Merge pull request #86 from obophenotype/20230919-release

20230919 Release
obophenotype · Sep 19, 2023 · aae8b65 · aae8b65
2 parents 90b2ed0 + 2778947
commit aae8b65
Showing 1 changed file with 32 additions and 53 deletions.
diff --git a/subsets/taxslim.obo b/subsets/taxslim.obo
@@ -7828,7 +7828,7 @@ property_value: has_rank NCBITaxon:species
 
 [Term]
 id: NCBITaxon:1052585
-name: Bacillus spizizenii TU-B-10
+name: Bacillus subtilis subsp. spizizenii TU-B-10
 namespace: ncbi_taxonomy
 synonym: "Bacillus subtilis subsp. spizizenii str. TU-B-10" EXACT equivalent_name []
 synonym: "Bacillus subtilis subsp. spizizenii strain TU-B-10" EXACT equivalent_name []
@@ -29867,7 +29867,7 @@ property_value: has_rank NCBITaxon:species
 
 [Term]
 id: NCBITaxon:1232713
-name: Xanthomonas euvesicatoria pv. viticola LMG 965
+name: Xanthomonas campestris pv. viticola LMG 965
 namespace: ncbi_taxonomy
 synonym: "Xanthomonas axonopodis pv. viticola LMG 965" RELATED synonym []
 synonym: "Xanthomonas campestris pv. viticola ICMP 3867" RELATED synonym []
@@ -31107,7 +31107,7 @@ property_value: has_rank NCBITaxon:species
 
 [Term]
 id: NCBITaxon:1246626
-name: Shouchella lehensis G1
+name: Alkalihalobacillus lehensis G1
 namespace: ncbi_taxonomy
 synonym: "Bacillus lehensis G1" RELATED synonym []
 xref: GC_ID:11
@@ -34019,7 +34019,7 @@ property_value: has_rank NCBITaxon:strain
 
 [Term]
 id: NCBITaxon:1263041
-name: Phocaeicola coprophilus CAG:333
+name: Bacteroides coprophilus CAG:333
 namespace: ncbi_taxonomy
 xref: GC_ID:11
 is_a: NCBITaxon:387090 ! Phocaeicola coprophilus
@@ -34051,7 +34051,7 @@ property_value: has_rank NCBITaxon:strain
 
 [Term]
 id: NCBITaxon:1263052
-name: Phocaeicola plebeius CAG:211
+name: Bacteroides plebeius CAG:211
 namespace: ncbi_taxonomy
 xref: GC_ID:11
 is_a: NCBITaxon:310297 ! Phocaeicola plebeius
@@ -34183,7 +34183,7 @@ property_value: has_rank NCBITaxon:strain
 
 [Term]
 id: NCBITaxon:1263078
-name: Anaerobutyricum hallii CAG:12
+name: Eubacterium hallii CAG:12
 namespace: ncbi_taxonomy
 xref: GC_ID:11
 is_a: NCBITaxon:39488 ! Anaerobutyricum hallii
@@ -40827,8 +40827,6 @@ property_value: has_rank NCBITaxon:strain
 id: NCBITaxon:13379
 name: Callistephus chinensis
 namespace: ncbi_taxonomy
-synonym: "Aster chinensis" RELATED synonym []
-synonym: "China aster" EXACT common_name []
 synonym: "Chinese aster" EXACT common_name []
 xref: GC_ID:1
 is_a: NCBITaxon:13378 ! Callistephus
@@ -45775,7 +45773,7 @@ property_value: has_rank NCBITaxon:genus
 
 [Term]
 id: NCBITaxon:1401074
-name: Hoylesella buccalis DNF00853
+name: Prevotella buccalis DNF00853
 namespace: ncbi_taxonomy
 xref: GC_ID:11
 is_a: NCBITaxon:28127 ! Hoylesella buccalis
@@ -48175,10 +48173,10 @@ property_value: has_rank NCBITaxon:strain
 
 [Term]
 id: NCBITaxon:1447716
-name: Bifidobacterium catenulatum PV20-2
+name: Bifidobacterium kashiwanohense PV20-2
 namespace: ncbi_taxonomy
 xref: GC_ID:11
-is_a: NCBITaxon:1686 ! Bifidobacterium catenulatum
+is_a: NCBITaxon:630129 ! Bifidobacterium catenulatum subsp. kashiwanohense
 property_value: has_rank NCBITaxon:strain
 
 [Term]
@@ -52397,7 +52395,6 @@ property_value: has_rank NCBITaxon:species
 id: NCBITaxon:1505
 name: Paeniclostridium sordellii
 namespace: ncbi_taxonomy
-alt_id: NCBITaxon:1796621
 alt_id: NCBITaxon:2998057
 alt_id: NCBITaxon:2998058
 alt_id: NCBITaxon:2998059
@@ -61283,7 +61280,6 @@ property_value: has_rank NCBITaxon:subspecies
 id: NCBITaxon:1680
 name: Bifidobacterium adolescentis
 namespace: ncbi_taxonomy
-alt_id: NCBITaxon:2881277
 alt_id: NCBITaxon:592977
 synonym: "Bifidobacterium stercoris" RELATED synonym []
 xref: GC_ID:11
@@ -79946,11 +79942,8 @@ property_value: has_rank NCBITaxon:genus
 id: NCBITaxon:203135
 name: Halomicrobium
 namespace: ncbi_taxonomy
-alt_id: NCBITaxon:1763447
-synonym: "Halosiccatus" RELATED synonym []
 xref: GC_ID:11
 xref: PMID:18836684
-xref: PMID:26596884
 is_a: NCBITaxon:1963268 ! Haloarculaceae
 property_value: has_rank NCBITaxon:genus
 
@@ -117648,7 +117641,7 @@ property_value: has_rank NCBITaxon:genus
 
 [Term]
 id: NCBITaxon:290434
-name: Borreliella bavariensis PBi
+name: Borrelia garinii subsp. bavariensis PBi
 namespace: ncbi_taxonomy
 alt_id: NCBITaxon:649587
 synonym: "Borrelia bavariensis PBi" EXACT equivalent_name []
@@ -126534,7 +126527,7 @@ name: Sulidae
 namespace: ncbi_taxonomy
 synonym: "gannets and boobies" EXACT genbank_common_name []
 xref: GC_ID:1
-is_a: NCBITaxon:3073854 ! Suliformes
+is_a: NCBITaxon:9205 ! Pelecaniformes
 property_value: has_rank NCBITaxon:family
 
 [Term]
@@ -131105,14 +131098,6 @@ xref: GC_ID:1
 is_a: NCBITaxon:3087 ! Scenedesmus
 property_value: has_rank NCBITaxon:species
 
-[Term]
-id: NCBITaxon:3073854
-name: Suliformes
-namespace: ncbi_taxonomy
-xref: GC_ID:1
-is_a: NCBITaxon:8825 ! Neognathae
-property_value: has_rank NCBITaxon:order
-
 [Term]
 id: NCBITaxon:3074
 name: Parachlorella kessleri
@@ -132523,14 +132508,16 @@ property_value: has_rank NCBITaxon:strain
 
 [Term]
 id: NCBITaxon:311403
-name: Rhizobium rhizogenes K84
+name: Agrobacterium radiobacter K84
 namespace: ncbi_taxonomy
-synonym: "Agrobacterium radiobacter K84" EXACT equivalent_name []
-synonym: "Agrobacterium tumefaciens K84" EXACT equivalent_name []
-synonym: "Rhizobium radiobacter K84" EXACT equivalent_name []
+synonym: "Agrobacterium radiobacter str. K84" EXACT equivalent_name []
+synonym: "Agrobacterium radiobacter strain K84" EXACT equivalent_name []
+synonym: "Agrobacterium rhizogenes K84" RELATED synonym []
+synonym: "Agrobacterium tumefaciens K84" RELATED synonym []
+synonym: "Rhizobium radiobacter K84" RELATED synonym []
 xref: GC_ID:11
 xref: PMID:19251847
-is_a: NCBITaxon:359 ! Rhizobium rhizogenes
+is_a: NCBITaxon:358 ! Agrobacterium tumefaciens
 property_value: has_rank NCBITaxon:strain
 
 [Term]
@@ -133315,7 +133302,6 @@ id: NCBITaxon:313354
 name: Liocarcinus depurator
 namespace: ncbi_taxonomy
 synonym: "harbour crab" EXACT common_name []
-synonym: "Polybius depurator" RELATED synonym []
 synonym: "Portunus depurator" RELATED synonym []
 xref: GC_ID:1
 is_a: NCBITaxon:313353 ! Liocarcinus
@@ -134805,7 +134791,7 @@ is_a: NCBITaxon:11120 ! Infectious bronchitis virus
 
 [Term]
 id: NCBITaxon:316273
-name: Xanthomonas euvesicatoria pv. vesicatoria str. 85-10
+name: Xanthomonas campestris pv. vesicatoria str. 85-10
 namespace: ncbi_taxonomy
 synonym: "Xanthomonas campestris pv. vesicatoria 85-10" EXACT equivalent_name []
 synonym: "Xanthomonas campestris pv. vesicatoria strain 85-10" EXACT equivalent_name []
@@ -140617,7 +140603,6 @@ name: [Ruminococcus] torques
 namespace: ncbi_taxonomy
 alt_id: NCBITaxon:46230
 synonym: "Mediterraneibacter torques" RELATED synonym []
-synonym: "Ruminococcus torques" RELATED synonym []
 xref: GC_ID:11
 xref: PMID:29855844
 is_a: NCBITaxon:2316020 ! Mediterraneibacter
@@ -148457,6 +148442,7 @@ namespace: ncbi_taxonomy
 synonym: "Bacillus coagulans 36D1" RELATED synonym []
 synonym: "Bacillus coagulans str. 36D1" EXACT equivalent_name []
 synonym: "Bacillus coagulans strain 36D1" EXACT equivalent_name []
+synonym: "Weizmannia coagulans 36D1" RELATED synonym []
 xref: GC_ID:11
 is_a: NCBITaxon:1398 ! Heyndrickxia coagulans
 property_value: has_rank NCBITaxon:strain
@@ -154506,22 +154492,21 @@ property_value: has_rank NCBITaxon:genus
 
 [Term]
 id: NCBITaxon:359
-name: Rhizobium rhizogenes
+name: Agrobacterium rhizogenes
 namespace: ncbi_taxonomy
 alt_id: NCBITaxon:270638
 alt_id: NCBITaxon:360
 synonym: "Agrobacterium biovar 2" RELATED synonym []
 synonym: "Agrobacterium genomic group 10" RELATED synonym []
 synonym: "Agrobacterium genomic species 10" RELATED synonym []
 synonym: "Agrobacterium genomosp. 10" RELATED synonym []
-synonym: "Agrobacterium rhizogenes" RELATED synonym []
-synonym: "Phytomonas rhizogenes" RELATED synonym []
+synonym: "Rhizobium rhizogenes" RELATED synonym []
 xref: GC_ID:11
 xref: PMID:11211278
 xref: PMID:11931171
 xref: PMID:16560572
 xref: PMID:8240952
-is_a: NCBITaxon:379 ! Rhizobium
+is_a: NCBITaxon:357 ! Agrobacterium
 property_value: has_rank NCBITaxon:species
 
 [Term]
@@ -155132,8 +155117,6 @@ property_value: has_rank NCBITaxon:species
 id: NCBITaxon:3605
 name: Vitis aestivalis
 namespace: ncbi_taxonomy
-alt_id: NCBITaxon:2448765
-synonym: "Vitis rufotomentosa" RELATED synonym []
 xref: GC_ID:1
 is_a: NCBITaxon:3603 ! Vitis
 property_value: has_rank NCBITaxon:species
@@ -185781,7 +185764,6 @@ name: Glutamicibacter uratoxydans
 namespace: ncbi_taxonomy
 synonym: "Arthrobacter uratoxydans" RELATED synonym []
 xref: GC_ID:11
-xref: PMID:23194805
 xref: PMID:26486726
 is_a: NCBITaxon:1742989 ! Glutamicibacter
 property_value: has_rank NCBITaxon:species
@@ -221421,7 +221403,7 @@ property_value: has_rank NCBITaxon:species
 
 [Term]
 id: NCBITaxon:582744
-name: Methylovorus glucosotrophus SIP3-4
+name: Methylovorus glucosetrophus SIP3-4
 namespace: ncbi_taxonomy
 synonym: "Methylovorus glucosetrophus str. SIP3-4" EXACT equivalent_name []
 synonym: "Methylovorus glucosetrophus strain SIP3-4" EXACT equivalent_name []
@@ -236112,7 +236094,7 @@ property_value: has_rank NCBITaxon:strain
 
 [Term]
 id: NCBITaxon:655816
-name: Bacillus spizizenii str. W23
+name: Bacillus subtilis subsp. spizizenii str. W23
 namespace: ncbi_taxonomy
 synonym: "Bacillus subtilis subsp. spizizenii strain W23" EXACT equivalent_name []
 xref: GC_ID:11
@@ -238599,7 +238581,7 @@ property_value: has_rank NCBITaxon:species
 
 [Term]
 id: NCBITaxon:66692
-name: Shouchella clausii KSM-K16
+name: Alkalihalobacillus clausii KSM-K16
 namespace: ncbi_taxonomy
 alt_id: NCBITaxon:296724
 synonym: "Bacillus clausii KSM-K16" RELATED synonym []
@@ -264371,13 +264353,12 @@ property_value: has_rank NCBITaxon:species
 
 [Term]
 id: NCBITaxon:81770
-name: Muscari comosum
+name: Leopoldia comosa
 namespace: ncbi_taxonomy
 alt_id: NCBITaxon:796800
-synonym: "Hyacinthus comosus" RELATED synonym []
-synonym: "Leopoldia comosa" RELATED synonym []
+synonym: "Muscari comosum" RELATED synonym []
 xref: GC_ID:1
-is_a: NCBITaxon:16161 ! Muscari
+is_a: NCBITaxon:796799 ! Leopoldia
 property_value: has_rank NCBITaxon:species
 
 [Term]
@@ -273901,7 +273882,7 @@ property_value: has_rank NCBITaxon:strain
 
 [Term]
 id: NCBITaxon:873533
-name: Hoylesella oralis ATCC 33269
+name: Prevotella oralis ATCC 33269
 namespace: ncbi_taxonomy
 synonym: "Prevotella oralis JCM 12251" RELATED synonym []
 synonym: "Prevotella oralis str. ATCC 33269" EXACT equivalent_name []
@@ -281103,7 +281084,7 @@ namespace: ncbi_taxonomy
 synonym: "cormorants and shags" EXACT genbank_common_name []
 xref: GC_ID:1
 xref: PMID:24994028
-is_a: NCBITaxon:3073854 ! Suliformes
+is_a: NCBITaxon:9205 ! Pelecaniformes
 property_value: has_rank NCBITaxon:family
 
 [Term]
@@ -281217,7 +281198,7 @@ namespace: ncbi_taxonomy
 synonym: "anhingas" EXACT genbank_common_name []
 synonym: "darters" EXACT common_name []
 xref: GC_ID:1
-is_a: NCBITaxon:3073854 ! Suliformes
+is_a: NCBITaxon:9205 ! Pelecaniformes
 property_value: has_rank NCBITaxon:family
 
 [Term]
@@ -287524,8 +287505,6 @@ property_value: has_rank NCBITaxon:species
 id: NCBITaxon:96241
 name: Bacillus spizizenii
 namespace: ncbi_taxonomy
-alt_id: NCBITaxon:1963032
-synonym: "Bacillus intestinalis" RELATED synonym []
 synonym: "Bacillus subtilis subsp. spizizenii" RELATED synonym []
 xref: GC_ID:11
 xref: PMID:10425781