mungall + causally downstream of - + - - - - - - Chris Mungall - immediately causally downstream of - - + + relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. + This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. +To define causal relations in an activity-flow type network, we make use of 3 primitives: - - - - - - - - - - - - - - - - - - - - - - - p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - Chris Mungall - indirectly activates - - indirectly positively regulates - - - - - - - - - - - - - - - - - - - - - - - p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - Chris Mungall - indirectly inhibits - - indirectly negatively regulates - - - - - - - - relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. - This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. - -To define causal relations in an activity-flow type network, we make use of 3 primitives: - - * Temporal: how do the intervals of the two occurrents relate? - * Is the causal relation regulatory? - * Is the influence positive or negative? + * Temporal: how do the intervals of the two occurrents relate? + * Is the causal relation regulatory? + * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. @@ -2822,7 +2434,7 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -2842,7 +2454,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - Chris Mungall + causally upstream of @@ -2850,19 +2462,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - Chris Mungall - - immediately causally upstream of - - - - @@ -2871,7 +2470,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - Chris Mungall + influences (processual) affects causally upstream of or within @@ -2885,7 +2484,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - Chris Mungall + causally downstream of or within @@ -2898,16 +2497,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - c involved in regulation of p if c is involved in some p' and p' regulates some p - Chris Mungall + involved in regulation of @@ -2917,16 +2512,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - c involved in regulation of p if c is involved in some p' and p' positively regulates some p - Chris Mungall + involved in positive regulation of @@ -2937,16 +2528,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - Chris Mungall + involved in negative regulation of @@ -2961,49 +2548,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - Chris Mungall + involved in or reguates involved in or involved in regulation of - - - - - - - - - - A protein that enables activity in a cytosol. - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - Chris Mungall - executes activity in - enables activity in - - is active in - - - - - - - - - true - - - - - c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm - GOC:dos - - - - @@ -3013,7 +2564,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' - Chris Mungall + Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with @@ -3024,22 +2575,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - Chris Mungall - binds - molecularly binds with - molecularly interacts with - - http://purl.obolibrary.org/obo/MI_0915 - - - - @@ -3049,7 +2584,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts. - Chris Mungall + interacts with on organism level biotically interacts with @@ -3059,104 +2594,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - An interaction relationship in which the partners are related via a feeding relationship. - Chris Mungall - - trophically interacts with - - - - - - - - - - Axiomatization to GO to be added later - Chris Mungall - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. - phosphorylates - - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. - -A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - Chris Mungall - Vasundra Touré - molecularly controls - directly regulates activity of - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré - directly inhibits - molecularly decreases activity of - directly negatively regulates activity of - - - - - - - - - - - - - - - - The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. -For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - Chris Mungall - Vasundra Touré - directly activates - molecularly increases activity of - directly positively regulates activity of - - - - - + - Chris Mungall + Inverse of provides nutrients for + Intended to be used when the target of the relation is not itself consumed, and does not have integral parts consumed, but provided nutrients in some other fashion. acquires nutrients from @@ -3164,21 +2608,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - Chris Mungall - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. - helper property (not for use in curation) - - - - - - Chris Mungall + + A biotic interaction where a material entity provides nutrition for an organism. + provides nutrients for @@ -3193,7 +2628,7 @@ For example, A and B may be gene products and binding of B by A positively regul 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - Chris Mungall + @@ -3212,7 +2647,7 @@ For example, A and B may be gene products and binding of B by A positively regul p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - Chris Mungall + has part that occurs in @@ -3228,23 +2663,13 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - Chris Mungall - is kinase activity - - - - x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - Chris Mungall + transformation of @@ -3256,7 +2681,7 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - Chris Mungall + immediate transformation of @@ -3282,7 +2707,7 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -3293,7 +2718,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + depends on @@ -3306,7 +2731,7 @@ For example, A and B may be gene products and binding of B by A positively regul q towards e2 if and only if q is a relational quality such that q inheres-in some e, and e != e2 and q is dependent on e2 This relation is provided in order to support the use of relational qualities such as 'concentration of'; for example, the concentration of C in V is a quality that inheres in V, but pertains to C. - Chris Mungall + towards @@ -3320,7 +2745,7 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - Chris Mungall + Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -3340,11 +2765,11 @@ For example, A and B may be gene products and binding of B by A positively regul A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future - Chris Mungall + determined by (system to material entity) - Chris Mungall - Pier Buttigieg + + determined by @@ -3356,7 +2781,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of determined by - Chris Mungall + determines (material entity to system) @@ -3377,7 +2802,7 @@ For example, A and B may be gene products and binding of B by A positively regul s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. - Chris Mungall + determined by part of @@ -3398,7 +2823,7 @@ For example, A and B may be gene products and binding of B by A positively regul - Chris Mungall + causally influenced by (entity-centric) causally influenced by @@ -3406,47 +2831,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - Chris Mungall - interaction relation helper property - - http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - - - - - - - - - Chris Mungall - molecular interaction relation helper property - - - - - - - - - - - - - - The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - Chris Mungall - Vasundra Touré + + causally influences (entity-centric) causally influences @@ -3458,48 +2851,16 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A relation that holds between elements of a musculoskeletal system or its analogs. - Chris Mungall + Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to - - - - - - - Chris Mungall - - participates in a biotic-biotic interaction with - - - - - - - - - - - p directly regulates q iff p is immediately causally upstream of q and p regulates q. - Chris Mungall - - directly regulates (processual) - - - - - directly regulates - - - - @@ -3511,7 +2872,7 @@ For example, A and B may be gene products and binding of B by A positively regul gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - Chris Mungall + has part structure that is capable of @@ -3525,7 +2886,7 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - Chris Mungall + causal relation between material entity and a process @@ -3590,40 +2951,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - - - - - directly positively regulates - - - - - - - - - - p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) - - - - - directly negatively regulates - - - - @@ -3638,7 +2965,7 @@ For example, A and B may be gene products and binding of B by A positively regul a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - Melissa Haendel + Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces @@ -3653,7 +2980,7 @@ For example, A and B may be gene products and binding of B by A positively regul a produced_by b iff some process that occurs_in b has_output a. - Melissa Haendel + produced by @@ -3671,150 +2998,60 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. - cjm + 2017-12-26T19:45:49Z realized in response to stimulus - + - - - - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. - cjm - 2018-01-25T23:20:13Z - enables subfunction + + + + + 2018-03-13T23:55:05Z + causally upstream of or within, negative effect + https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect - + - - - - - - - - cjm - 2018-01-26T23:49:30Z - - acts upstream of or within, positive effect - + + + + + 2018-03-13T23:55:19Z + causally upstream of or within, positive effect + - + - - - - - - - - cjm - 2018-01-26T23:49:51Z - - acts upstream of or within, negative effect + + + + muffin 'has substance added' some 'baking soda' + + "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. + The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. + + has substance added - + - - - - - - - - c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - - cjm - 2018-01-26T23:53:14Z - - acts upstream of, positive effect - - - - - - - - - - - - - - - c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative - - cjm - 2018-01-26T23:53:22Z - - acts upstream of, negative effect - - - - - - - - - - - cjm - 2018-03-13T23:55:05Z - causally upstream of or within, negative effect - - - - - - - - - - cjm - 2018-03-13T23:55:19Z - causally upstream of or within, positive effect - - - - - - - - - - - muffin 'has substance added' some 'baking soda' - - "has substance added" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time. - The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients. - Damion Dooley - has substance added - - - - - - - - - - + + + + @@ -3823,10 +3060,10 @@ For example, A and B may be gene products and binding of B by A positively regul An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut) Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph. r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. - Austin Meier - Chris Mungall - David Osumi-Sutherland - Marie Angelique Laporte + + + + triggered by process realized in response to https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit @@ -3835,7 +3072,7 @@ For example, A and B may be gene products and binding of B by A positively regul triggered by process - RO:cjm + @@ -3882,44 +3119,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - Vasundra Touré - regulates activity of - - - - - - - - - p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. - pg - 2022-09-26T06:07:17Z - indirectly causally upstream of - - - - - - - - - - p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. - pg - 2022-09-26T06:08:01Z - indirectly regulates - - - - @@ -3929,68 +3128,17 @@ For example, A and B may be gene products and binding of B by A positively regul A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - https://orcid.org/0000-0001-9625-1899 - https://orcid.org/0000-0003-2620-0345 A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 - 2021-11-08T12:00:00Z + + + 2021-11-08T12:00:00Z utilizes device utilizes material - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. - - regulates characteristic - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. - - positively regulates characteristic - - - - - - - - - - - - - - - - - A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. - - negatively regulates characteristic - - - - - - - - - - - - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. - continuant @@ -4027,222 +3166,79 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. - occurrent - - - - - - - - - - - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. - independent continuant - + - - - spatial region - + - - - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. - process - + - - - - disposition - + - - - - - - - - - - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. - realizable entity - + - - - - - - - - - quality - + - - - - - - - - - - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. - specifically dependent continuant - + - - - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. - role - + - - - - - - - - - A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. - generically dependent continuant - + - - - function - + - - - - - - - - - - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. - material entity - - - - - - - - - - - - - - - immaterial entity - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -4252,9 +3248,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + @@ -4264,16 +3260,15 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - - - true - - - + + + + + + + @@ -4307,13 +3302,31 @@ For example, A and B may be gene products and binding of B by A positively regul A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 - Chris Mungall + http://www.jbiomedsem.com/content/4/1/43 system + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + diff --git a/src/envo/imports/seed.txt b/src/envo/imports/seed.txt index 1c844f6c..86850c4c 100644 --- a/src/envo/imports/seed.txt +++ b/src/envo/imports/seed.txt @@ -4308,6 +4308,12 @@ http://purl.obolibrary.org/obo/ENVO_03605006 http://purl.obolibrary.org/obo/ENVO_03605007 http://purl.obolibrary.org/obo/ENVO_03605008 http://purl.obolibrary.org/obo/ENVO_03605009 +http://purl.obolibrary.org/obo/ENVO_03605201 +http://purl.obolibrary.org/obo/ENVO_03605202 +http://purl.obolibrary.org/obo/ENVO_03605203 +http://purl.obolibrary.org/obo/ENVO_03606003 +http://purl.obolibrary.org/obo/ENVO_03606004 +http://purl.obolibrary.org/obo/ENVO_03606009 http://purl.obolibrary.org/obo/ENVO_04000000 http://purl.obolibrary.org/obo/ENVO_04000001 http://purl.obolibrary.org/obo/ENVO_04000002 @@ -4851,6 +4857,7 @@ http://purl.obolibrary.org/obo/PATO_0001693 http://purl.obolibrary.org/obo/PATO_0001731 http://purl.obolibrary.org/obo/PATO_0001733 http://purl.obolibrary.org/obo/PATO_0001734 +http://purl.obolibrary.org/obo/PATO_0001739 http://purl.obolibrary.org/obo/PATO_0001741 http://purl.obolibrary.org/obo/PATO_0001757 http://purl.obolibrary.org/obo/PATO_0001759 @@ -5056,6 +5063,7 @@ http://purl.org/dc/elements/1.1/contributor http://purl.org/dc/elements/1.1/creator http://purl.org/dc/elements/1.1/date http://purl.org/dc/elements/1.1/description +http://purl.org/dc/elements/1.1/source http://purl.org/dc/elements/1.1/title http://purl.org/dc/terms/created http://purl.org/dc/terms/license @@ -5592,6 +5600,7 @@ https://orcid.org/0000-0003-0632-7576 https://orcid.org/0000-0003-1072-8081 https://orcid.org/0000-0003-1264-1166 https://orcid.org/0000-0003-1336-5554 +https://orcid.org/0000-0003-2179-0745 https://orcid.org/0000-0003-3138-4118 https://orcid.org/0000-0003-4808-4736 https://pesticidestewardship.org/water/runoff/ @@ -5692,6 +5701,12 @@ https://www.wmo.int/pages/prog/lsp/meteoterm_wmo_en.html https://www.worldwildlife.org/biomes/deserts-and-xeric-shrublands https://www.worldwildlife.org/biomes/tropical-and-subtropical-dry-broadleaf-forests https://www.worldwildlife.org/biomes/tropical-and-subtropical-moist-broadleaf-forests +https://www.worldwildlife.org/ecoregions/at1003 +https://www.worldwildlife.org/ecoregions/at1004 +https://www.worldwildlife.org/ecoregions/at1009 +https://www.worldwildlife.org/ecoregions/at1201 +https://www.worldwildlife.org/ecoregions/at1202 +https://www.worldwildlife.org/ecoregions/at1203 https://www.worldwildlife.org/ecoregions/im1303 https://www.worldwildlife.org/ecoregions/im1304 term diff --git a/src/envo/imports/uberon_import.owl b/src/envo/imports/uberon_import.owl index 454733af..ae5adcc8 100644 --- a/src/envo/imports/uberon_import.owl +++ b/src/envo/imports/uberon_import.owl @@ -15562,5 +15562,5 @@ - +