diff --git a/cob-base.owl b/cob-base.owl index d971095..59b959f 100644 --- a/cob-base.owl +++ b/cob-base.owl @@ -8,16 +8,14 @@ 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:skos="http://www.w3.org/2004/02/skos/core#" - xmlns:sssom="https://w3id.org/sssom/" xmlns:terms="http://purl.org/dc/terms/"> - + COB brings together key terms from a wide range of OBO projects to improve interoperability. Core Ontology for Biology and Biomedicine - 2024-09-20 + 2024-12-12 @@ -33,14 +31,6 @@ - - - - based on - - - - @@ -51,31 +41,17 @@ - - - - - - - - - - - - - - - - - - - + + editor note + - + - + + term replaced by + @@ -85,12 +61,6 @@ - - - - - - @@ -109,42 +79,6 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - part of - part of - - - - - - - - - - - - - has part - has part - - - - - - - - - - - - - - - realized in - realized in - + - - - - - - - - - realizes - realizes - - - - - - - - - - - - - - - occurs in - occurs in - - - - - - - - - - - - - - - contains process - contains process - - - - - - - - - - is concretized as - - - - - - - is concretized as - is concretized as - + - - - executed by - - - - - - - topObjectProperty - executed by - - - - - - - - - - characteristic of - - - - - - - inheres in - characteristic of - - - - - - - - - - participates in - - - - - - - participates in - participates in - - - - - - - - - - - is specified input of - - - - - - - is_specified_input_of - is specified input of - - - - - - - - - - - is specified output of - - - - - - - is_specified_output_of - is specified output of - - - - - - - - - realized in - - - - - - - - - contains process - - - - - - - - - - - has specified input - - - - - - - has_specified_input - has specified input - - - - - - - - - - - has specified output - - - - - - - has_specified_output - has specified output - - - - - - - - - has part - - - - - - - - - - has participant - - - - - - - has participant - has participant - - - - - - - - - occurs in - - - - - - - - - part of - - - - - - - - - - enabled by - - - - - - - enabled by - enabled by - - - - - - - - - concretizes + executed by - - - - - - concretizes - concretizes - @@ -522,99 +134,12 @@ - - - - - - - - - executes - - - - - - - executes - executes - - - - - - - - - - realizes - - - - - - - - - - - - has characteristic - https://github.com/oborel/obo-relations/pull/284 - - - - - - - bearer of - has characteristic - - - - - - Anything can have a characteristic - - - - - - - - - is about - - - - - - - is about - is about - - - - - - - - - - - - - - - - @@ -627,51 +152,15 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - + @@ -689,20 +178,8 @@ - - - The range of this property should be a user-defined unit datatype, e.g 182^:cm has quantity - https://github.com/OBOFoundry/COB/issues/35 - - - - - - topDataProperty - has quantity - @@ -710,10 +187,8 @@ - Number of protons in an atomic nucleus - We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning - has atomic number + has atomic number @@ -721,9 +196,8 @@ - - - has number of atomic nuclei + + has number of atomic nuclei @@ -731,8 +205,7 @@ - - has inchi string + has inchi string @@ -750,2343 +223,307 @@ - - - - - - - - - process - process - + - + - - - - - - - - - disposition - disposition - + - + - - - - - - - - - realizable entity - realizable - + - + - - + + - - - - - - specifically dependent continuant - characteristic - - + - - + + obsolete elementary charge + true - - - - - - role - role - - + - - + + + + + + + + + + A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. + atom - - - - - - site - site - - + - - + + + + + + + + + A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. + This molecular entity is different than ChEBI's 'molecular entity'. + We would like to have cardinality restrictions on the logic, but there are some technical limitations. + molecule - - - - - - function - function - - + - - + + obsolete macromolecular entity + true - - - - - - material entity - material entity - - + - - + + + obsolete subcellular structure + true - - - - - - immaterial entity - immaterial entity - - + - - + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism - - - - - - gross anatomical part - gross anatomical part - - + - - + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity - - - - - - cellular organism - cellular organism - - + - - + + obsolete geographical location + true - - - - - - electron - electron - - + - - + + + + + + + + + + completely executed planned process - - - - - - protein polypeptide chain - protein - - + - - + + + A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. + nucleic acid chain - - - - - - proton - proton - - - - - - - - - - - - monoatomic ion - monoatomic ion - - - - - - - - - - - - - - - neutron - neutron - - - - - - - - - - - - - - - atom - uncharged atom - - - - - - - - - - - - - - - atomic nucleus - atomic nucleus - - - - - - - - - - - - - - - nucleic acid - nucleic acid polymer - - - - - - - - - - - - - - - subatomic particle - subatomic particle - - - - - - - - - - - - - - - characteristic - role - - - - - - - - - - - - - - - cell - cell - - - - - - - - - - - - - - - native cell - native cell - - - - - - - - - - - - - - - cell in vitro - cell in vitro - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/PATO_0000125 - mass - - - - - - - mass - mass - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/PATO_0002193 - charge - - - - - - - electric - charge - - - - - + - - - no longer needed - obsolete_elementary charge + + + obsolete immaterial anatomical entity true - - - - - - owl:Thing - elementary charge - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000040 - material entity - - - - - - http://purl.obolibrary.org/obo/CHEBI_36342 - subatomic particle - - - - - + - - - http://purl.obolibrary.org/obo/CHEBI_24636 - proton + + obsolete gene product + true - + - - - http://purl.obolibrary.org/obo/CHEBI_30222 - neutron + + + obsolete action specification + true - + - - + + - - 0 + + - http://purl.obolibrary.org/obo/CHEBI_10545 - electron + A complex of two or more molecular entities that are not covalently bound. + complex of molecules - + - - - - - 1 - - - - - - - - - - - A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. - This atom is closely related to ChEBI's atom, but not exactly equivalent to. - atom - + + + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + planned process - - - - - - atom - atom - - + - - - http://purl.obolibrary.org/obo/CHEBI_33252 - Some people may be uncomfortable calling every proton an atomic nucleus - This is equivalent to CHEBI:33252 - atomic nucleus + + + failed planned process - + - - + + - - - - + + + + + + + + + + + + - - A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. - This molecular entity is different than ChEBI's 'molecular entity'. - We would like to have cardinality restrictions on the logic, but there are some technical limitations. - molecular entity - - + A planned process that intends to output material entities from input material entities + material processing - - - - - - molecular entity - molecular entity - - - - - - - molecule - molecular entity - - + - - A material entity consisting of multiple atoms that are completely connected by covalent bonds and structured in subunits, and where the most determinate class identity of the macromolecule is not necessarily changed when there is an addition or subtraction of atoms or bonds. - Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 - obsolete macromolecular entity + + obsolete cellular membrane true - - - - - - http://purl.obolibrary.org/obo/CHEBI_16541 - http://purl.obolibrary.org/obo/PR_000000001 - protein - - - - - - - protein - protein - - - - - - - - - http://purl.obolibrary.org/obo/CL_0000000 - A material entity that has a plasma membrane and results from cellular division. - CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. - We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. - cell - - - - - - - - - http://purl.obolibrary.org/obo/CL_0000003 - native cell - - - - - - - - - http://purl.obolibrary.org/obo/CL_0001034 - cell in vitro - - - - - - - - - - - - - - - - A material entity consisting of at least two macromolecular entities derived from a cell as parts, and that has a function for the cell. - Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. - Overlaps with some cellular components from GO - subcellular structure - - - - - - - owl:Thing - subcellular structure - - - - - - - - - http://purl.obolibrary.org/obo/CARO_0001008 - A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. - Bodily fluids, such as urine, are currently defined as anatomical entities in UBERON. We should make sure there is a proper home for these here. - gross anatomical part - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0100026 - A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. - "Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'. - Includes virus - we will later have a class for cellular organisms. - organism - - - - - - - organism - organism - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000245 - Should revisit if we can place outside of material entity - a collection of roles. - organization - - - - - - - organization - organization - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000047 - A material entity that is created or changed during material processing. - processed material entity - - - - - - - processed material - processed material entity - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000141 - immaterial entity - - - - - - - - - - geographical location - - - - - - - owl:Thing - geographical location - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000017 - realizable - - - - - + - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000015 - process + + obsolete physical information carrier + true - + - - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000011 - completely executed planned process + + characteristic - - - - - - planned process - completely executed planned process - - + - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - - - - http://purl.obolibrary.org/obo/GO_0008150 - A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. - A biological process is an evolved process - biological process + A process during which an organism comes into contact with another entity. + exposure of organism - - - - - - biological process - biological process - - + - - - + + - - - - - - - - - + + - - - http://purl.obolibrary.org/obo/GO_0003674 - This is the same as GO molecular function - gene product or complex activity - - - - - - - molecular function - gene product or complex activity - - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_24867 - monoatomic ion + A processed material entity which is designed to be capable of a process. + device - - - - - http://purl.obolibrary.org/obo/CHEBI_33250 - uncharged atom - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_33696 - nucleic acid polymer - - - - - - - - - - http://purl.obolibrary.org/obo/PCO_0000000 - collection of organisms - - - - - - - collection of organisms - collection of organisms - - - - - - - - - immaterial anatomical entity - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000029 - site - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0001909 - conclusion based on data - - - - - - - conclusion based on data - conclusion based on data - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000030 - Pier: 'data, information or knowledge'. OR 'representation - information - - - - - - - information content entity - information - - - - - - - - - - http://purl.obolibrary.org/obo/OGMS_0000073 - disease diagnosis - - - - - - - diagnosis - disease diagnosis - - - - - - - - - - http://purl.obolibrary.org/obo/OGMS_0000014 - phenotypic finding - - - - - - - clinical finding - phenotypic finding - - - - - - - - - - http://purl.obolibrary.org/obo/OGMS_0000063 - disease course - - - - - - - disease course - disease course - - - - - - - - - - - http://purl.obolibrary.org/obo/ENVO_02500000 - environmental process - - - - - - - environmental system process - environmental process - - - - - - - - - - http://purl.obolibrary.org/obo/MOP_0000543 - This is meant to capture processes that are more fundamental than macromolecular activities - physico-chemical process - - - - - - - molecular process - physico-chemical process - - - - - - - - - - http://purl.obolibrary.org/obo/ENVO_01001110 - ecosystem - - - - - - - ecosystem - ecosystem - - - - - - - - - - http://purl.obolibrary.org/obo/ENVO_01000813 - geophysical entity - - - - - - - astronomical body part - geophysical entity - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000033 - directive information entity - - - - - - - directive information entity - directive information entity - - - - - - - - - - gene product - - - - - - - owl:Thing - gene product - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/GO_0032991 - This is not covalently bonded, which conflicts with changes to the parent definition. - protein-containing macromolecular complex - - - - - - - protein-containing complex - protein-containing macromolecular complex - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000005 - objective specification - - - - - - - objective specification - objective specification - - - - - - - - - - - - - - - - - - - - - action specification - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000104 - plan specification - - - - - - - plan specification - plan specification - - - - - - - - - - - - - - - - A complex of two or more molecular entities that are not covalently bound. - >=2 parts (not we cannot use cardinality with transitive properties) - complex of molecular entities - - - - - - - owl:Thing - complex of molecular entities - - - - - - - - - - - - - - - - - - - - - A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. - planned process - - - - - - - - - failed planned process - - - - - - - - - - http://purl.obolibrary.org/obo/DRON_00000005 - A processed material entity created to be administered to an individual with the intent to improve health. - drug product - - - - - - - - drug product - drug product - - - - - - - drug - drug product - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000310 - document - - - - - - - document - document - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000027 - data item - - - - - - - data item - data item - - - - - - - - - - http://purl.obolibrary.org/obo/GO_0005634 - cell nucleus - - - - - - - nucleus - cell nucleus - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000070 - assay - - - - - - - assay - assay - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0200000 - data transformation - - - - - - - data transformation - data transformation - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000066 - investigation - - - - - - - investigation - investigation - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000094 - material processing - - - - - - - material processing - material processing - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000016 - disposition - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000034 - function - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000260 - plan - - - - - - - plan - plan - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000023 - role - - - - - - - - - - cellular membrane - - - - - - - owl:Thing - cellular membrane - - - - - - - - - - http://purl.obolibrary.org/obo/CARO_0010004 - http://purl.obolibrary.org/obo/NCBITaxon_131567 - cellular organism - - - - - - - cellular organisms - cellular organism - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000067 - evaluant role - - - - - - - evaluant role - evaluant role - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000015 - Pier 'representational entity' - This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc - information representation - - - - - - - information carrier - information representation - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000109 - measurement datum - - - - - - - measurement datum - measurement datum - - - - - - - - - - - - - - - - - - - - physical information carrier - - - - - - - - - - http://purl.obolibrary.org/obo/SEPIO_0000048 - A role realized by a participant in a process such that the participant causes the process. - agent role - - - - - - - agent role - agent role - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000020 - http://purl.obolibrary.org/obo/PATO_0000001 - characteristic - https://github.com/OBOFoundry/COB/issues/65 - https://github.com/oborel/obo-relations/pull/284 - - - - - - - quality - characteristic - - - - - - - - - A process during which an organism comes into contact with another entity. - exposure of organism - - - - - - - - - - - - - - - - - - - - - A processed material entity which is designed to perform a function. - In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device. - -We say "designed" to emphasize a device's primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight. - -Regarding usage then, we don't say a naturally formed rock is a hammering device - it wasn't designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering "tool", which does not necessarily convey intentional design. - -Example of use: A whole device like an engine; a component like a bolt is also a device. - - 2023-03-24T16:04:27Z - device - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - geophysical entity - geographical entity - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - organism - Viruses - - - - - - - - - - - - - - - organism - cellular organisms - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agent role - investigation agent role - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cellular organism - whole plant - - - - - - - - - - - - - - - cell - plant cell - - - - - - - - - - - - - - - immaterial anatomical entity - plant anatomical space - - - - - - - - - - - - - - - native cell - native plant cell - - - - - - - - - - - - - - - - - - - - - - - - - - - material entity - sequence_feature - - - - - - - - - - - - - - - characteristic - sequence_attribute - - - - - - - - - - - - - - - material entity - sequence_variant - - - - - - - - - - - - - - - material entity - sequence_collection - - - - - - - - - - - - - - - immaterial anatomical entity - immaterial anatomical entity - - - - - - - - - - - - - - - cellular organism - multicellular organism - - - - - - - - - - - - - - - gross anatomical part - multicellular anatomical structure - - - - - - - - - - - - - - - native cell - xenopus cell - - - - - - - - - - - - - - - native cell - zebrafish cell - diff --git a/cob-full.owl b/cob-full.owl deleted file mode 100644 index f29dcdc..0000000 --- a/cob-full.owl +++ /dev/null @@ -1,1456 +0,0 @@ - - - - - COB brings together key terms from a wide range of OBO projects to improve interoperability. - - Core Ontology for Biology and Biomedicine - 2024-09-20 - - - - - - - - - - - - - based on - - - - - - - - definition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is concretized as - - - - - - - - - executed by - - - - - - - - - characteristic of - - - - - - - - - participates in - - - - - - - - - - is specified input of - - - - - - - - - - is specified output of - - - - - - - - - realized in - - - - - - - - - contains process - - - - - - - - - - has specified input - - - - - - - - - - has specified output - - - - - - - - - has part - - - - - - - - - has participant - - - - - - - - - occurs in - - - - - - - - - part of - - - - - - - - - enabled by - - - - - - - - concretizes - - - - - - - - intended to realize - - - - - - - - has plan - - - - - - - - intended plan process type - - - - - - - - - - - - executes - - - - - - - - - - realizes - - - - - - - - - - - has characteristic - https://github.com/oborel/obo-relations/pull/284 - - - - - - Anything can have a characteristic - - - - - - - - is about - - - - - - - - - - - - - - The range of this property should be a user-defined unit datatype, e.g 182^:cm - has quantity - https://github.com/OBOFoundry/COB/issues/35 - - - - - - - - - - Number of protons in an atomic nucleus - We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning - has atomic number - - - - - - - - - - has number of atomic nuclei - - - - - - - - - has inchi string - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/PATO_0000125 - mass - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/PATO_0002193 - charge - - - - - - - - no longer needed - obsolete_elementary charge - true - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000040 - material entity - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_36342 - subatomic particle - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_24636 - proton - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_30222 - neutron - - - - - - - - - - - - 0 - - - http://purl.obolibrary.org/obo/CHEBI_10545 - electron - - - - - - - - - - - 1 - - - - - - - - - - - A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. - This atom is closely related to ChEBI's atom, but not exactly equivalent to. - atom - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_33252 - Some people may be uncomfortable calling every proton an atomic nucleus - This is equivalent to CHEBI:33252 - atomic nucleus - - - - - - - - - - - - - - - - A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. - This molecular entity is different than ChEBI's 'molecular entity'. - We would like to have cardinality restrictions on the logic, but there are some technical limitations. - molecular entity - - - - - - - - A material entity consisting of multiple atoms that are completely connected by covalent bonds and structured in subunits, and where the most determinate class identity of the macromolecule is not necessarily changed when there is an addition or subtraction of atoms or bonds. - Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 - obsolete macromolecular entity - true - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_16541 - http://purl.obolibrary.org/obo/PR_000000001 - protein - - - - - - - - - http://purl.obolibrary.org/obo/CL_0000000 - A material entity that has a plasma membrane and results from cellular division. - CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. - We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. - cell - - - - - - - - - http://purl.obolibrary.org/obo/CL_0000003 - native cell - - - - - - - - - http://purl.obolibrary.org/obo/CL_0001034 - cell in vitro - - - - - - - - - - - - - - - A material entity consisting of at least two macromolecular entities derived from a cell as parts, and that has a function for the cell. - Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. - Overlaps with some cellular components from GO - subcellular structure - - - - - - - - - http://purl.obolibrary.org/obo/CARO_0001008 - A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. - Bodily fluids, such as urine, are currently defined as anatomical entities in UBERON. We should make sure there is a proper home for these here. - gross anatomical part - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0100026 - A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. - "Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'. - Includes virus - we will later have a class for cellular organisms. - organism - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000245 - Should revisit if we can place outside of material entity - a collection of roles. - organization - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000047 - A material entity that is created or changed during material processing. - processed material entity - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000141 - immaterial entity - - - - - - - - - geographical location - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000017 - realizable - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000015 - process - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000011 - completely executed planned process - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/GO_0008150 - A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. - A biological process is an evolved process - biological process - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/GO_0003674 - This is the same as GO molecular function - gene product or complex activity - - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_24867 - monoatomic ion - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_33250 - uncharged atom - - - - - - - - - http://purl.obolibrary.org/obo/CHEBI_33696 - nucleic acid polymer - - - - - - - - - http://purl.obolibrary.org/obo/PCO_0000000 - collection of organisms - - - - - - - - - immaterial anatomical entity - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000029 - site - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0001909 - conclusion based on data - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000030 - Pier: 'data, information or knowledge'. OR 'representation - information - - - - - - - - - http://purl.obolibrary.org/obo/OGMS_0000073 - disease diagnosis - - - - - - - - - http://purl.obolibrary.org/obo/OGMS_0000014 - phenotypic finding - - - - - - - - - http://purl.obolibrary.org/obo/OGMS_0000063 - disease course - - - - - - - - - - http://purl.obolibrary.org/obo/ENVO_02500000 - environmental process - - - - - - - - - http://purl.obolibrary.org/obo/MOP_0000543 - This is meant to capture processes that are more fundamental than macromolecular activities - physico-chemical process - - - - - - - - - http://purl.obolibrary.org/obo/ENVO_01001110 - ecosystem - - - - - - - - - http://purl.obolibrary.org/obo/ENVO_01000813 - geophysical entity - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000033 - directive information entity - - - - - - - - - gene product - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/GO_0032991 - This is not covalently bonded, which conflicts with changes to the parent definition. - protein-containing macromolecular complex - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000005 - objective specification - - - - - - - - - - - - - - - - - - - - - action specification - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000104 - plan specification - - - - - - - - - - - - - - - A complex of two or more molecular entities that are not covalently bound. - >=2 parts (not we cannot use cardinality with transitive properties) - complex of molecular entities - - - - - - - - - - - - - - - - - - - - - A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. - planned process - - - - - - - - - failed planned process - - - - - - - - - http://purl.obolibrary.org/obo/DRON_00000005 - A processed material entity created to be administered to an individual with the intent to improve health. - drug product - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000310 - document - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000027 - data item - - - - - - - - - http://purl.obolibrary.org/obo/GO_0005634 - cell nucleus - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000070 - assay - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0200000 - data transformation - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000066 - investigation - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000094 - material processing - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000016 - disposition - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000034 - function - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000260 - plan - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000023 - role - - - - - - - - - cellular membrane - - - - - - - - - http://purl.obolibrary.org/obo/CARO_0010004 - http://purl.obolibrary.org/obo/NCBITaxon_131567 - cellular organism - - - - - - - - - http://purl.obolibrary.org/obo/OBI_0000067 - evaluant role - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000015 - Pier 'representational entity' - This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc - information representation - - - - - - - - - http://purl.obolibrary.org/obo/IAO_0000109 - measurement datum - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - physical information carrier - - - - - - - - - http://purl.obolibrary.org/obo/SEPIO_0000048 - A role realized by a participant in a process such that the participant causes the process. - agent role - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/BFO_0000020 - http://purl.obolibrary.org/obo/PATO_0000001 - characteristic - https://github.com/OBOFoundry/COB/issues/65 - https://github.com/oborel/obo-relations/pull/284 - - - - - - - - - A process during which an organism comes into contact with another entity. - exposure of organism - - - - - - - - - - - - - - - - - - - - - A processed material entity which is designed to perform a function. - In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device. - -We say "designed" to emphasize a device's primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight. - -Regarding usage then, we don't say a naturally formed rock is a hammering device - it wasn't designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering "tool", which does not necessarily convey intentional design. - -Example of use: A whole device like an engine; a component like a bolt is also a device. - - 2023-03-24T16:04:27Z - device - - - - - - - diff --git a/cob-root.owl b/cob-root.owl new file mode 100644 index 0000000..b2730fa --- /dev/null +++ b/cob-root.owl @@ -0,0 +1,1369 @@ + + + + + COB brings together key terms from a wide range of OBO projects to improve interoperability. + + Core Ontology for Biology and Biomedicine + 2024-12-12 + + + + + + + + + + + + + definition + + + + + + + + editor note + + + + + + + + term replaced by + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + a core relation that holds between a part and its whole + part of + + + + + + + + a core relation that holds between a whole and its part + has part + + + + + + + + + + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process + realizes + + + + + + + + executed by + + + + + + + + intended to realize + + + + + + + + has plan + + + + + + + + intended plan process type + + + + + + + + + is about + + + + + + + + + The inverse property of is_specified_input_of + has specified input + + + + + + + + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + is specified input of + + + + + + + + + The inverse property of is_specified_output_of + has specified output + + + + + + + + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + is specified output of + + + + + + + + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + characteristic of + + + + + + + + Inverse of characteristic_of + has characteristic + + + + + + + + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates in + + + + + + + + a relation between a process and a continuant, in which the continuant is somehow involved in the process + has participant + + + + + + + + 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. + is concretized as + + + + + + + + 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. + concretizes + + + + + + + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + derives from + + + + + + + + a relation between two independent continuants, the location and the target, in which the target is entirely within the location + location of + + + + + + + + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + located in + + + + + + + + + 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. + capable of + + + + + + + + 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 + surrounded by + + + + + + + + inverse of surrounded by + surrounds + + + + + + + + + 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. + has input + + + + + + + + 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. + has output + + + + + + + + inverse of enables + enabled by + + + + + + + + + + + + + has quantity + + + + + + + + + Number of protons in an atomic nucleus + has atomic number + + + + + + + + + has number of atomic nuclei + + + + + + + + has inchi string + + + + + + + + + + + + + + process + + + + + + + + + disposition + + + + + + + + + realizable entity + + + + + + + + + role + + + + + + + + + site + + + + + + + + + function + + + + + + + + + Elucidation: 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 + + + + + + + + + Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. + electron + + + + + + + + + Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. + proton + + + + + + + + + Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. + neutron + + + + + + + + + + + + + + + A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 + atomic nucleus + + + + + + + + + + A particle smaller than an atom. + subatomic particle + + + + + + + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. + CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. + We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. + cell + + + + + + + + + A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. + cell in vitro + + + + + + + + + obsolete elementary charge + true + + + + + + + + + + + + + + + + A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. + atom + + + + + + + + + + + + + + + A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. + This molecular entity is different than ChEBI's 'molecular entity'. + We would like to have cardinality restrictions on the logic, but there are some technical limitations. + molecule + + + + + + + + + obsolete macromolecular entity + true + + + + + + + + + + obsolete subcellular structure + true + + + + + + + + + A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. + gross anatomical part + + + + + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + + + + + + + + + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity + + + + + + + + + obsolete geographical location + true + + + + + + + + + + + + + + + + completely executed planned process + + + + + + + + + A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. + nucleic acid chain + + + + + + + + + + obsolete immaterial anatomical entity + true + + + + + + + + + obsolete gene product + true + + + + + + + + + + obsolete action specification + true + + + + + + + + + + + + + + + A complex of two or more molecular entities that are not covalently bound. + complex of molecules + + + + + + + + + A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. + planned process + + + + + + + + + failed planned process + + + + + + + + + + + + + + + + + + + + + + + A planned process that intends to output material entities from input material entities + material processing + + + + + + + + + obsolete cellular membrane + true + + + + + + + + + obsolete physical information carrier + true + + + + + + + + + characteristic + + + + + + + + + + + + + + + A process during which an organism comes into contact with another entity. + exposure of organism + + + + + + + + + + + + + + + A processed material entity which is designed to be capable of a process. + device + + + + + + + + + a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role + drug product + + + + + + + + + A material part of an astronomical body. + geophysical entity + + + + + + + + + An environmental system which includes both living and non-living components. + ecosystem + + + + + + + + + A process in which includes the components of an environmental system as participants. + environmental process + + + + + + + + + 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 material + + + + + + + + + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. + This is the same as GO molecular function + gene product or complex activity + + + + + + + + + + + + + + + + + + A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). + cellular_component + + + + + + + + + + + + + + + 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 + + + + + + + + + + + + + + + + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. + This is not covalently bonded, which conflicts with changes to the parent definition. + protein-containing complex + + + + + + + + + Any constituent part of a virion, a complete fully infectious extracellular virus particle. + virion component + + + + + + + + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. + Overlaps with some cellular components from GO + cellular anatomical entity + + + + + + + + + A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. + objective specification + + + + + + + + + A directive information entity that describes an action the bearer will take. + action specification + + + + + + + + + An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + data item + + + + + + + + + A generically dependent continuant that is about some thing. + Pier: 'data, information or knowledge'. OR 'representation' + information content entity + + + + + + + + + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + directive information entity + + + + + + + + + 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 + + + + + + + + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + measurement datum + + + + + + + + + A process in which at least one of the participants is a molecule. + This is meant to capture processes that are more fundamental than macromolecular activities + physico-chemical process + + + + + + + + + cellular organism + + + + + + + + + a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). + investigation + + + + + + + + + + + + + + + + + + + + + + + A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. + assay + + + + + + + + + + + + + + + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + plan + + + + + + + + + + + + + + + + + + + + + + + A planned process with the objective of collecting a specimen. + specimen collection + + + + + + + + + + + + + + + A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). + specimen from organism + + + + + + + + + + + + + + + A material entity that has the specimen role. + specimen + + + + + + + + + + + + + + + + + + + + + + + A planned process that produces output data from input data. + data transformation + + + + + + + + + A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. + mass + + + + + + + + + A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. + electric charge + + + + + + + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + collection of organisms + + + + + + + + + A cell which is a plant structure (PO:0009011). + plant cell + + + + + + + + + An anatomical entity that is or was part of a plant. + plant anatomical entity + + + + + + + + + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. + protein + + + + + + + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + amino acid chain + + + + + + + + + Any extent of continuous biological sequence. + sequence_feature + + + + + + + + + A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. + sequence_variant + + + + + + + + + A collection of discontinuous sequences. + sequence_collection + + + + + + + + + + + + + + + + + + + + Anatomical entity that has mass. + material anatomical entity + + + + + + + + + + Anatomical entity that has no mass. + immaterial anatomical entity + + + + + + + + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity + + + + + + + + + Material entity that is manufactured to realize the vaccine function. + vaccine + + + + + + + diff --git a/cob.owl b/cob.owl index f21dc97..9e4005c 100644 --- a/cob.owl +++ b/cob.owl @@ -1,22 +1,19 @@ + xmlns:terms="http://purl.org/dc/terms/"> - - COB brings together key terms from a wide range of OBO projects to improve interoperability. - - Core Ontology for Biology and Biomedicine - This version of COB includes native OBO URIs, only using COB IRIs where equivalent natives could not be found. To see the edition that includes native IRIs, consult cob-edit.owl. - 2024-09-20 + + COB brings together key terms from a wide range of OBO projects to improve interoperability. + + Core Ontology for Biology and Biomedicine + 2024-12-12 @@ -42,37 +39,17 @@ - - - - - - - - - - - - - - - - - - - - - - - - - + + editor note + - + - + + term replaced by + @@ -94,12 +71,6 @@ - - - - - - - - + a core relation that holds between a part and its whole part of @@ -124,53 +94,27 @@ + a core relation that holds between a whole and its part has part - - - - - realized in - - - - + Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes - - - - - - occurs in - - - - - - - - contains process - - - - - - executed by + executed by @@ -202,6 +146,7 @@ + is about @@ -210,10 +155,9 @@ - - - - has specified input + + The inverse property of is_specified_input_of + has specified input @@ -221,8 +165,9 @@ - - is specified input of + + A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. + is specified input of @@ -230,10 +175,9 @@ - - - - has specified output + + The inverse property of is_specified_output_of + has specified output @@ -241,8 +185,9 @@ - - is specified output of + + A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. + is specified output of @@ -250,8 +195,8 @@ - - characteristic of + a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. + characteristic of @@ -259,26 +204,17 @@ - - - + Inverse of characteristic_of has characteristic - https://github.com/oborel/obo-relations/pull/284 - - - - - Anything can have a characteristic - - - participates in + a relation between a continuant and a process, in which the continuant is somehow involved in the process + participates in @@ -286,7 +222,7 @@ - + a relation between a process and a continuant, in which the continuant is somehow involved in the process has participant @@ -295,8 +231,8 @@ - - is concretized as + 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. + is concretized as @@ -304,28 +240,91 @@ + 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. concretizes - + - - - enabled by + + a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity + derives from - + - - - - - - executes + + a relation between two independent continuants, the location and the target, in which the target is entirely within the location + location of + + + + + + + + a relation between two independent continuants, the target and the location, in which the target is entirely within the location + located in + + + + + + + + + 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. + capable of + + + + + + + + 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 + surrounded by + + + + + + + + inverse of surrounded by + surrounds + + + + + + + + + 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. + has input + + + + + + + + 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. + has output + + + + + + + + inverse of enables + enabled by @@ -344,10 +343,7 @@ - - The range of this property should be a user-defined unit datatype, e.g 182^:cm has quantity - https://github.com/OBOFoundry/COB/issues/35 @@ -356,10 +352,8 @@ - Number of protons in an atomic nucleus - We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning - has atomic number + has atomic number @@ -368,8 +362,7 @@ - - has number of atomic nuclei + has number of atomic nuclei @@ -377,8 +370,7 @@ - - has inchi string + has inchi string @@ -398,13 +390,7 @@ - - - - - - - process + process @@ -413,7 +399,7 @@ - disposition + disposition @@ -421,31 +407,8 @@ - - realizable - - - - - - - - - - - - - - - - - - - - - characteristic - https://github.com/OBOFoundry/COB/issues/65 - https://github.com/oborel/obo-relations/pull/284 + + realizable entity @@ -454,7 +417,7 @@ - role + role @@ -472,7 +435,7 @@ - function + function @@ -481,7 +444,8 @@ - material entity + Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + material entity @@ -490,27 +454,7 @@ - immaterial entity - - - - - - - - - A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. - Bodily fluids, such as urine, are currently defined as anatomical entities in UBERON. We should make sure there is a proper home for these here. - gross anatomical part - - - - - - - - - cellular organism + immaterial entity @@ -519,13 +463,8 @@ - - - - 0 - - - electron + Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. + electron @@ -534,17 +473,8 @@ - proton - - - - - - - - - - monoatomic ion + Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. + proton @@ -553,16 +483,8 @@ - neutron - - - - - - - - - uncharged atom + Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. + neutron @@ -571,18 +493,16 @@ + + + + + + + A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. Some people may be uncomfortable calling every proton an atomic nucleus This is equivalent to CHEBI:33252 - atomic nucleus - - - - - - - - - nucleic acid polymer + atomic nucleus @@ -591,7 +511,9 @@ - subatomic particle + + A particle smaller than an atom. + subatomic particle @@ -599,29 +521,11 @@ - - A material entity that has a plasma membrane and results from cellular division. + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. - cell - - - - - - - - - native cell - - - - - - - - - cell in vitro + cell @@ -630,8 +534,7 @@ - no longer needed - obsolete_elementary charge + obsolete elementary charge true @@ -640,12 +543,6 @@ - - - - 1 - - @@ -656,7 +553,7 @@ A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. This atom is closely related to ChEBI's atom, but not exactly equivalent to. - atom + atom @@ -671,11 +568,10 @@ - A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. This molecular entity is different than ChEBI's 'molecular entity'. We would like to have cardinality restrictions on the logic, but there are some technical limitations. - molecular entity + molecule @@ -684,9 +580,7 @@ - A material entity consisting of multiple atoms that are completely connected by covalent bonds and structured in subunits, and where the most determinate class identity of the macromolecule is not necessarily changed when there is an addition or subtraction of atoms or bonds. - Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 - obsolete macromolecular entity + obsolete macromolecular entity true @@ -695,17 +589,49 @@ + + + obsolete subcellular structure + true + + + + + + + + + A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. + gross anatomical part + + + + + + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome + 'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. + Includes virus - we will later have a class for cellular organisms. + organism + + + + + + + - - + + - A material entity consisting of at least two macromolecular entities derived from a cell as parts, and that has a function for the cell. - Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. - Overlaps with some cellular components from GO - subcellular structure + A material entity processed by human activity with an intent to produce it. + In the COB 2024 workshop there was much disagreement about this label. + processed material entity @@ -713,8 +639,35 @@ - - geographical location + + obsolete geographical location + true + + + + + + + + + + + + + + + + completely executed planned process + + + + + + + + + A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. + nucleic acid chain @@ -722,8 +675,10 @@ - - immaterial anatomical entity + + + obsolete immaterial anatomical entity + true @@ -731,8 +686,9 @@ - - gene product + + obsolete gene product + true @@ -740,20 +696,10 @@ - - - - - - - - - - - - - - action specification + + + obsolete action specification + true @@ -769,8 +715,7 @@ A complex of two or more molecular entities that are not covalently bound. - >=2 parts (not we cannot use cardinality with transitive properties) - complex of molecular entities + complex of molecules @@ -779,18 +724,6 @@ - - - - - - - - - - - - A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. planned process @@ -801,17 +734,41 @@ - failed planned process + + + + + + + + + + + + + + + + + + + A planned process that intends to output material entities from input material entities + material processing + + + + - - cellular membrane + + obsolete cellular membrane + true @@ -819,19 +776,18 @@ - - - - - - - - - - - - - physical information carrier + + obsolete physical information carrier + true + + + + + + + + + characteristic @@ -840,8 +796,14 @@ + + + + + + A process during which an organism comes into contact with another entity. - exposure of organism + exposure of organism @@ -849,40 +811,15 @@ - + - - - - - - - - + + - A processed material entity which is designed to perform a function. - In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device. - -We say "designed" to emphasize a device's primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight. - -Regarding usage then, we don't say a naturally formed rock is a hammering device - it wasn't designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering "tool", which does not necessarily convey intentional design. - -Example of use: A whole device like an engine; a component like a bolt is also a device. - - 2023-03-24T16:04:27+00:00 - device - - - - - - - - - A processed material entity created to be administered to an individual with the intent to improve health. - drug product + A processed material entity which is designed to be capable of a process. + device @@ -891,6 +828,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a + A material part of an astronomical body. geophysical entity @@ -900,6 +838,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a + An environmental system which includes both living and non-living components. ecosystem @@ -909,9 +848,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - - - + A process in which includes the components of an environmental system as participants. environmental process @@ -921,32 +858,28 @@ Example of use: A whole device like an engine; a component like a bolt is also a - - - - - - - - - - - - - - - + A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. This is the same as GO molecular function - gene product or complex activity + gene product or complex activity - + - - - cell nucleus + + + + + + + + + + + + A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). + cellular_component @@ -955,39 +888,14 @@ Example of use: A whole device like an engine; a component like a bolt is also a - - - - - - - - - - - - - - - - - - - - - - - - - A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. - A biological process is an evolved process - biological process + 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 @@ -996,14 +904,45 @@ Example of use: A whole device like an engine; a component like a bolt is also a + - + + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. This is not covalently bonded, which conflicts with changes to the parent definition. - protein-containing macromolecular complex + protein-containing complex + + + + + + + + + Any constituent part of a virion, a complete fully infectious extracellular virus particle. + virion component + + + + + + + + + + + + + + + + A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. + Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. + Overlaps with some cellular components from GO + cellular anatomical entity @@ -1012,24 +951,18 @@ Example of use: A whole device like an engine; a component like a bolt is also a + A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. objective specification - + - - - - - - - - - Pier 'representational entity' - This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc - information representation + + + A directive information entity that describes an action the bearer will take. + action specification @@ -1038,7 +971,8 @@ Example of use: A whole device like an engine; a component like a bolt is also a - data item + An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + data item @@ -1047,20 +981,9 @@ Example of use: A whole device like an engine; a component like a bolt is also a - - - - - - - - - - - - - Pier: 'data, information or knowledge'. OR 'representation - information + A generically dependent continuant that is about some thing. + Pier: 'data, information or knowledge'. OR 'representation' + information content entity @@ -1069,6 +992,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a + An information content entity whose concretizations indicate to their bearer how to realize them in a process. directive information entity @@ -1078,18 +1002,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - - - - - - - - - - - - + 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 @@ -1099,51 +1012,28 @@ Example of use: A whole device like an engine; a component like a bolt is also a + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. measurement datum - - - - - document - - - - + A process in which at least one of the participants is a molecule. This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process - - - - - - - - - - - completely executed planned process - - - - - + - - - A material entity that is created or changed during material processing. - processed material entity + + + cellular organism @@ -1151,17 +1041,9 @@ Example of use: A whole device like an engine; a component like a bolt is also a - - investigation - - - - - - - - - evaluant role + + a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). + investigation @@ -1169,69 +1051,23 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + - assay - - - - - - - - - material processing - - - - - - - - - Should revisit if we can place outside of material entity - a collection of roles. - organization + A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. + assay @@ -1240,135 +1076,154 @@ Example of use: A whole device like an engine; a component like a bolt is also a - - - - - - - - plan + A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. + plan - - - - - conclusion based on data - - - - - + - - - A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. - "Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'. - Includes virus - we will later have a class for cellular organisms. - organism + + + + + + + + + + + + + + + + + A planned process that produces output data from input data. + data transformation - + - - - data transformation + + + A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. + mass - + - - - phenotypic finding + + + A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. + electric charge - + - - - disease course + + + + + + + + + A material entity that consists of two or more organisms, viruses, or viroids. + collection of organisms - + - - - disease diagnosis + + + An anatomical entity that is or was part of a plant. + plant anatomical entity - + - - - - - - - - - mass + + + An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. + protein - + - - - - - - - - - charge + + + An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. + amino acid chain - + - + + + + + + + + + + + - collection of organisms + + Anatomical entity that has mass. + material anatomical entity - + - - - protein + + + + Anatomical entity that has no mass. + immaterial anatomical entity - + - - - A role realized by a participant in a process such that the participant causes the process. - agent role + + + + + + + + + + + Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. + anatomical entity diff --git a/cob.tsv b/cob.tsv index 1093964..cc64a53 100644 --- a/cob.tsv +++ b/cob.tsv @@ -1,75 +1,69 @@ ID ID [LABEL] definition subClassOf [ID NAMED] subClassOf [LABEL NAMED] subClassOf [ID ANON] subClassOf [LABEL ANON] -BFO:0000015 process BFO:0000050 only BFO:0000015 part of only process -BFO:0000016 disposition BFO:0000017 realizable -BFO:0000017 realizable BFO:0000020 characteristic -BFO:0000020 characteristic BFO:0000051 only BFO:0000020|RO:0000052 some owl:Thing characteristic of some |has part only characteristic -BFO:0000023 role BFO:0000017 realizable +BFO:0000015 process +BFO:0000016 disposition BFO:0000017 realizable entity +BFO:0000017 realizable entity COB:0000502 characteristic +BFO:0000023 role BFO:0000017 realizable entity BFO:0000029 site BFO:0000141 immaterial entity BFO:0000034 function BFO:0000016 disposition BFO:0000040 material entity BFO:0000141 immaterial entity -CARO:0001008 gross anatomical part A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. BFO:0000040 material entity -CARO:0010004 cellular organism OBI:0100026 organism -CHEBI:10545 electron CHEBI:36342 subatomic particle COB:0000801 value 0 has number of atomic nuclei value 0 -CHEBI:24636 proton CHEBI:36342 subatomic particle -CHEBI:24867 monoatomic ion COB:0000011 atom -CHEBI:30222 neutron CHEBI:36342 subatomic particle -CHEBI:33250 uncharged atom COB:0000011 atom -CHEBI:33252 atomic nucleus CHEBI:36342 subatomic particle -CHEBI:33696 nucleic acid polymer COB:0000013 molecular entity -CHEBI:36342 subatomic particle BFO:0000040 material entity -CL:0000000 cell A material entity that has a plasma membrane and results from cellular division. BFO:0000040 material entity -CL:0000003 native cell CL:0000000 cell -CL:0001034 cell in vitro CL:0000000 cell -COB:0000005 obsolete_elementary charge +CHEBI:10545 electron Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. CHEBI:36342 subatomic particle +CHEBI:24636 proton Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. CHEBI:36342 subatomic particle +CHEBI:30222 neutron Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. CHEBI:36342 subatomic particle +CHEBI:33252 atomic nucleus A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. CHEBI:36342 subatomic particle BFO:0000051 some CHEBI:24636 has part some proton +CHEBI:36342 subatomic particle A particle smaller than an atom. BFO:0000040 material entity +CL:0000000 cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. UBERON:0000465 material anatomical entity +COB:0000005 obsolete elementary charge COB:0000011 atom A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. BFO:0000040 material entity BFO:0000051 some CHEBI:33252 has part some atomic nucleus -COB:0000013 molecular entity A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. BFO:0000040 material entity BFO:0000051 some COB:0000011 has part some atom -COB:0000014 obsolete macromolecular entity A material entity consisting of multiple atoms that are completely connected by covalent bonds and structured in subunits, and where the most determinate class identity of the macromolecule is not necessarily changed when there is an addition or subtraction of atoms or bonds. -COB:0000020 subcellular structure A material entity consisting of at least two macromolecular entities derived from a cell as parts, and that has a function for the cell. BFO:0000040 material entity BFO:0000051 some COB:0000013 has part some molecular entity -COB:0000032 geographical location BFO:0000141 immaterial entity -COB:0000056 immaterial anatomical entity BFO:0000141 immaterial entity -COB:0000073 gene product COB:0000013 molecular entity -COB:0000077 action specification IAO:0000033 directive information entity BFO:0000051 some COB:0000077|BFO:0000051 some IAO:0000005 has part some action specification|has part some objective specification -COB:0000080 complex of molecular entities A complex of two or more molecular entities that are not covalently bound. BFO:0000040 material entity BFO:0000051 some COB:0000013 has part some molecular entity -COB:0000082 planned process A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. BFO:0000015 process BFO:0000055 some SEPIO:0000048|COB:0000081 some OBI:0000260 intended to realize some plan|realizes some agent role +COB:0000013 molecule A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. BFO:0000040 material entity BFO:0000051 some COB:0000011 has part some atom +COB:0000014 obsolete macromolecular entity +COB:0000020 obsolete subcellular structure +COB:0000021 gross anatomical part A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. UBERON:0000465 material anatomical entity +COB:0000022 organism A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome UBERON:0000465 material anatomical entity +COB:0000026 processed material entity A material entity processed by human activity with an intent to produce it. BFO:0000040 material entity OBI:0000312 some COB:0000110 is specified output of some material processing +COB:0000032 obsolete geographical location +COB:0000035 completely executed planned process COB:0000082 planned process BFO:0000055 some OBI:0000260 realizes some plan +COB:0000049 nucleic acid chain A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. COB:0000013 molecule +COB:0000056 obsolete immaterial anatomical entity +COB:0000073 obsolete gene product +COB:0000077 obsolete action specification +COB:0000080 complex of molecules A complex of two or more molecular entities that are not covalently bound. BFO:0000040 material entity BFO:0000051 some COB:0000013 has part some molecule +COB:0000082 planned process A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. BFO:0000015 process COB:0000083 failed planned process COB:0000082 planned process -COB:0000116 cellular membrane COB:0000020 subcellular structure -COB:0000122 physical information carrier BFO:0000040 material entity -COB:0001000 exposure of organism A process during which an organism comes into contact with another entity. BFO:0000015 process -COB:0001300 device A processed material entity which is designed to perform a function. OBI:0000047 processed material entity OBI:0000312 some OBI:0000094|RO:0000053 some BFO:0000034 has characteristic some function|is specified output of some material processing -DRON:00000005 drug product A processed material entity created to be administered to an individual with the intent to improve health. OBI:0000047 processed material entity -ENVO:01000813 geophysical entity BFO:0000040 material entity -ENVO:01001110 ecosystem BFO:0000040 material entity -ENVO:02500000 environmental process BFO:0000015 process -GO:0003674 gene product or complex activity BFO:0000015 process RO:0002333 some (COB:0000073 or GO:0032991) enabled by some (gene product or protein-containing macromolecular complex) -GO:0005634 cell nucleus COB:0000020 subcellular structure -GO:0008150 biological process A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. BFO:0000015 process (BFO:0000066 some OBI:0100026) or (RO:0000057 some OBI:0100026) or (RO:0000057 some (BFO:0000050 some OBI:0100026))|BFO:0000051 some GO:0003674 (occurs in some organism) or (has participant some organism) or (has participant some (part of some organism))|has part some gene product or complex activity -GO:0032991 protein-containing macromolecular complex COB:0000080 complex of molecular entities BFO:0000051 some COB:0000073 has part some gene product -IAO:0000005 objective specification IAO:0000033 directive information entity -IAO:0000015 information representation BFO:0000020 characteristic -IAO:0000027 data item IAO:0000030 information -IAO:0000030 information IAO:0000136 some owl:Thing|RO:0000058 some IAO:0000015 is about some |is concretized as some information representation -IAO:0000033 directive information entity IAO:0000030 information -IAO:0000104 plan specification IAO:0000033 directive information entity BFO:0000051 some COB:0000077|BFO:0000051 some IAO:0000005 has part some action specification|has part some objective specification -IAO:0000109 measurement datum IAO:0000027 data item -IAO:0000310 document IAO:0000030 information -MOP:0000543 physico-chemical process BFO:0000015 process -OBI:0000011 completely executed planned process COB:0000082 planned process BFO:0000055 some OBI:0000260 realizes some plan -OBI:0000047 processed material entity A material entity that is created or changed during material processing. BFO:0000040 material entity -OBI:0000066 investigation OBI:0000011 completely executed planned process -OBI:0000067 evaluant role BFO:0000023 role -OBI:0000070 assay OBI:0000011 completely executed planned process OBI:0000293 some (BFO:0000040 and (RO:0000053 some OBI:0000067))|OBI:0000299 some (IAO:0000109 and (IAO:0000136 some (BFO:0000040 and (RO:0000053 some OBI:0000067)))) has specified input some (material entity and (has characteristic some evaluant role))|has specified output some (measurement datum and (is about some (material entity and (has characteristic some evaluant role)))) -OBI:0000094 material processing OBI:0000011 completely executed planned process -OBI:0000245 organization BFO:0000040 material entity -OBI:0000260 plan BFO:0000017|IAO:0000015 information representation|realizable BFO:0000054 only COB:0000082|RO:0000059 some IAO:0000104 concretizes some plan specification|realized in only planned process -OBI:0001909 conclusion based on data IAO:0000030 information -OBI:0100026 organism A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. BFO:0000040 material entity -OBI:0200000 data transformation OBI:0000011 completely executed planned process -OGMS:0000014 phenotypic finding IAO:0000030 information -OGMS:0000063 disease course BFO:0000015 process -OGMS:0000073 disease diagnosis IAO:0000030 information -PATO:0000125 mass BFO:0000020 characteristic RO:0000052 some BFO:0000040 characteristic of some material entity -PATO:0002193 charge BFO:0000020 characteristic RO:0000052 some BFO:0000040 characteristic of some material entity -PCO:0000000 collection of organisms BFO:0000040 material entity -PR:000000001 protein COB:0000013 molecular entity -SEPIO:0000048 agent role BFO:0000023 role +COB:0000110 material processing A planned process that intends to output material entities from input material entities COB:0000035 completely executed planned process (OBI:0000293 some BFO:0000040) and (OBI:0000299 some BFO:0000040) (has specified input some material entity) and (has specified output some material entity) +COB:0000116 obsolete cellular membrane +COB:0000122 obsolete physical information carrier +COB:0000502 characteristic +COB:0001000 exposure of organism A process during which an organism comes into contact with another entity. BFO:0000015 process RO:0000057 some COB:0000022 has participant some organism +COB:0001300 device A processed material entity which is designed to be capable of a process. COB:0000026 processed material entity RO:0002215 some BFO:0000015 capable of some process +ENVO:01000813 geophysical entity A material part of an astronomical body. BFO:0000040 material entity +ENVO:01001110 ecosystem An environmental system which includes both living and non-living components. BFO:0000040 material entity +ENVO:02500000 environmental process A process in which includes the components of an environmental system as participants. BFO:0000015 process +GO:0003674 gene product or complex activity A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. BFO:0000015 process +GO:0005575 cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). BFO:0000040 material entity +GO:0008150 biological process 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. BFO:0000015 process BFO:0000051 some GO:0003674 has part some gene product or complex activity +GO:0032991 protein-containing complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. COB:0000080|GO:0005575 cellular_component|complex of molecules BFO:0000051 some PR:000000001 has part some protein +GO:0044423 virion component Any constituent part of a virion, a complete fully infectious extracellular virus particle. GO:0005575 cellular_component +GO:0110165 cellular anatomical entity A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. GO:0005575|UBERON:0000465 cellular_component|material anatomical entity BFO:0000051 some COB:0000013 has part some molecule +IAO:0000005 objective specification A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. IAO:0000033 directive information entity +IAO:0000007 action specification A directive information entity that describes an action the bearer will take. IAO:0000033 directive information entity +IAO:0000027 data item An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. IAO:0000030 information content entity +IAO:0000030 information content entity A generically dependent continuant that is about some thing. +IAO:0000033 directive information entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. IAO:0000030 information content entity +IAO:0000104 plan specification 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. IAO:0000033 directive information entity +IAO:0000109 measurement datum A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. IAO:0000027 data item +MOP:0000543 physico-chemical process A process in which at least one of the participants is a molecule. BFO:0000015 process +NCBITaxon:131567 cellular organism COB:0000022 organism +OBI:0000066 investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). COB:0000035 completely executed planned process +OBI:0000070 assay A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. COB:0000035 completely executed planned process (OBI:0000293 some BFO:0000040) and (OBI:0000299 some IAO:0000027) (has specified input some material entity) and (has specified output some data item) +OBI:0000260 plan A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. BFO:0000017 realizable entity RO:0000059 some IAO:0000104 concretizes some plan specification +OBI:0200000 data transformation A planned process that produces output data from input data. COB:0000082 planned process (OBI:0000293 some IAO:0000027) and (OBI:0000299 some IAO:0000027) (has specified input some data item) and (has specified output some data item) +PATO:0000125 mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. COB:0000502 characteristic +PATO:0002193 electric charge A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. COB:0000502 characteristic +PCO:0000000 collection of organisms A material entity that consists of two or more organisms, viruses, or viroids. BFO:0000040 material entity BFO:0000051 some COB:0000022 has part some organism +PO:0025131 plant anatomical entity An anatomical entity that is or was part of a plant. UBERON:0000465 material anatomical entity +PR:000000001 protein An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. PR:000018263 amino acid chain +PR:000018263 amino acid chain An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. COB:0000013 molecule +UBERON:0000465 material anatomical entity Anatomical entity that has mass. BFO:0000040|UBERON:0001062 anatomical entity|material entity +UBERON:0000466 immaterial anatomical entity Anatomical entity that has no mass. BFO:0000141|UBERON:0001062 anatomical entity|immaterial entity +UBERON:0001062 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index b570bb9..fb013ab 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -16,8 +16,6 @@ These are the current imports in COB | Import | URL | Type | | ------ | --- | ---- | -| ro | http://purl.obolibrary.org/obo/ro.owl | custom | -| omo | http://purl.obolibrary.org/obo/omo.owl | mirror | ## Components Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases: @@ -26,9 +24,4 @@ Components, in contrast to imports, are considered full members of the ontology. 2. A part of the ontology is managed in ROBOT templates 3. The expressivity of the component is higher than the format of the edit file. For example, people still choose to manage their ontology in OBO format (they should not) missing out on a lot of owl features. They may choose to manage logic that is beyond OBO in a specific OWL component. -These are the components in COB -| Filename | URL | -| -------- | --- | -| cob-annotations.owl | None | -| cob-to-external.owl | None | diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 0c14749..6d49e67 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -19,7 +19,7 @@ # 6. [Run everything (COB products and release pipeline)](all) # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 5daef41d99e802417bd9ad0f378f72168e2d30f0488f5b2423330cbc561ec834 +CONFIG_HASH= 0cb0824fc712dd1bbe3e3067c8a9d6d4212a769da65f9ec96e0020e31e2cafb9 # ---------------------------------------- @@ -62,13 +62,13 @@ OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') VERSION= $(TODAY) ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION) ANNOTATE_CONVERT_FILE = annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@ -OTHER_SRC = $(COMPONENTSDIR)/cob-annotations.owl $(COMPONENTSDIR)/cob-to-external.owl +OTHER_SRC = ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt EDIT_PREPROCESSED = $(TMPDIR)/$(ONT)-preprocess.owl FORMATS = $(sort owl owl) FORMATS_INCL_TSV = $(sort $(FORMATS) tsv) -RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full cob-base-reasoned cob-examples-reasoned cob-native ) +RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-root ) ifeq ($(ODK_DEBUG),yes) ODK_DEBUG_FILE = debug.log @@ -168,7 +168,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = ro omo +IMPORTS = IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -375,16 +375,6 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt .PRECIOUS: $(IMPORTDIR)/%_import.owl -## Module for ontology: ro - -$(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl - echo "ERROR: You have configured your default module type to be custom; this behavior needs to be overwritten in cob.Makefile!" && false -## Module for ontology: omo - -$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/omo.owl $(IMPORTDIR)/omo_terms_combined.txt - if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ - $(ANNOTATE_CONVERT_FILE); fi - .PHONY: refresh-imports refresh-imports: @@ -406,39 +396,6 @@ refresh-%: no-mirror-refresh-%: $(MAKE) IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B - -# ---------------------------------------- -# Components -# ---------------------------------------- -# Some ontologies contain external and internal components. A component is included in the ontology in its entirety. - -COMP=true # Global parameter to bypass component generation - -.PHONY: all_components -all_components: $(OTHER_SRC) - -.PHONY: recreate-components -recreate-components: - $(MAKE) COMP=true IMP=false MIR=true PAT=true IMP_LARGE=false all_components -B - -.PHONY: no-mirror-recreate-components -no-mirror-recreate-components: - $(MAKE) COMP=true IMP=false MIR=false PAT=true IMP_LARGE=false all_components -B - -.PHONY: recreate-% -recreate-%: - $(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=true PAT=true $(COMPONENTSDIR)/$*.owl -B - -.PHONY: no-mirror-recreate-% -no-mirror-recreate-%: - $(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl -B - -$(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR) - test -f $@ || touch $@ -.PRECIOUS: $(COMPONENTSDIR)/%.owl - - - # ---------------------------------------- # Mirroring upstream ontologies # ---------------------------------------- @@ -450,22 +407,6 @@ IMP_LARGE=true # Global parameter to bypass handling of large imports ifeq ($(strip $(MIR)),true) -## ONTOLOGY: ro -.PHONY: mirror-ro -.PRECIOUS: $(MIRRORDIR)/ro.owl -mirror-ro: | $(TMPDIR) - curl -L $(OBOBASE)/ro.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \ - $(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl - - -## ONTOLOGY: omo -.PHONY: mirror-omo -.PRECIOUS: $(MIRRORDIR)/omo.owl -mirror-omo: | $(TMPDIR) - curl -L $(OBOBASE)/omo.owl --create-dirs -o $(TMPDIR)/omo-download.owl --retry 4 --max-time 200 && \ - $(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl - - $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ cp $(TMPDIR)/mirror-$*.owl $@; fi; fi @@ -549,15 +490,6 @@ $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) relax \ reduce -r ELK \ $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ - -cob-base-reasoned.owl: - echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in cob.Makefile!" && false - -cob-examples-reasoned.owl: - echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in cob.Makefile!" && false - -cob-native.owl: - echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in cob.Makefile!" && false # ---------------------------------------- # Debugging Tools # ---------------------------------------- diff --git a/src/ontology/cob-edit.owl b/src/ontology/cob-edit.owl deleted file mode 100644 index bdc191b..0000000 --- a/src/ontology/cob-edit.owl +++ /dev/null @@ -1,1368 +0,0 @@ - - - - - COB brings together key terms from a wide range of OBO projects to improve interoperability. - - Core Ontology for Biology and Biomedicine - - - - - - - - - - - - - definition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - is concretized as - - - - - - - - - executed by - - - - - - - - - characteristic of - - - - - - - - - participates in - - - - - - - - - - is specified input of - - - - - - - - - - is specified output of - - - - - - - - - realized in - - - - - - - - - contains process - - - - - - - - - - has specified input - - - - - - - - - - has specified output - - - - - - - - - has part - - - - - - - - - has participant - - - - - - - - - occurs in - - - - - - - - - part of - - - - - - - - - enabled by - - - - - - - - concretizes - - - - - - - - intended to realize - - - - - - - - has plan - - - - - - - - intended plan process type - - - - - - - - - - - - executes - - - - - - - - - - realizes - - - - - - - - - - - has characteristic - https://github.com/oborel/obo-relations/pull/284 - - - - - - Anything can have a characteristic - - - - - - - - is about - - - - - - - - - - - - - - The range of this property should be a user-defined unit datatype, e.g 182^:cm - has quantity - https://github.com/OBOFoundry/COB/issues/35 - - - - - - - - - - Number of protons in an atomic nucleus - We are undecided as to whether to ultimately model this as a data property of object property + cardinality, but for now we are using DPs as these are faster for reasoning - has atomic number - - - - - - - - - - has number of atomic nuclei - - - - - - - - - has inchi string - - - - - - - - - - - - - - - - - - - - mass - - - - - - - - - - - - - - - charge - - - - - - - - no longer needed - obsolete_elementary charge - true - - - - - - - - material entity - - - - - - - - - subatomic particle - - - - - - - - - proton - - - - - - - - - neutron - - - - - - - - - - - - 0 - - - electron - - - - - - - - - - - 1 - - - - - - - - - - - A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. - This atom is closely related to ChEBI's atom, but not exactly equivalent to. - atom - - - - - - - - - Some people may be uncomfortable calling every proton an atomic nucleus - This is equivalent to CHEBI:33252 - atomic nucleus - - - - - - - - - - - - - - - - A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. - This molecular entity is different than ChEBI's 'molecular entity'. - We would like to have cardinality restrictions on the logic, but there are some technical limitations. - molecular entity - - - - - - - - A material entity consisting of multiple atoms that are completely connected by covalent bonds and structured in subunits, and where the most determinate class identity of the macromolecule is not necessarily changed when there is an addition or subtraction of atoms or bonds. - Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 - obsolete macromolecular entity - true - - - - - - - - - protein - - - - - - - - - A material entity that has a plasma membrane and results from cellular division. - CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. - We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism. - cell - - - - - - - - - native cell - - - - - - - - - cell in vitro - - - - - - - - - - - - - - - A material entity consisting of at least two macromolecular entities derived from a cell as parts, and that has a function for the cell. - Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. - Overlaps with some cellular components from GO - subcellular structure - - - - - - - - - A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. - Bodily fluids, such as urine, are currently defined as anatomical entities in UBERON. We should make sure there is a proper home for these here. - gross anatomical part - - - - - - - - - A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. - "Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'. - Includes virus - we will later have a class for cellular organisms. - organism - - - - - - - - - Should revisit if we can place outside of material entity - a collection of roles. - organization - - - - - - - - - A material entity that is created or changed during material processing. - processed material entity - - - - - - - - immaterial entity - - - - - - - - - geographical location - - - - - - - - - realizable - - - - - - - - - - - - - - process - - - - - - - - - - - - - - - - completely executed planned process - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective. - A biological process is an evolved process - biological process - - - - - - - - - - - - - - - - - - - - - - - - This is the same as GO molecular function - gene product or complex activity - - - - - - - - - - monoatomic ion - - - - - - - - - uncharged atom - - - - - - - - - nucleic acid polymer - - - - - - - - - collection of organisms - - - - - - - - - immaterial anatomical entity - - - - - - - - - site - - - - - - - - - conclusion based on data - - - - - - - - - - - - - - - - - - - - Pier: 'data, information or knowledge'. OR 'representation - information - - - - - - - - - disease diagnosis - - - - - - - - - phenotypic finding - - - - - - - - - disease course - - - - - - - - - - environmental process - - - - - - - - - This is meant to capture processes that are more fundamental than macromolecular activities - physico-chemical process - - - - - - - - - ecosystem - - - - - - - - - geophysical entity - - - - - - - - - directive information entity - - - - - - - - - gene product - - - - - - - - - - - - - - - This is not covalently bonded, which conflicts with changes to the parent definition. - protein-containing macromolecular complex - - - - - - - - - objective specification - - - - - - - - - - - - - - - - - - - - - action specification - - - - - - - - - - - - - - - - - - - - - plan specification - - - - - - - - - - - - - - - A complex of two or more molecular entities that are not covalently bound. - >=2 parts (not we cannot use cardinality with transitive properties) - complex of molecular entities - - - - - - - - - - - - - - - - - - - - - A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. - planned process - - - - - - - - - failed planned process - - - - - - - - - A processed material entity created to be administered to an individual with the intent to improve health. - drug product - - - - - - - - - document - - - - - - - - - data item - - - - - - - - - cell nucleus - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - assay - - - - - - - - - data transformation - - - - - - - - - investigation - - - - - - - - - material processing - - - - - - - - - disposition - - - - - - - - - function - - - - - - - - - - - - - - - - - - - - - plan - - - - - - - - - role - - - - - - - - - cellular membrane - - - - - - - - - cellular organism - - - - - - - - - evaluant role - - - - - - - - - - - - - - - Pier 'representational entity' - This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc - information representation - - - - - - - - - measurement datum - - - - - - - - - - - - - - - - - - - - physical information carrier - - - - - - - - - A role realized by a participant in a process such that the participant causes the process. - agent role - - - - - - - - - - - - - - - - - - - - characteristic - https://github.com/OBOFoundry/COB/issues/65 - https://github.com/oborel/obo-relations/pull/284 - - - - - - - - - A process during which an organism comes into contact with another entity. - exposure of organism - - - - - - - - - - - - - - - - - - - - - A processed material entity which is designed to perform a function. - - 2023-03-24T16:04:27Z - In this definition we assume devices are made of processed material, not natural artifacts, so we involve artifactual function rather than biological function, but align with a general BFO function sense where functions such as pumping, lifting can occur in both contexts. Thus we can compare a biological arm with a robotic arm device. - -We say "designed" to emphasize a device's primary function rather than all the other possible dispositions a device may have that may also be useful. E.g. one can use a hammer for a paper weight. - -Regarding usage then, we don't say a naturally formed rock is a hammering device - it wasn't designed to bear a hammering function per se. However, a given rock may still happen to have the disposition to bear a hammering function, and so we could say it is a hammering "tool", which does not necessarily convey intentional design. - -Example of use: A whole device like an engine; a component like a bolt is also a device. - device - - - - - - - diff --git a/src/ontology/cob-edit.tsv b/src/ontology/cob-edit.tsv new file mode 100644 index 0000000..3d2a500 --- /dev/null +++ b/src/ontology/cob-edit.tsv @@ -0,0 +1,150 @@ +Ontology ID Label Type Definition Editor Note COB Module COB Module Reason Parent Class Subclass Axiom Equivalent Class Axiom Disjoint Class Parent Property Domain Range Inverse Property Replacement ID Replacement Label Comment +ID LABEL TYPE A IAO:0000115 A IAO:0000116 SPLIT=| A COB:module A COB:module-reason C % SC % SPLIT=| EC % SPLIT=| DC % SP % DOMAIN RANGE IP % + We use some basic annotation properties. +IAO:0000115 definition owl:AnnotationProperty BASE required annotations +IAO:0000116 editor note owl:AnnotationProperty BASE required annotations +IAO:0100001 term replaced by owl:AnnotationProperty BASE required annotations + Existing object properties listed in the Replacement columns will be used in place of more specific COB object properties in this sheet. +BFO:0000050 part of owl:ObjectProperty a core relation that holds between a part and its whole REPLACEMENT +BFO:0000051 has part owl:ObjectProperty a core relation that holds between a whole and its part REPLACEMENT +BFO:0000055 realizes owl:ObjectProperty Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process REPLACEMENT process realizable entity +OBI:0000293 has specified input owl:ObjectProperty The inverse property of is_specified_input_of REPLACEMENT planned process +OBI:0000295 is specified input of owl:ObjectProperty A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. REPLACEMENT planned process +OBI:0000299 has specified output owl:ObjectProperty The inverse property of is_specified_output_of REPLACEMENT planned process +OBI:0000312 is specified output of owl:ObjectProperty A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. REPLACEMENT planned process +RO:0000052 characteristic of owl:ObjectProperty a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. REPLACEMENT +RO:0000053 has characteristic owl:ObjectProperty Inverse of characteristic_of REPLACEMENT +RO:0000056 participates in owl:ObjectProperty a relation between a continuant and a process, in which the continuant is somehow involved in the process REPLACEMENT +RO:0000057 has participant owl:ObjectProperty a relation between a process and a continuant, in which the continuant is somehow involved in the process REPLACEMENT +RO:0000058 is concretized as owl:ObjectProperty 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. REPLACEMENT +RO:0000059 concretizes owl:ObjectProperty 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. REPLACEMENT +RO:0001000 derives from owl:ObjectProperty a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity REPLACEMENT +RO:0001015 location of owl:ObjectProperty a relation between two independent continuants, the location and the target, in which the target is entirely within the location REPLACEMENT +RO:0001025 located in owl:ObjectProperty a relation between two independent continuants, the target and the location, in which the target is entirely within the location REPLACEMENT +RO:0002215 capable of owl:ObjectProperty 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. REPLACEMENT process +RO:0002219 surrounded by owl:ObjectProperty 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 REPLACEMENT +RO:0002221 surrounds owl:ObjectProperty inverse of surrounded by REPLACEMENT +RO:0002233 has input owl:ObjectProperty 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. REPLACEMENT process +RO:0002234 has output owl:ObjectProperty 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. REPLACEMENT +RO:0002333 enabled by owl:ObjectProperty inverse of enables REPLACEMENT + Material entities are the core of OBO. They are easy to individuate. We start with naturally occurring material entities. +BFO:0000040 material entity owl:Class Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. FULL required top-level term +COB:has-material-part has material part owl:ObjectProperty REPLACED material entity material entity BFO:0000051 has part +COB:material-part-of material part of owl:ObjectProperty REPLACED material entity material entity has material part BFO:0000050 part of +CHEBI:36342 subatomic particle owl:Class A particle smaller than an atom. FULL used as parent of 'atomic nucleus' material entity +CHEBI:10545 electron owl:Class Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV. FULL included for completeness subatomic particle +CHEBI:24636 proton owl:Class Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u. FULL used to define 'subatomic particle' subatomic particle +CHEBI:30222 neutron owl:Class Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u. FULL included for completeness subatomic particle +CHEBI:33252 atomic nucleus owl:Class A nucleus is the positively charged central portion of an atom, excluding the orbital electrons. This is equivalent to CHEBI:33252|Some people may be uncomfortable calling every proton an atomic nucleus FULL used to define 'atom' subatomic particle 'has material part' some proton +COB:0000011 atom owl:Class A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. This atom is closely related to ChEBI's atom, but not exactly equivalent to. BASE material entity 'has material part' some 'atomic nucleus' subatomic particle +COB:0000013 molecule owl:Class A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom. We would like to have cardinality restrictions on the logic, but there are some technical limitations.|This molecular entity is different than ChEBI's 'molecular entity'. BASE material entity 'has material part' some atom atom +COB:0000049 nucleic acid chain owl:Class A molecule that consists of nucleotides (unmodified nucleotide residues and/or modified nucleotide residues) linked by phosphodiester bonds or derivatives of such bonds. BASE molecule +PR:000018263 amino acid chain owl:Class An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds. FULL included for contrast with 'protein' molecule COB injects: subclass of 'material entity' +PR:000000001 protein owl:Class An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. FULL used to define 'protein-containing complex' amino acid chain +SO:0000110 sequence_feature owl:Class Any extent of continuous biological sequence. ROOT root of Sequence Ontology material entity COB injects: subclass of 'material entity' +SO:0001060 sequence_variant owl:Class A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. ROOT root of Sequence Ontology material entity COB injects: subclass of 'material entity' +SO:0001260 sequence_collection owl:Class A collection of discontinuous sequences. ROOT root of Sequence Ontology material entity COB injects: subclass of 'material entity' +COB:0000080 complex of molecules owl:Class A complex of two or more molecular entities that are not covalently bound. BASE material entity 'has material part' some 'molecule' +GO:0032991 protein-containing complex owl:Class A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. This is not covalently bonded, which conflicts with changes to the parent definition. FULL member of 'cellular component' root group union complex of molecules 'has material part' some protein +GO:0044423 virion component owl:Class Any constituent part of a virion, a complete fully infectious extracellular virus particle. ROOT GROUP: MEMBER member of 'cellular component' root group union material entity +GO:0110165 cellular anatomical entity owl:Class A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Overlaps with some cellular components from GO|Components are larger than individual macromolecular entities. It is tricky to define distinction between 'cell component' and 'macromolecular entity', e.g. ribosome. We would like to exclude most protein complexes. FULL member of 'cellular component' root group union material entity 'has material part' some 'molecule' +GO:0005575 cellular_component owl:Class A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex). ROOT GROUP material entity 'protein-containing complex' or 'virion component' or 'cellular anatomical entity' +CL:0000000 cell owl:Class A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. We struggled with this definition. We are worried about circularity. We also considered requiring the capability of metabolism.|CL and GO definitions of cell differ based on inclusive or exclusive of cell wall, etc. FULL in scope & unmodified from CL material entity +PO:0009002 plant cell owl:Class A cell which is a plant structure (PO:0009011). ROOT root of Plant Ontology cell +CL:0001034 cell in vitro owl:Class A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. ROOT root of Cell Ontology cell +COB:0000021 gross anatomical part owl:Class A part of a multicellular organism that is a collection of cell components that are not all contained in one cell. FULL temporarily has a COB ID; waiting on Uberon's 'gross anatomical part' term material entity +UBERON:0000465 material anatomical entity owl:Class Anatomical entity that has mass. ROOT GROUP material entity 'cellular anatomical entity' or 'cell' or 'gross anatomical part' or 'organism' +PO:0025131 plant anatomical entity owl:Class An anatomical entity that is or was part of a plant. ROOT GROUP: CHILD material anatomical entity +COB:0000022 organism owl:Class A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome Includes virus - we will later have a class for cellular organisms.|'Maximal functionally integrated unit' is intended to express unity, which Barry considers synonymous with BFO 'object'. BASE material entity +NCBITaxon:131567 cellular organism owl:Class FULL unmodified & in scope organism +PCO:0000000 collection of organisms owl:Class A material entity that consists of two or more organisms, viruses, or viroids. FULL unmodified & in scope material entity 'has material part' some organism +ENVO:01000813 geophysical entity owl:Class A material part of an astronomical body. FULL in scope & only label modified material entity ENVO calls this 'astronomical body part' +ENVO:01001110 ecosystem owl:Class An environmental system which includes both living and non-living components. FULL unmodified & in scope material entity + Immaterial entities, such as cavities and anatomical spaces, can be individuated by their material boundaries. Material entities can be located in immaterial entities. +BFO:0000141 immaterial entity owl:Class FULL unmodified & in scope +COB:has-immaterial-part has immaterial part owl:ObjectProperty REPLACED immaterial entity immaterial entity BFO:0000051 has part +COB:immaterial-part-of immaterial part of owl:ObjectProperty REPLACED immaterial entity immaterial entity has immaterial part BFO:0000050 part of +COB:located-in located in owl:ObjectProperty REPLACED material entity immaterial entity RO:0001025 located in not quite RO located in +COB:location-of location of owl:ObjectProperty REPLACED immaterial entity material entity located in RO:0001015 location of +UBERON:0000466 immaterial anatomical entity owl:Class Anatomical entity that has no mass. ROOT GROUP: MEMBER root of Uberon immaterial entity +UBERON:0001062 anatomical entity owl:Class Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. ROOT GROUP 'material anatomical entity' or 'immaterial anatomical entity' +COB:has-material-boundary has material boundary owl:ObjectProperty REPLACED immaterial entity material entity RO:0002219 surrounded by like RO has 2D boundary? RO surrounded by? +COB:material-boundary-of material boundary of owl:ObjectProperty REPLACED material entity immaterial entity has material boundary RO:0002221 surrounds +BFO:0000029 site owl:Class FULL TO DISCUSS: in previous COB release immaterial entity + Characteristics specifically depend on other entities. Characteristics of characteristics are not allowed. characteristics of information? length, size? +COB:0000502 characteristic owl:Class BASE replace by SDC? +COB:has-characteristic has characteristic owl:ObjectProperty REPLACED characteristic RO:0000053 has characteristic domain: not characteristic ? +COB:characteristic-of characteristic of owl:ObjectProperty REPLACED characteristic has characteristic RO:0000052 characteristic of range: not characteristic ? +PATO:0000125 mass owl:Class A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. FULL in previous COB characteristic +PATO:0002193 electric charge owl:Class A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. FULL in previous COB characteristic + Information entities generically depends on other entities. Information can be copied. Information is about some other thing. +IAO:0000030 information content entity owl:Class A generically dependent continuant that is about some thing. Pier: 'data, information or knowledge'. OR 'representation' FULL unmodified & in scope +IAO:0000136 is about owl:ObjectProperty FULL information content entity +COB:concretizes concretizes owl:ObjectProperty REPLACED characteristic information content entity RO:0000059 concretizes +COB:concretized-as concretized as owl:ObjectProperty REPLACED information content entity characteristic concretizes RO:0000058 is concretized as + Processes ... have participants, have process parts +BFO:0000015 process owl:Class FULL unmodified & in scope +COB:has-process-part has process part owl:ObjectProperty REPLACED process process BFO:0000051 has part +COB:process-part-of process part of owl:ObjectProperty REPLACED process process has process part BFO:0000050 part of +COB:has-material-participant has material participant owl:ObjectProperty REPLACED process material entity RO:0000057 has participant +COB:material-participates-in material participates in owl:ObjectProperty REPLACED material entity process has material participant RO:0000056 participates in +COB:has-material-input has material input owl:ObjectProperty REPLACED has material participant RO:0002233 has input +COB:has-material-output has material output owl:ObjectProperty REPLACED has material participant RO:0002234 has output +COB:has-information-participant has information participant owl:ObjectProperty REPLACED process information content entity RO:0000057 has participant by virtue of the material basis for that information +COB:has-information-input has information input owl:ObjectProperty REPLACED has information participant RO:0002233 has input +COB:has-information-output has information output owl:ObjectProperty REPLACED has information participant RO:0002234 has output +COB:capable-of capable of owl:ObjectProperty REPLACED material entity process RO:0002215 capable of +COB:enabled-by enabled by owl:ObjectProperty REPLACED has material participant RO:0002333 enabled by +MOP:0000543 physico-chemical process owl:Class A process in which at least one of the participants is a molecule. This is meant to capture processes that are more fundamental than macromolecular activities FULL in scope, COB injects label process +GO:0003674 gene product or complex activity owl:Class A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. This is the same as GO molecular function FULL unmodified & in scope process physico-chemical process GO's 'molecular function'; this subClassOf axioms requires a 'gene product' term: 'enabled by' some ('gene product' or 'protein-containing complex') +GO:0008150 biological process owl:Class 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. FULL unmodified & in scope process 'has process part' some 'gene product or complex activity' gene product or complex activity +COB:0001000 exposure of organism owl:Class A process during which an organism comes into contact with another entity. BASE process 'has material participant' some organism +ENVO:02500000 environmental process owl:Class A process in which includes the components of an environmental system as participants. FULL unmodified & in scope process + A realizable is a special characteristic that is realized by a processes; a role is a realizable that depends on a physical, social, or institutional context; a disposition does not depend on context; a function is a designed (intended) disposition +BFO:0000017 realizable entity owl:Class FULL unmodified & in scope characteristic +COB:realizes realizes owl:ObjectProperty REPLACED process realizable entity BFO:0000055 realizes +BFO:0000023 role owl:Class FULL unmodified & in scope realizable entity +BFO:0000016 disposition owl:Class FULL TO DISCUSS: in previous COB release realizable entity +BFO:0000034 function owl:Class FULL TO DISCUSS: in previous COB release disposition + A plan specification is information about how a plan can be realized; a plan concretizes a plan specification; a plan is a characteristic of an agent; a completely executed planned process realizes a plan, and has specified inputs and outputs +OBI:0000260 plan owl:Class A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. FULL used to define planned process realizable entity 'concretizes' some 'plan specification' +IAO:0000033 directive information entity owl:Class An information content entity whose concretizations indicate to their bearer how to realize them in a process. FULL unmodified & in scope information content entity +IAO:0000007 action specification owl:Class A directive information entity that describes an action the bearer will take. FULL unmodified & in scope directive information entity +IAO:0000005 objective specification owl:Class A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. FULL unmodified & in scope directive information entity +IAO:0000104 plan specification owl:Class 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. FULL used to define plan directive information entity +COB:0000082 planned process owl:Class A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. BASE process Maybe add axiom: 'realizes' some 'agent role' +COB:0000083 failed planned process owl:Class BASE planned process +COB:0000035 completely executed planned process owl:Class BASE planned process 'realizes' some 'plan' failed planned process +COB:has-specified-material-input has specified material input owl:ObjectProperty REPLACED has material input completely executed planned process material entity OBI:0000293 has specified input +COB:has-specified-material-output has specified material output owl:ObjectProperty REPLACED has material output completely executed planned process material entity OBI:0000299 has specified output +COB:specified-material-output-of specified material output of owl:ObjectProperty REPLACED has specified material output OBI:0000312 is specified output of +COB:has-specified-information-input has specified information input owl:ObjectProperty REPLACED has information input completely executed planned process information content entity OBI:0000293 has specified input +COB:has-specified-information-output has specified information output owl:ObjectProperty REPLACED has information output completely executed planned process information content entity OBI:0000299 has specified output +COB:specified-information-output-of specified information output of owl:ObjectProperty REPLACED has specified information output OBI:0000312 specified output of + A device is the output of a material processing, which is a completely executed planned process. +COB:0000110 material processing owl:Class A planned process that intends to output material entities from input material entities BASE completely executed planned process 'has specified material input' some 'material entity' and 'has specified material output' some 'material entity' +COB:0000026 processed material entity owl:Class A material entity processed by human activity with an intent to produce it. In the COB 2024 workshop there was much disagreement about this label. BASE material entity 'specified material output of' some 'material processing' +COB:0001300 device owl:Class A processed material entity which is designed to be capable of a process. BASE processed material entity 'capable of' some process device function +VO:0000001 vaccine owl:Class Material entity that is manufactured to realize the vaccine function. ROOT root of the Vaccine Ontology processed material entity vaccine function +DRON:00000005 drug product owl:Class a material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role ROOT root of the Drug Ontology processed material entity clinical drug function +FOODON:00002403 food material owl:Class 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 ROOT root of the Food Ontology material entity + OBI assay model +OBI:0000066 investigation owl:Class a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). FULL unmodified & in scope completely executed planned process +OBI:0000070 assay owl:Class A planned process that has the objective to produce information about a material entity (the evaluant) by examining it. FULL unmodified & in scope completely executed planned process 'has specified material input' some 'material entity' and 'has specified information output' some 'data item' +IAO:0000027 data item owl:Class An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. FULL unmodified & in scope information content entity +IAO:0000109 measurement datum owl:Class A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. FULL in previous COB data item +OBI:0200000 data transformation owl:Class A planned process that produces output data from input data. FULL unmodified & in scope planned process 'has specified information input' some 'data item' and 'has specified information output' some 'data item' + Specimens from OBI +OBI:0000659 specimen collection owl:Class A planned process with the objective of collecting a specimen. ROOT unmodified & in scope process 'has specified material input' some 'material entity' and 'has specified material output' some 'specimen' +OBI:0100051 specimen owl:Class A material entity that has the specimen role. ROOT material entity 'specified material output of' some 'specimen collection' +COB:derives-from derives from owl:ObjectProperty REPLACED material entity material entity RO:0001000 derives from +OBI:0001479 specimen from organism owl:Class A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm). ROOT specimen 'derives from' some 'material anatomical entity' + Previous COB properties: These still need discussion +COB:0000016 executed by owl:ObjectProperty BASE TO DISCUSS: in previous COB release +COB:0000081 intended to realize owl:ObjectProperty BASE TO DISCUSS: in previous COB release +COB:0000084 has plan owl:ObjectProperty BASE TO DISCUSS: in previous COB release +COB:0000085 intended plan process type owl:ObjectProperty BASE TO DISCUSS: in previous COB release +COB:0000511 has quantity owl:DataProperty BASE TO DISCUSS: in previous COB release +COB:0000800 has atomic number owl:DataProperty Number of protons in an atomic nucleus BASE TO DISCUSS: in previous COB release atom +COB:0000801 has number of atomic nuclei owl:DataProperty BASE TO DISCUSS: in previous COB release material entity +COB:0000803 has inchi string owl:DataProperty BASE TO DISCUSS: in previous COB release diff --git a/src/ontology/cob-odk.yaml b/src/ontology/cob-odk.yaml index a92b2c7..f2736f4 100644 --- a/src/ontology/cob-odk.yaml +++ b/src/ontology/cob-odk.yaml @@ -10,10 +10,7 @@ workflows: - docs release_artefacts: - base - - full - - custom-cob-base-reasoned - - custom-cob-examples-reasoned - - custom-cob-native + - root import_group: module_type: filter annotation_properties: @@ -21,16 +18,6 @@ import_group: - IAO:0000115 - IAO:0000116 - IAO:0000111 - products: - - id: ro - module_type: custom - slme_individuals: exclude - - id: omo - module_type: mirror -components: - products: - - filename: cob-annotations.owl - - filename: cob-to-external.owl robot_java_args: '-Xmx8G' custom_makefile_header: | ### Workflow @@ -47,4 +34,4 @@ custom_makefile_header: | # 6. [Run everything (COB products and release pipeline)](all) create_obo_metadata: FALSE documentation: - documentation_system: mkdocs \ No newline at end of file + documentation_system: mkdocs diff --git a/src/ontology/cob.Makefile b/src/ontology/cob.Makefile index 67e5776..8f3956e 100644 --- a/src/ontology/cob.Makefile +++ b/src/ontology/cob.Makefile @@ -10,16 +10,17 @@ SHELL := bash .SUFFIXES: .SECONDARY: -COB_TO_EXTERNAL = $(COMPONENTSDIR)/cob-to-external.owl -COB_ANNOTATIONS = $(COMPONENTSDIR)/cob-annotations.owl -COB_EXAMPLES = $(COMPONENTSDIR)/cob-examples.owl +ANNOTATE_ONTOLOGY_METADATA := \ + --prefix "dcterms: http://purl.org/dc/terms/" \ + --language-annotation dcterms:title "Core Ontology for Biology and Biomedicine" en \ + --language-annotation dcterms:description "COB brings together key terms from a wide range of OBO projects to improve interoperability." en \ + --link-annotation dcterms:license https://creativecommons.org/publicdomain/zero/1.0/ .PHONY: prepare_release prepare_release: $(ASSETS) $(PATTERN_RELEASE_FILES) cob.tsv rsync -R $(RELEASE_ASSETS) cob.tsv $(RELEASEDIR) &&\ - rm -f $(CLEANFILES) &&\ - rm -f cob.tsv &&\ - echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab" + rm -f $(CLEANFILES) &&\ + echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab" .PHONY: prepare_cob_products prepare_cob_products: test @@ -36,88 +37,56 @@ products/: $(TMPDIR)/robot.jar: | $(TMPDIR) if [ $(ROBOT_DOWNLOAD) = true ]; then curl -L -o $@ https://build.obolibrary.io/job/ontodev/job/robot/job/master/lastSuccessfulBuild/artifact/bin/robot.jar; fi + ######################################## -# -- MAIN RELEASE PRODUCTS -- +# -- TEMPLATES -- ######################################## -# build main release product -REWIRE_PRECEDENCE = PR CHEBI -cob.ttl: components/cob-to-external.tsv cob-native.owl - sssom rewire -I xml -m $< $(patsubst %,--precedence %,$(REWIRE_PRECEDENCE)) cob-native.owl -o $@ - -cob.owl: cob.ttl - robot merge --include-annotations true -i $< -i ontology-metadata.owl \ - annotate --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ - --output $@.tmp.owl && mv $@.tmp.owl $@ -.PRECIOUS: cob.owl - -cob-native.owl: $(SRC) - $(ROBOT) remove --input $< --select imports --trim false \ - reason -r HERMIT \ - annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ - --output $@.tmp.owl && mv $@.tmp.owl $@ - -# base file is main cob plus linking axioms -#cob-base.owl: cob.owl $(COB_TO_EXTERNAL) -# $(ROBOT) merge $(patsubst %, -i %, $^) -o $@ - -$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) - $(ROBOT_RELEASE_IMPORT_MODE_BASE) \ - $(SHARED_ROBOT_COMMANDS) \ - annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ - --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ - --output $@.tmp.owl && mv $@.tmp.owl $@ - -cob-base-reasoned.owl: cob-base.owl - $(ROBOT) remove --input $< --select imports --trim false \ - reason -r HERMIT \ - annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ - --output $@.tmp.owl && mv $@.tmp.owl $@ - -cob-examples-reasoned.owl: cob-base.owl $(COB_EXAMPLES) - $(ROBOT) remove --input $< --select imports --trim false \ - merge $(patsubst %, -i %, $^) \ - reason -r HERMIT \ - annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ - --output $@.tmp.owl && mv $@.tmp.owl $@ +$(TMPDIR)/cob-%.tsv: $(SCRIPTSDIR)/split-cob-edit.py cob-edit.tsv + $^ $(TMPDIR) # TSV export (may depend on dev version of robot export) cob.tsv: cob.owl - $(ROBOT) export -i $< -c "ID|ID [LABEL]|definition|subClassOf [ID NAMED]|subClassOf [LABEL NAMED]|subClassOf [ID ANON]|subClassOf [LABEL ANON]" -e $@ -# $(ROBOT) export -i $< --entity-select NAMED -c "ID|ID [LABEL]|definition|subClassOf [ID]|subClassOf [LABEL]|subClassOf [ID ANON]|subClassOf [LABEL ANON]" -e $@ + $(ROBOT) export -i $< -c "ID|ID [LABEL]|definition|subClassOf [ID NAMED]|subClassOf [LABEL NAMED]|subClassOf [ID ANON]|subClassOf [LABEL ANON]" -e $@ -# -- BRIDGING AXIOMS TO OBO ROOTS -- -# -# the source file is cob-to-external.tsv -# -# OWL is generated from this -# -$(TMPDIR)/cob-to-external.sssom.owl: $(COMPONENTSDIR)/cob-to-external.tsv | $(TMPDIR) - sssom convert $< --output-format owl -o $@ +######################################## +# -- MAIN RELEASE PRODUCTS -- +######################################## -$(COB_TO_EXTERNAL): $(TMPDIR)/cob-to-external.sssom.owl - $(ROBOT) merge -i $< \ +$(ONT)-edit.owl: $(TMPDIR)/cob-root.tsv $(COMPONENTSDIR)/obsolete.tsv + $(ROBOT) template \ + $(foreach X,$(filter %.tsv,$^),--template $(X)) \ + reason -r HERMIT \ annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ - convert -f owl -o $@ + $(ANNOTATE_ONTOLOGY_METADATA) \ + --output $@.tmp.owl && mv $@.tmp.owl $@ -$(TMPDIR)/cob-annotations.ttl: $(COB_TO_EXTERNAL) $(SPARQLDIR)/external-links.rq | $(TMPDIR) - $(ROBOT) query --input $< --query $(word 2,$^) $@ +# COB "Full" +$(ONT).owl: $(TMPDIR)/cob-full.tsv $(COMPONENTSDIR)/obsolete.tsv + $(ROBOT) template \ + $(foreach X,$(filter %.tsv,$^),--template $(X)) \ + reason -r HERMIT \ + annotate --ontology-iri $(ONTBASE).owl $(ANNOTATE_ONTOLOGY_VERSION) \ + $(ANNOTATE_ONTOLOGY_METADATA) \ + --output $@.tmp.owl && mv $@.tmp.owl $@ -$(COB_ANNOTATIONS): $(TMPDIR)/cob-annotations.ttl - $(ROBOT) annotate --input $< \ - --ontology-iri "http://purl.obolibrary.org/obo/cob/$@" \ - --annotation owl:versionInfo $(TODAY) \ - --output $@ +$(ONT)-base.owl: $(ONT).owl $(TMPDIR)/cob-base.tsv $(COMPONENTSDIR)/obsolete.tsv + $(ROBOT) template --input $< \ + $(foreach X,$(filter %.tsv,$^),--template $(X)) \ + annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ + --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + $(ANNOTATE_ONTOLOGY_METADATA) \ + --output $@.tmp.owl && mv $@.tmp.owl $@ -# This is the custom import: removing all COB related axioms from RO, but otherwise pulling in logical dependencies. +$(ONT)-root.owl: $(TMPDIR)/cob-root.tsv $(COMPONENTSDIR)/obsolete.tsv + $(ROBOT) template \ + $(foreach X,$(filter %.tsv,$^),--template $(X)) \ + reason -r HERMIT \ + annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + $(ANNOTATE_ONTOLOGY_METADATA) \ + --output $@.tmp.owl && mv $@.tmp.owl $@ -$(IMPORTDIR)/ro_import.owl: $(MIRRORDIR)/ro.owl $(IMPORTDIR)/ro_terms_combined.txt - if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ - extract -T $(IMPORTDIR)/ro_terms_combined.txt --copy-ontology-annotations true --force true --individuals exclude --method BOT \ - remove --base-iri http://purl.obolibrary.org/obo/COB_ --axioms internal --preserve-structure false --trim false \ - query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ - $(ANNOTATE_CONVERT_FILE); fi ######################################## # -- TESTING -- @@ -151,7 +120,7 @@ cob_test: main_test itest # main test: should be run via CI on every PR # this tests COB's internal consistency .PHONY: main_test -main_test: $(REPORTDIR)/$(SRC)-obo-report.tsv cob.owl cob-base-reasoned.owl cob-examples-reasoned.owl +main_test: $(REPORTDIR)/$(SRC)-obo-report.tsv $(RELEASEDIR)/cob-root.owl test: main_test # integration tests: for now, run these on commmand line diff --git a/src/ontology/components/cob-annotations.owl b/src/ontology/components/cob-annotations.owl deleted file mode 100644 index 315e89c..0000000 --- a/src/ontology/components/cob-annotations.owl +++ /dev/null @@ -1,226 +0,0 @@ - - - - 2024-09-20 - - - - - - - - - - - - - based on - - - - - - - - http://purl.obolibrary.org/obo/PATO_0000125 - - - http://purl.obolibrary.org/obo/PATO_0002193 - - - http://purl.obolibrary.org/obo/BFO_0000040 - - - http://purl.obolibrary.org/obo/CHEBI_36342 - - - http://purl.obolibrary.org/obo/CHEBI_24636 - - - http://purl.obolibrary.org/obo/CHEBI_30222 - - - http://purl.obolibrary.org/obo/CHEBI_10545 - - - http://purl.obolibrary.org/obo/CHEBI_33252 - - - http://purl.obolibrary.org/obo/CHEBI_16541 - http://purl.obolibrary.org/obo/PR_000000001 - - - http://purl.obolibrary.org/obo/CL_0000000 - - - http://purl.obolibrary.org/obo/CL_0000003 - - - http://purl.obolibrary.org/obo/CL_0001034 - - - http://purl.obolibrary.org/obo/CARO_0001008 - - - http://purl.obolibrary.org/obo/OBI_0100026 - - - http://purl.obolibrary.org/obo/OBI_0000245 - - - http://purl.obolibrary.org/obo/OBI_0000047 - - - http://purl.obolibrary.org/obo/BFO_0000141 - - - http://purl.obolibrary.org/obo/BFO_0000017 - - - http://purl.obolibrary.org/obo/BFO_0000015 - - - http://purl.obolibrary.org/obo/OBI_0000011 - - - http://purl.obolibrary.org/obo/GO_0008150 - - - http://purl.obolibrary.org/obo/GO_0003674 - - - http://purl.obolibrary.org/obo/CHEBI_24867 - - - http://purl.obolibrary.org/obo/CHEBI_33250 - - - http://purl.obolibrary.org/obo/CHEBI_33696 - - - http://purl.obolibrary.org/obo/PCO_0000000 - - - http://purl.obolibrary.org/obo/BFO_0000029 - - - http://purl.obolibrary.org/obo/OBI_0001909 - - - http://purl.obolibrary.org/obo/IAO_0000030 - - - http://purl.obolibrary.org/obo/OGMS_0000073 - - - http://purl.obolibrary.org/obo/OGMS_0000014 - - - http://purl.obolibrary.org/obo/OGMS_0000063 - - - http://purl.obolibrary.org/obo/ENVO_02500000 - - - http://purl.obolibrary.org/obo/MOP_0000543 - - - http://purl.obolibrary.org/obo/ENVO_01001110 - - - http://purl.obolibrary.org/obo/ENVO_01000813 - - - http://purl.obolibrary.org/obo/IAO_0000033 - - - http://purl.obolibrary.org/obo/GO_0032991 - - - http://purl.obolibrary.org/obo/IAO_0000005 - - - http://purl.obolibrary.org/obo/IAO_0000104 - - - http://purl.obolibrary.org/obo/DRON_00000005 - - - http://purl.obolibrary.org/obo/IAO_0000310 - - - http://purl.obolibrary.org/obo/IAO_0000027 - - - http://purl.obolibrary.org/obo/GO_0005634 - - - http://purl.obolibrary.org/obo/OBI_0000070 - - - http://purl.obolibrary.org/obo/OBI_0200000 - - - http://purl.obolibrary.org/obo/OBI_0000066 - - - http://purl.obolibrary.org/obo/OBI_0000094 - - - http://purl.obolibrary.org/obo/BFO_0000016 - - - http://purl.obolibrary.org/obo/BFO_0000034 - - - http://purl.obolibrary.org/obo/OBI_0000260 - - - http://purl.obolibrary.org/obo/BFO_0000023 - - - http://purl.obolibrary.org/obo/CARO_0010004 - http://purl.obolibrary.org/obo/NCBITaxon_131567 - - - http://purl.obolibrary.org/obo/OBI_0000067 - - - http://purl.obolibrary.org/obo/IAO_0000015 - - - http://purl.obolibrary.org/obo/IAO_0000109 - - - http://purl.obolibrary.org/obo/SEPIO_0000048 - - - http://purl.obolibrary.org/obo/BFO_0000020 - http://purl.obolibrary.org/obo/PATO_0000001 - - - - - - - diff --git a/src/ontology/components/cob-examples.owl b/src/ontology/components/cob-examples.owl deleted file mode 100644 index 5eee0ae..0000000 --- a/src/ontology/components/cob-examples.owl +++ /dev/null @@ -1,552 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - Example subclass of 'nucleotide' - guanine - - - - - - - - - Example subclass of 'nucleotide' - adenine - - - - - - - - - Example subclass of 'molecular entity' - salicylic acid - - - - - - - - - deoxyribonucleic acid - - - - - - - - - thymidine - - - - - - - - - - - - - - 8 - - - - - - oxygen atom - - - - - - - - - - - - - - - - - - - - - - - - Example subclass of 'atom' - nickel atom (uncharged) - - - - - - - - - - - InChI=1S/O2/c1-2/q+2 - - - - dioxygen(2+) - - - - - - - - - - - - - - - - - - 2 - - - diatomic oxygen - - - - - - - - - nucleoside - - - - - - - - - - - - - - - - - - - - polyatomic ion - - - - - - - - - Example subclass of 'molecular entity' - nucleotide - - - - - - - - - - - - - - - double-stranded DNA - https://github.com/OBOFoundry/COB/issues/103 - - - - - - - - - tritiated thymidine - - - - - - - - - - - - - - - - - - - - Example subclass of 'atom' - nickel ion - - - - - - - - - Example subclass of 'nucleic acid polymer' - RNA polymer - - - - - - - - - Example subclass of 'nucleic acid polymer' - DNA polyanion - - - - - - - - - single-stranded DNA - - - - - - - - - TODO: add has_neutron_number=34 - nickel 58 - - - - - - - - - - - - - - - - - - - - diatomic oxygen ion - - - - - - - - - - - - - - - - - - - - - - - - uncharged diatomic oxygen - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >1, where the parts are not transitively covalently connected - - - - - - - - - Example subclass of 'geophysical entity' - mountain - - - - - - - - - Example subclass of 'ecosystem' - tidal pool - - - - - - - - - - - - - - - chromosome - - - - - - - - - - - min 2 - - - - - - - - - Example subclass of 'cellular membrane' - plasma membrane - - - - - - - - - Example subclass of 'cellular organism' - human - - - - - - - - - Example subclass of 'planned process' - informed consent process - - - - - - - - - Example subclass of 'processed material entity' - device - - - - - - - - - Example subclass of 'processed material entity' - reagent - - - - - - - - - Example subclass of 'plan specification' - study design - - - - - - - - - Example subclass of 'gross anatomical part' - lung - - - - - - - - - Example subclass of 'processed material entity' - vaccine - - - - - - - - - - - - - - 28 - - - - - - Example subclass of 'atom' - nickel atom - - - - - - - - - Example subclass of 'gross anatomical part' - tumor - - - - - - - - - Example subclass of 'protein' - glycosylated protein - - - - - - - - - Example subclass of 'processed material entity' - drug product - - - - - - - diff --git a/src/ontology/components/cob-to-external.owl b/src/ontology/components/cob-to-external.owl deleted file mode 100644 index 5089e3a..0000000 --- a/src/ontology/components/cob-to-external.owl +++ /dev/null @@ -1,2338 +0,0 @@ - - - - - https://creativecommons.org/publicdomain/zero/1.0/ - 2024-09-18 - http://purl.obolibrary.org/obo/cob/components/cob-to-external.tsv - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - part of - part of - - - - - - - - - - - - - - - has part - has part - - - - - - - - - - - - - - - realized in - realized in - - - - - - - - - - - - - - - realizes - realizes - - - - - - - - - - - - - - - occurs in - occurs in - - - - - - - - - - - - - - - contains process - contains process - - - - - - - - - - - - - - - is concretized as - is concretized as - - - - - - - - - - - - - - - topObjectProperty - executed by - - - - - - - - - - - - - - - inheres in - characteristic of - - - - - - - - - - - - - - - participates in - participates in - - - - - - - - - - - - - - - is_specified_input_of - is specified input of - - - - - - - - - - - - - - - is_specified_output_of - is specified output of - - - - - - - - - - - - - - - - - - - - - - - - - - - has_specified_input - has specified input - - - - - - - - - - - - - - - has_specified_output - has specified output - - - - - - - - - - - - - - - - - - - - - has participant - has participant - - - - - - - - - - - - - - - - - - - - - - - - - - - enabled by - enabled by - - - - - - - - - - - - - - - concretizes - concretizes - - - - - - - - - - - - - - - executes - executes - - - - - - - - - - - - - - - - - - - - - bearer of - has characteristic - - - - - - - - - - - - - - - is about - is about - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - topDataProperty - has quantity - - - - - - - - - - - - - - - - - - - - process - process - - - - - - - - - - - - - - - disposition - disposition - - - - - - - - - - - - - - - realizable entity - realizable - - - - - - - - - - - - - - - specifically dependent continuant - characteristic - - - - - - - - - - - - - - - role - role - - - - - - - - - - - - - - - site - site - - - - - - - - - - - - - - - function - function - - - - - - - - - - - - - - - material entity - material entity - - - - - - - - - - - - - - - immaterial entity - immaterial entity - - - - - - - - - - - - - - - gross anatomical part - gross anatomical part - - - - - - - - - - - - - - - cellular organism - cellular organism - - - - - - - - - - - - - - - electron - electron - - - - - - - - - - - - - - - protein polypeptide chain - protein - - - - - - - - - - - - - - - proton - proton - - - - - - - - - - - - - - - monoatomic ion - monoatomic ion - - - - - - - - - - - - - - - neutron - neutron - - - - - - - - - - - - - - - atom - uncharged atom - - - - - - - - - - - - - - - atomic nucleus - atomic nucleus - - - - - - - - - - - - - - - nucleic acid - nucleic acid polymer - - - - - - - - - - - - - - - subatomic particle - subatomic particle - - - - - - - - - - - - - - - characteristic - role - - - - - - - - - - - - - - - cell - cell - - - - - - - - - - - - - - - native cell - native cell - - - - - - - - - - - - - - - cell in vitro - cell in vitro - - - - - - - - - - - - - - - mass - mass - - - - - - - - - - - - - - - electric - charge - - - - - - - - - - - - - - - owl:Thing - elementary charge - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - protein - protein - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - owl:Thing - subcellular structure - - - - - - - - - - - - - - - - - - - - - organism - organism - - - - - - - - - - - - - - - organization - organization - - - - - - - - - - - - - - - processed material - processed material entity - - - - - - - - - - - - - - - - - - - - - owl:Thing - geographical location - - - - - - - - - - - - - - - - - - - - - - - - - - - planned process - completely executed planned process - - - - - - - - - - - - - - - biological process - biological process - - - - - - - - - - - - - - - molecular function - gene product or complex activity - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - collection of organisms - collection of organisms - - - - - - - - - - - - - - - - - - - - - - - - - - - conclusion based on data - conclusion based on data - - - - - - - - - - - - - - - information content entity - information - - - - - - - - - - - - - - - diagnosis - disease diagnosis - - - - - - - - - - - - - - - clinical finding - phenotypic finding - - - - - - - - - - - - - - - disease course - disease course - - - - - - - - - - - - - - - environmental system process - environmental process - - - - - - - - - - - - - - - molecular process - physico-chemical process - - - - - - - - - - - - - - - ecosystem - ecosystem - - - - - - - - - - - - - - - astronomical body part - geophysical entity - - - - - - - - - - - - - - - directive information entity - directive information entity - - - - - - - - - - - - - - - owl:Thing - gene product - - - - - - - - - - - - - - - protein-containing complex - protein-containing macromolecular complex - - - - - - - - - - - - - - - objective specification - objective specification - - - - - - - - - - - - - - - plan specification - plan specification - - - - - - - - - - - - - - - owl:Thing - complex of molecular entities - - - - - - - - - - - - - - - - drug product - drug product - - - - - - - drug - drug product - - - - - - - - - - - - - - - document - document - - - - - - - - - - - - - - - data item - data item - - - - - - - - - - - - - - - nucleus - cell nucleus - - - - - - - - - - - - - - - assay - assay - - - - - - - - - - - - - - - data transformation - data transformation - - - - - - - - - - - - - - - investigation - investigation - - - - - - - - - - - - - - - material processing - material processing - - - - - - - - - - - - - - - - - - - - - - - - - - - plan - plan - - - - - - - - - - - - - - - - - - - - - owl:Thing - cellular membrane - - - - - - - - - - - - - - - cellular organisms - cellular organism - - - - - - - - - - - - - - - evaluant role - evaluant role - - - - - - - - - - - - - - - information carrier - information representation - - - - - - - - - - - - - - - measurement datum - measurement datum - - - - - - - - - - - - - - - agent role - agent role - - - - - - - - - - - - - - - quality - characteristic - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - geophysical entity - geographical entity - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - organism - Viruses - - - - - - - - - - - - - - - organism - cellular organisms - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agent role - investigation agent role - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cellular organism - whole plant - - - - - - - - - - - - - - - cell - plant cell - - - - - - - - - - - - - - - immaterial anatomical entity - plant anatomical space - - - - - - - - - - - - - - - native cell - native plant cell - - - - - - - - - - - - - - - - - - - - - - - - - - - material entity - sequence_feature - - - - - - - - - - - - - - - characteristic - sequence_attribute - - - - - - - - - - - - - - - material entity - sequence_variant - - - - - - - - - - - - - - - material entity - sequence_collection - - - - - - - - - - - - - - - immaterial anatomical entity - immaterial anatomical entity - - - - - - - - - - - - - - - cellular organism - multicellular organism - - - - - - - - - - - - - - - gross anatomical part - multicellular anatomical structure - - - - - - - - - - - - - - - native cell - xenopus cell - - - - - - - - - - - - - - - native cell - zebrafish cell - - - - - - - - - - - - - - - atom - atom - - - - - - - - - - - molecular entity - molecular entity - - - - - - - molecule - molecular entity - - - - - - - diff --git a/src/ontology/components/cob-to-external.tsv b/src/ontology/components/cob-to-external.tsv deleted file mode 100644 index 9b39a6c..0000000 --- a/src/ontology/components/cob-to-external.tsv +++ /dev/null @@ -1,142 +0,0 @@ -#license: "https://creativecommons.org/publicdomain/zero/1.0/" -#mapping_set_id: "http://purl.obolibrary.org/obo/cob/components/cob-to-external.tsv" -#curie_map: -# rdfs: "http://www.w3.org/2000/01/rdf-schema#" -# skos: "http://www.w3.org/2004/02/skos/core#" -# owl: "http://www.w3.org/2002/07/owl#" -# BFO: "http://purl.obolibrary.org/obo/BFO_" -# CARO: "http://purl.obolibrary.org/obo/CARO_" -# CHEBI: "http://purl.obolibrary.org/obo/CHEBI_" -# CL: "http://purl.obolibrary.org/obo/CL_" -# COB: "http://purl.obolibrary.org/obo/COB_" -# ENVO: "http://purl.obolibrary.org/obo/ENVO_" -# GEO: "http://purl.obolibrary.org/obo/GEO_" -# GO: "http://purl.obolibrary.org/obo/GO_" -# IAO: "http://purl.obolibrary.org/obo/IAO_" -# MOP: "http://purl.obolibrary.org/obo/MOP_" -# NCBITaxon: "http://purl.obolibrary.org/obo/NCBITaxon_" -# OBI: "http://purl.obolibrary.org/obo/OBI_" -# OGMS: "http://purl.obolibrary.org/obo/OGMS_" -# PATO: "http://purl.obolibrary.org/obo/PATO_" -# PCO: "http://purl.obolibrary.org/obo/PCO_" -# PO: "http://purl.obolibrary.org/obo/PO_" -# PR: "http://purl.obolibrary.org/obo/PR_" -# SO: "http://purl.obolibrary.org/obo/SO_" -# RO: "http://purl.obolibrary.org/obo/RO_" -# UBERON: "http://purl.obolibrary.org/obo/UBERON_" -# XAO: "http://purl.obolibrary.org/obo/XAO_" -# ZFA: "http://purl.obolibrary.org/obo/ZFA_" -# SEPIO: "http://purl.obolibrary.org/obo/SEPIO_" -# STATO: "http://purl.obolibrary.org/obo/STATO_" -# DRON: "http://purl.obolibrary.org/obo/DRON_" -subject_id subject_label predicate_id object_id object_label notes mapping_justification -COB:0000003 mass owl:equivalentClass PATO:0000125 mass . semapv:ManualMappingCuration -COB:0000004 charge owl:equivalentClass PATO:0002193 electric . semapv:ManualMappingCuration -COB:0000005 elementary charge rdfs:subClassOf owl:Thing owl:Thing Making ticket in PATO tracker semapv:ManualMappingCuration -COB:0000006 material entity owl:equivalentClass BFO:0000040 material entity . semapv:ManualMappingCuration -COB:0000006 material entity sssom:superClassOf SO:0000110 sequence_feature . semapv:ManualMappingCuration -COB:0000006 material entity sssom:superClassOf SO:0001060 sequence_variant . semapv:ManualMappingCuration -COB:0000006 material entity sssom:superClassOf SO:0001260 sequence_collection . semapv:ManualMappingCuration -COB:0000007 subatomic particle owl:equivalentClass CHEBI:36342 subatomic particle . semapv:ManualMappingCuration -COB:0000008 proton owl:equivalentClass CHEBI:24636 proton . semapv:ManualMappingCuration -COB:0000009 neutron owl:equivalentClass CHEBI:30222 neutron . semapv:ManualMappingCuration -COB:0000010 electron owl:equivalentClass CHEBI:10545 electron . semapv:ManualMappingCuration -COB:0000011 atom skos:closeMatch CHEBI:33250 atom . semapv:ManualMappingCuration -COB:0000012 atomic nucleus owl:equivalentClass CHEBI:33252 atomic nucleus . semapv:ManualMappingCuration -COB:0000013 molecular entity skos:closeMatch CHEBI:23367 molecular entity No exact match in CHEBI semapv:ManualMappingCuration -COB:0000013 molecular entity skos:closeMatch CHEBI:25367 molecule This is electrically neutral in CHEBI but in COB it is generic. We should make it union of molecule and polyatomic ion semapv:ManualMappingCuration -COB:0000015 protein owl:equivalentClass CHEBI:16541 protein polypeptide chain . semapv:ManualMappingCuration -COB:0000015 protein owl:equivalentClass PR:000000001 protein . semapv:ManualMappingCuration -COB:0000017 cell owl:equivalentClass CL:0000000 cell . semapv:ManualMappingCuration -COB:0000017 cell sssom:superClassOf PO:0009002 plant cell . semapv:ManualMappingCuration -COB:0000018 native cell owl:equivalentClass CL:0000003 native cell . semapv:ManualMappingCuration -COB:0000018 native cell sssom:superClassOf XAO:0003012 xenopus cell . semapv:ManualMappingCuration -COB:0000018 native cell sssom:superClassOf ZFA:0009000 zebrafish cell . semapv:ManualMappingCuration -COB:0000018 native cell sssom:superClassOf PO:0025606 native plant cell . semapv:ManualMappingCuration -COB:0000019 cell in vitro owl:equivalentClass CL:0001034 cell in vitro . semapv:ManualMappingCuration -COB:0000020 subcellular structure rdfs:subClassOf owl:Thing owl:Thing Chris will follow up semapv:ManualMappingCuration -COB:0000021 gross anatomical part owl:equivalentClass CARO:0001008 gross anatomical part . semapv:ManualMappingCuration -COB:0000021 gross anatomical part sssom:superClassOf UBERON:0010000 multicellular anatomical structure . semapv:ManualMappingCuration -COB:0000022 organism sssom:superClassOf NCBITaxon:10239 Viruses . semapv:ManualMappingCuration -COB:0000022 organism sssom:superClassOf NCBITaxon:131567 cellular organisms . semapv:ManualMappingCuration -COB:0000022 organism owl:equivalentClass OBI:0100026 organism . semapv:ManualMappingCuration -COB:0000025 organization owl:equivalentClass OBI:0000245 organization . semapv:ManualMappingCuration -COB:0000026 processed material entity owl:equivalentClass OBI:0000047 processed material . semapv:ManualMappingCuration -COB:0000031 immaterial entity owl:equivalentClass BFO:0000141 immaterial entity . semapv:ManualMappingCuration -COB:0000032 geographical location rdfs:subClassOf owl:Thing owl:Thing semapv:ManualMappingCuration -COB:0000033 realizable owl:equivalentClass BFO:0000017 realizable entity . semapv:ManualMappingCuration -COB:0000034 process owl:equivalentClass BFO:0000015 process . semapv:ManualMappingCuration -COB:0000035 completely executed planned process owl:equivalentClass OBI:0000011 planned process . semapv:ManualMappingCuration -COB:0000037 biological process owl:equivalentClass GO:0008150 biological process . semapv:ManualMappingCuration -COB:0000038 gene product or complex activity owl:equivalentClass GO:0003674 molecular function . semapv:ManualMappingCuration -COB:0000042 monoatomic ion owl:equivalentClass CHEBI:24867 monoatomic ion . semapv:ManualMappingCuration -COB:0000043 uncharged atom owl:equivalentClass CHEBI:33250 atom "we think our uncharged atom is actually chebi:atom, to be discussed with CHEBI people" semapv:ManualMappingCuration -COB:0000049 nucleic acid polymer owl:equivalentClass CHEBI:33696 nucleic acid follow up with CHEBI on nomenclature semapv:ManualMappingCuration -COB:0000055 collection of organisms owl:equivalentClass PCO:0000000 collection of organisms . semapv:ManualMappingCuration -COB:0000056 immaterial anatomical entity sssom:superClassOf UBERON:0000466 immaterial anatomical entity . semapv:ManualMappingCuration -COB:0000056 immaterial anatomical entity sssom:superClassOf PO:0025117 plant anatomical space . semapv:ManualMappingCuration -COB:0000057 site owl:equivalentClass BFO:0000029 site . semapv:ManualMappingCuration -COB:0000058 conclusion based on data owl:equivalentClass OBI:0001909 conclusion based on data . semapv:ManualMappingCuration -COB:0000061 information owl:equivalentClass IAO:0000030 information content entity . semapv:ManualMappingCuration -COB:0000062 disease diagnosis owl:equivalentClass OGMS:0000073 diagnosis . semapv:ManualMappingCuration -COB:0000063 phenotypic finding owl:equivalentClass OGMS:0000014 clinical finding . semapv:ManualMappingCuration -COB:0000064 disease course owl:equivalentClass OGMS:0000063 disease course . semapv:ManualMappingCuration -COB:0000065 environmental process owl:equivalentClass ENVO:02500000 environmental system process . semapv:ManualMappingCuration -COB:0000066 physico-chemical process owl:equivalentClass MOP:0000543 molecular process "we are not sure if these are equivalent, or if we even want to retain this. Follow up with Colin" semapv:ManualMappingCuration -COB:0000067 ecosystem owl:equivalentClass ENVO:01001110 ecosystem . semapv:ManualMappingCuration -COB:0000068 geophysical entity owl:equivalentClass ENVO:01000813 astronomical body part . semapv:ManualMappingCuration -COB:0000068 geophysical entity sssom:superClassOf GEO:000000370 geographical entity See https://github.com/OBOFoundry/COB/issues/91 semapv:ManualMappingCuration -COB:0000069 directive information entity owl:equivalentClass IAO:0000033 directive information entity . semapv:ManualMappingCuration -COB:0000073 gene product rdfs:subClassOf owl:Thing owl:Thing semapv:ManualMappingCuration -COB:0000075 protein-containing macromolecular complex owl:equivalentClass GO:0032991 protein-containing complex . semapv:ManualMappingCuration -COB:0000076 objective specification owl:equivalentClass IAO:0000005 objective specification . semapv:ManualMappingCuration -COB:0000079 plan specification owl:equivalentClass IAO:0000104 plan specification . semapv:ManualMappingCuration -COB:0000080 complex of molecular entities rdfs:subClassOf owl:Thing owl:Thing semapv:ManualMappingCuration -COB:0000088 drug product owl:equivalentClass DRON:00000005 drug product we currently use a different text definition but we believe they do not contradict semapv:ManualMappingCuration -COB:0000088 drug product rdfs:seeAlso CHEBI:23888 drug These can't be equivalent because COB drug product is a material entity, and ChEBI's drug is a role. See issue #140 for more information. semapv:ManualMappingCuration -COB:0000101 document owl:equivalentClass IAO:0000310 document . semapv:ManualMappingCuration -COB:0000102 data item owl:equivalentClass IAO:0000027 data item . semapv:ManualMappingCuration -COB:0000103 cell nucleus owl:equivalentClass GO:0005634 nucleus . semapv:ManualMappingCuration -COB:0000107 assay owl:equivalentClass OBI:0000070 assay . semapv:ManualMappingCuration -COB:0000108 data transformation owl:equivalentClass OBI:0200000 data transformation . semapv:ManualMappingCuration -COB:0000109 investigation owl:equivalentClass OBI:0000066 investigation . semapv:ManualMappingCuration -COB:0000110 material processing owl:equivalentClass OBI:0000094 material processing . semapv:ManualMappingCuration -COB:0000111 disposition owl:equivalentClass BFO:0000016 disposition . semapv:ManualMappingCuration -COB:0000112 function owl:equivalentClass BFO:0000034 function . semapv:ManualMappingCuration -COB:0000113 plan owl:equivalentClass OBI:0000260 plan . semapv:ManualMappingCuration -COB:0000114 role owl:equivalentClass BFO:0000023 role . semapv:ManualMappingCuration -COB:0000502 characteristic sssom:superClassOf CHEBI:50906 role The ChEBI notion of a role doesn't strictly follow the BFO sense of either being a role or disposition, meaning that it's hard, if not impossible, to impose BFO order to this branch of ChEBI. See issue #173 semapv:ManualMappingCuration -COB:0000116 cellular membrane rdfs:subClassOf owl:Thing owl:Thing semapv:ManualMappingCuration -COB:0000118 cellular organism owl:equivalentClass NCBITaxon:131567 cellular organisms . semapv:ManualMappingCuration -COB:0000118 cellular organism owl:equivalentClass CARO:0010004 cellular organism . semapv:ManualMappingCuration -COB:0000118 cellular organism sssom:superClassOf UBERON:0000468 multicellular organism . semapv:ManualMappingCuration -COB:0000118 cellular organism sssom:superClassOf PO:0000003 whole plant . semapv:ManualMappingCuration -COB:0000119 evaluant role owl:equivalentClass OBI:0000067 evaluant role . semapv:ManualMappingCuration -COB:0000120 information representation owl:equivalentClass IAO:0000015 information carrier . semapv:ManualMappingCuration -COB:0000121 measurement datum owl:equivalentClass IAO:0000109 measurement datum . semapv:ManualMappingCuration -COB:0000036 contains process owl:equivalentProperty BFO:0000067 contains process . semapv:ManualMappingCuration -COB:0000047 has part owl:equivalentProperty BFO:0000051 has part . semapv:ManualMappingCuration -COB:0000070 has participant owl:equivalentProperty RO:0000057 has participant . semapv:ManualMappingCuration -COB:0000071 occurs in owl:equivalentProperty BFO:0000066 occurs in . semapv:ManualMappingCuration -COB:0000072 part of owl:equivalentProperty BFO:0000050 part of . semapv:ManualMappingCuration -COB:0000074 enabled by owl:equivalentProperty RO:0002333 enabled by . semapv:ManualMappingCuration -COB:0000502 characteristic owl:equivalentClass PATO:0000001 quality https://github.com/OBOFoundry/COB/issues/124 semapv:ManualMappingCuration -COB:0000502 characteristic owl:equivalentClass BFO:0000020 specifically dependent continuant may be revised to be narrower semapv:ManualMappingCuration -COB:0000502 characteristic sssom:superClassOf SO:0000400 sequence_attribute . semapv:ManualMappingCuration -COB:0000511 has quantity rdfs:subPropertyOf owl:topDataProperty topDataProperty . semapv:ManualMappingCuration -COB:0000512 has characteristic owl:equivalentProperty RO:0000053 bearer of . semapv:ManualMappingCuration -COB:0000002 is concretized as owl:equivalentProperty RO:0000058 is concretized as . semapv:ManualMappingCuration -COB:0000078 concretizes owl:equivalentProperty RO:0000059 concretizes . semapv:ManualMappingCuration -COB:0000086 executes owl:equivalentProperty STATO:0000102 executes . semapv:ManualMappingCuration -COB:0000016 executed by rdfs:subPropertyOf owl:topObjectProperty topObjectProperty "There is no inverse for 'executes' STATO, only in COB." semapv:ManualMappingCuration -COB:0000023 characteristic of owl:equivalentProperty RO:0000052 inheres in "In RO, 'inheres in' is the inverse of 'bearer of'." semapv:ManualMappingCuration -COB:0000024 participates in owl:equivalentProperty RO:0000056 participates in . semapv:ManualMappingCuration -COB:0000027 is specified input of owl:equivalentProperty OBI:0000295 is_specified_input_of . semapv:ManualMappingCuration -COB:0000028 is specified output of owl:equivalentProperty OBI:0000312 is_specified_output_of . semapv:ManualMappingCuration -COB:0000039 has specified input owl:equivalentProperty OBI:0000293 has_specified_input . semapv:ManualMappingCuration -COB:0000040 has specified output owl:equivalentProperty OBI:0000299 has_specified_output . semapv:ManualMappingCuration -COB:0000087 realizes owl:equivalentProperty BFO:0000055 realizes . semapv:ManualMappingCuration -COB:0000029 realized in owl:equivalentProperty BFO:0000054 realized in . semapv:ManualMappingCuration -COB:0000513 is about owl:equivalentProperty IAO:0000136 is about There is no inverse for 'is about' in IAO. semapv:ManualMappingCuration -COB:0000123 agent role owl:equivalentClass SEPIO:0000048 agent role semapv:ManualMappingCuration -COB:0000123 agent role sssom:superClassOf OBI:0000202 investigation agent role semapv:ManualMappingCuration diff --git a/src/ontology/components/obsolete.tsv b/src/ontology/components/obsolete.tsv new file mode 100644 index 0000000..6d1a6b6 --- /dev/null +++ b/src/ontology/components/obsolete.tsv @@ -0,0 +1,11 @@ +Ontology ID Label Type Definition Deprecated Term Replaced By +ID LABEL TYPE A IAO:0000115 AT owl:deprecated^^xsd:boolean AI IAO:0100001 +COB:0000005 obsolete elementary charge owl:Class true +COB:0000014 obsolete macromolecular entity owl:Class true +COB:0000020 obsolete subcellular structure owl:Class true GO:0110165 +COB:0000032 obsolete geographical location owl:Class true +COB:0000056 obsolete immaterial anatomical entity owl:Class true UBERON:0000466 +COB:0000073 obsolete gene product owl:Class true +COB:0000077 obsolete action specification owl:Class true IAO:0000007 +COB:0000116 obsolete cellular membrane owl:Class true +COB:0000122 obsolete physical information carrier owl:Class true diff --git a/src/scripts/split-cob-edit.py b/src/scripts/split-cob-edit.py new file mode 100755 index 0000000..4b80409 --- /dev/null +++ b/src/scripts/split-cob-edit.py @@ -0,0 +1,98 @@ +#!/usr/bin/env python3 +# +# Split the cob-edit.tsv file into three ROBOT templates: +# cob-base.tsv cob-full.tsv cob-root.tsv + +import argparse +import csv +import os +import re + + +def initialize_tsv(output_dir, filename, fieldnames, robot_row): + '''Initialize and return a DictWriter for a ROBOT template.''' + path = os.path.join(output_dir, filename) + path_fh = open(path, 'w') + writer = csv.DictWriter(path_fh, fieldnames, delimiter='\t', lineterminator='\n', extrasaction='ignore') + writer.writeheader() + writer.writerow(robot_row) + return writer + + +def split(input_path, output_dir): + '''Split the COB term template into base, full, and root templates.''' + header_row = None + robot_row, terms, replacements = {}, {}, {} + + with open(input_path) as f: + rows = csv.DictReader(f, delimiter='\t') + for row in rows: + if not header_row: + header_row = list(row.keys()) + id = row['Ontology ID'].strip() + if id == '': + continue + if id == 'ID': + robot_row = row + continue + + # Handle the Replacement columns + # by collecting a dictionary of replacements. + replacement_id = row['Replacement ID'].strip() + replacement_label = row['Replacement Label'].strip() + if replacement_label and replacement_label != '': + # removed exception for non-base IDs... TBD if needed/wanted + replacements[row['Label'].strip()] = { + 'ID': id, + 'Replacement Label': replacement_label, + 'Replacement ID': replacement_id, + } + # Otherwise just add this row to 'terms'. + else: + terms[id] = row + + ignore = [ + 'COB Module', 'COB Module Reason', + 'Replacement ID', 'Replacement Label', + 'Comment' + ] + fieldnames = [x for x in header_row if x not in ignore] + + # Apply replacements to the axioms in all the logical columns + axiom_cols = [ + 'Parent Class', 'Subclass Axiom', 'Equivalent Class Axiom', + 'Disjoint Class', 'Parent Property', 'Domain', 'Range', + 'Inverse Property' + ] + for id, row in terms.items(): + for repl_label, repl_dict in replacements.items(): + for col in axiom_cols: + if col not in row: + continue + row[col] = re.sub(repl_label, repl_dict['Replacement Label'], row[col]) + + base_writer = initialize_tsv(output_dir, 'cob-base.tsv', fieldnames, robot_row) + full_writer = initialize_tsv(output_dir, 'cob-full.tsv', fieldnames, robot_row) + root_writer = initialize_tsv(output_dir, 'cob-root.tsv', fieldnames, robot_row) + + for id, row in terms.items(): + module = row['COB Module'].strip() + if module == 'BASE': + base_writer.writerow(row) + if module not in ['', 'ROOT']: + full_writer.writerow(row) + if module != '': + root_writer.writerow(row) + + +def main(): + parser = argparse.ArgumentParser(description='Split the main COB term template into multiple module templates') + parser.add_argument('input', type=str, help='The input COB term template') + parser.add_argument('outdir', type=str, help='The output directory') + args = parser.parse_args() + + split(args.input, args.outdir) + + +if __name__ == '__main__': + main()