From 882bfd814f936809b7c963d36e14acb357e0c815 Mon Sep 17 00:00:00 2001 From: jamesaoverton Date: Fri, 20 Sep 2024 13:54:53 +0000 Subject: [PATCH] Update release files --- cob-base-reasoned.owl | 270 ++++++++++------- cob-base.owl | 252 ++++++++++------ cob-examples-reasoned.owl | 265 ++++++++++------- cob-full.owl | 150 +++++----- cob-native.owl | 154 +++++----- cob.owl | 314 ++++++++++---------- cob.tsv | 28 +- src/ontology/components/cob-annotations.owl | 211 ++++++++++++- 8 files changed, 995 insertions(+), 649 deletions(-) diff --git a/cob-base-reasoned.owl b/cob-base-reasoned.owl index 10419da..04ad068 100644 --- a/cob-base-reasoned.owl +++ b/cob-base-reasoned.owl @@ -12,12 +12,12 @@ 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 + + COB brings together key terms from a wide range of OBO projects to improve interoperability. - 2023-11-16 + Core Ontology for Biology and Biomedicine + 2024-09-20 @@ -85,12 +85,30 @@ + + + + + + + + + + + + + + + + + + @@ -186,6 +204,22 @@ + + + + + + + + + + + realizes + realizes + + + + @@ -450,8 +484,17 @@ + concretizes + + + + + + concretizes + concretizes + @@ -532,7 +575,7 @@ - Anything can have a characteristic + Anything can have a characteristic @@ -541,7 +584,6 @@ - http://purl.obolibrary.org/obo/IAO_0000136 is about @@ -615,6 +657,12 @@ + + + + + + @@ -643,7 +691,7 @@ - The range of this property should be a user-defined unit datatype, e.g 182^:cm + 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 @@ -664,7 +712,7 @@ 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 + 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 @@ -877,29 +925,10 @@ - - - - - - - - - - - - - organism or virus or viroid - organism - - - - - @@ -1296,7 +1325,7 @@ 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. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. atom @@ -1317,8 +1346,8 @@ http://purl.obolibrary.org/obo/CHEBI_33252 - Some people may be uncomfortable calling every proton an atomic nucleus - This is equivalent to CHEBI:33252 + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 atomic nucleus @@ -1337,8 +1366,8 @@ 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. + 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 @@ -1367,7 +1396,7 @@ 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 + Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 obsolete macromolecular entity true @@ -1401,8 +1430,8 @@ 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. + 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 @@ -1443,8 +1472,8 @@ 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 + 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 @@ -1465,7 +1494,7 @@ 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. + 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 @@ -1477,11 +1506,10 @@ - http://purl.obolibrary.org/obo/CARO_0001010 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. + "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 @@ -1502,7 +1530,7 @@ http://purl.obolibrary.org/obo/OBI_0000245 - Should revisit if we can place outside of material entity - a collection of roles. + Should revisit if we can place outside of material entity - a collection of roles. organization @@ -1523,7 +1551,7 @@ http://purl.obolibrary.org/obo/OBI_0000047 - A material entity processed by human activity with an intent to produce + A material entity that is created or changed during material processing. processed material entity @@ -1615,7 +1643,7 @@ planned process - planned process + completely executed planned process @@ -1660,7 +1688,7 @@ 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 + A biological process is an evolved process biological process @@ -1696,7 +1724,7 @@ http://purl.obolibrary.org/obo/GO_0003674 - This is the same as GO molecular function + This is the same as GO molecular function gene product or complex activity @@ -1809,22 +1837,18 @@ - - + + - - - - - - + + http://purl.obolibrary.org/obo/IAO_0000030 - Pier: 'data, information or knowledge'. OR 'representation + Pier: 'data, information or knowledge'. OR 'representation information @@ -1926,7 +1950,7 @@ http://purl.obolibrary.org/obo/MOP_0000543 - This is meant to capture processes that are more fundamental than macromolecular activities + This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process @@ -2030,7 +2054,7 @@ http://purl.obolibrary.org/obo/GO_0032991 - This is not covalently bonded, which conflicts with changes to the parent definition. + This is not covalently bonded, which conflicts with changes to the parent definition. protein-containing macromolecular complex @@ -2124,14 +2148,16 @@ - + + + + + + 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 - - - - @@ -2140,12 +2166,6 @@ owl:Thing complex of molecular entities - - - - - >=2 parts (not we cannot use cardinality with transitive properties) - @@ -2184,11 +2204,10 @@ - + - - http://purl.obolibrary.org/obo/DRON_0000005 + 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 @@ -2196,7 +2215,7 @@ - + drug product drug product @@ -2422,6 +2441,7 @@ + @@ -2430,11 +2450,7 @@ - - - - - + @@ -2485,7 +2501,6 @@ - http://purl.obolibrary.org/obo/CARO_0010004 @@ -2506,17 +2521,27 @@ + - OBI:0000067 + http://purl.obolibrary.org/obo/OBI_0000067 evaluant role + + + + + + evaluant role + evaluant role + + @@ -2527,21 +2552,38 @@ 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 + 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 + @@ -2592,7 +2634,12 @@ - + + + + + + @@ -2605,14 +2652,6 @@ https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 - - - - - - - - @@ -2621,12 +2660,6 @@ quality characteristic - - - - - We should name the inverse in COB and avoid the confusing inverse(..) construct - @@ -2659,23 +2692,23 @@ 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. + 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. +Example of use: A whole device like an engine; a component like a bolt is also a device. + + 2023-03-24T16:04:27Z device - + - + @@ -2769,6 +2802,16 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + + + + + + @@ -2804,6 +2847,15 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + + + + + @@ -2825,7 +2877,6 @@ Example of use: A whole device like an engine; a component like a bolt is also a - @@ -2843,7 +2894,6 @@ Example of use: A whole device like an engine; a component like a bolt is also a - @@ -2884,6 +2934,15 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + + + + + @@ -2934,6 +2993,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a + @@ -3269,5 +3329,5 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + diff --git a/cob-base.owl b/cob-base.owl index a5c88b9..d971095 100644 --- a/cob-base.owl +++ b/cob-base.owl @@ -12,12 +12,12 @@ 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 + + COB brings together key terms from a wide range of OBO projects to improve interoperability. - 2023-11-16 + Core Ontology for Biology and Biomedicine + 2024-09-20 @@ -85,12 +85,30 @@ + + + + + + + + + + + + + + + + + + @@ -186,6 +204,22 @@ + + + + + + + + + + + realizes + realizes + + + + @@ -450,8 +484,17 @@ + concretizes + + + + + + concretizes + concretizes + @@ -532,7 +575,7 @@ - Anything can have a characteristic + Anything can have a characteristic @@ -541,7 +584,6 @@ - http://purl.obolibrary.org/obo/IAO_0000136 is about @@ -615,6 +657,12 @@ + + + + + + @@ -643,7 +691,7 @@ - The range of this property should be a user-defined unit datatype, e.g 182^:cm + 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 @@ -664,7 +712,7 @@ 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 + 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 @@ -860,22 +908,6 @@ - - - - - - - - - - - organism or virus or viroid - organism - - - - @@ -1242,7 +1274,7 @@ 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. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. atom @@ -1262,8 +1294,8 @@ http://purl.obolibrary.org/obo/CHEBI_33252 - Some people may be uncomfortable calling every proton an atomic nucleus - This is equivalent to CHEBI:33252 + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 atomic nucleus @@ -1281,8 +1313,8 @@ 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. + 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 @@ -1310,7 +1342,7 @@ 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 + Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 obsolete macromolecular entity true @@ -1343,8 +1375,8 @@ 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. + 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 @@ -1382,8 +1414,8 @@ 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 + 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 @@ -1403,7 +1435,7 @@ 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. + 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 @@ -1414,11 +1446,10 @@ - http://purl.obolibrary.org/obo/CARO_0001010 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. + "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 @@ -1438,7 +1469,7 @@ http://purl.obolibrary.org/obo/OBI_0000245 - Should revisit if we can place outside of material entity - a collection of roles. + Should revisit if we can place outside of material entity - a collection of roles. organization @@ -1458,7 +1489,7 @@ http://purl.obolibrary.org/obo/OBI_0000047 - A material entity processed by human activity with an intent to produce + A material entity that is created or changed during material processing. processed material entity @@ -1545,7 +1576,7 @@ planned process - planned process + completely executed planned process @@ -1589,7 +1620,7 @@ 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 + A biological process is an evolved process biological process @@ -1624,7 +1655,7 @@ http://purl.obolibrary.org/obo/GO_0003674 - This is the same as GO molecular function + This is the same as GO molecular function gene product or complex activity @@ -1732,22 +1763,18 @@ - - + + - - - - - - + + http://purl.obolibrary.org/obo/IAO_0000030 - Pier: 'data, information or knowledge'. OR 'representation + Pier: 'data, information or knowledge'. OR 'representation information @@ -1844,7 +1871,7 @@ http://purl.obolibrary.org/obo/MOP_0000543 - This is meant to capture processes that are more fundamental than macromolecular activities + This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process @@ -1945,7 +1972,7 @@ http://purl.obolibrary.org/obo/GO_0032991 - This is not covalently bonded, which conflicts with changes to the parent definition. + This is not covalently bonded, which conflicts with changes to the parent definition. protein-containing macromolecular complex @@ -2035,14 +2062,16 @@ - + + + + + + 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 - - - - @@ -2051,12 +2080,6 @@ owl:Thing complex of molecular entities - - - - - >=2 parts (not we cannot use cardinality with transitive properties) - @@ -2094,10 +2117,9 @@ - + - - http://purl.obolibrary.org/obo/DRON_0000005 + 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 @@ -2105,7 +2127,7 @@ - + drug product drug product @@ -2329,11 +2351,7 @@ - - - - - + @@ -2402,16 +2420,26 @@ + - OBI:0000067 + http://purl.obolibrary.org/obo/OBI_0000067 evaluant role + + + + + + evaluant role + evaluant role + + @@ -2420,20 +2448,37 @@ 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 + 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 + @@ -2481,7 +2526,12 @@ - + + + + + + @@ -2494,14 +2544,6 @@ https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 - - - - - - - - @@ -2510,12 +2552,6 @@ quality characteristic - - - - - We should name the inverse in COB and avoid the confusing inverse(..) construct - @@ -2546,23 +2582,23 @@ 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. + 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. +Example of use: A whole device like an engine; a component like a bolt is also a device. + + 2023-03-24T16:04:27Z device - + - + @@ -2630,6 +2666,12 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + + @@ -2654,6 +2696,12 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + + @@ -2716,6 +2764,12 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + + @@ -3037,5 +3091,5 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + diff --git a/cob-examples-reasoned.owl b/cob-examples-reasoned.owl index cddfdf1..4226c1e 100644 --- a/cob-examples-reasoned.owl +++ b/cob-examples-reasoned.owl @@ -12,12 +12,12 @@ 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 + + COB brings together key terms from a wide range of OBO projects to improve interoperability. - 2023-11-16 + Core Ontology for Biology and Biomedicine + 2024-09-20 @@ -85,12 +85,30 @@ + + + + + + + + + + + + + + + + + + @@ -186,6 +204,22 @@ + + + + + + + + + + + realizes + realizes + + + + @@ -456,8 +490,17 @@ + concretizes + + + + + + concretizes + concretizes + @@ -538,7 +581,7 @@ - Anything can have a characteristic + Anything can have a characteristic @@ -547,7 +590,6 @@ - http://purl.obolibrary.org/obo/IAO_0000136 is about @@ -621,6 +663,12 @@ + + + + + + @@ -649,7 +697,7 @@ - The range of this property should be a user-defined unit datatype, e.g 182^:cm + 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 @@ -670,7 +718,7 @@ 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 + 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 @@ -883,29 +931,10 @@ - - - - - - - - - - - - - organism or virus or viroid - organism - - - - - @@ -1603,7 +1632,7 @@ 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. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. atom @@ -1624,8 +1653,8 @@ http://purl.obolibrary.org/obo/CHEBI_33252 - Some people may be uncomfortable calling every proton an atomic nucleus - This is equivalent to CHEBI:33252 + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 atomic nucleus @@ -1644,8 +1673,8 @@ 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. + 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 @@ -1674,7 +1703,7 @@ 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 + Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 obsolete macromolecular entity true @@ -1708,8 +1737,8 @@ 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. + 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 @@ -1750,8 +1779,8 @@ 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 + 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 @@ -1772,7 +1801,7 @@ 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. + 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 @@ -1784,11 +1813,10 @@ - http://purl.obolibrary.org/obo/CARO_0001010 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. + "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 @@ -1809,7 +1837,7 @@ http://purl.obolibrary.org/obo/OBI_0000245 - Should revisit if we can place outside of material entity - a collection of roles. + Should revisit if we can place outside of material entity - a collection of roles. organization @@ -1830,7 +1858,7 @@ http://purl.obolibrary.org/obo/OBI_0000047 - A material entity processed by human activity with an intent to produce + A material entity that is created or changed during material processing. processed material entity @@ -1922,7 +1950,7 @@ planned process - planned process + completely executed planned process @@ -1967,7 +1995,7 @@ 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 + A biological process is an evolved process biological process @@ -2003,7 +2031,7 @@ http://purl.obolibrary.org/obo/GO_0003674 - This is the same as GO molecular function + This is the same as GO molecular function gene product or complex activity @@ -2116,22 +2144,18 @@ - - + + - - - - - - + + http://purl.obolibrary.org/obo/IAO_0000030 - Pier: 'data, information or knowledge'. OR 'representation + Pier: 'data, information or knowledge'. OR 'representation information @@ -2233,7 +2257,7 @@ http://purl.obolibrary.org/obo/MOP_0000543 - This is meant to capture processes that are more fundamental than macromolecular activities + This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process @@ -2337,7 +2361,7 @@ http://purl.obolibrary.org/obo/GO_0032991 - This is not covalently bonded, which conflicts with changes to the parent definition. + This is not covalently bonded, which conflicts with changes to the parent definition. protein-containing macromolecular complex @@ -2433,6 +2457,7 @@ 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 @@ -2453,12 +2478,6 @@ >1, where the parts are not transitively covalently connected - - - - - >=2 parts (not we cannot use cardinality with transitive properties) - @@ -2497,11 +2516,10 @@ - + - - http://purl.obolibrary.org/obo/DRON_0000005 + 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 @@ -2509,7 +2527,7 @@ - + drug product drug product @@ -2735,6 +2753,7 @@ + @@ -2743,11 +2762,7 @@ - - - - - + @@ -2798,7 +2813,6 @@ - http://purl.obolibrary.org/obo/CARO_0010004 @@ -2819,17 +2833,27 @@ + - OBI:0000067 + http://purl.obolibrary.org/obo/OBI_0000067 evaluant role + + + + + + evaluant role + evaluant role + + @@ -2840,21 +2864,38 @@ 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 + 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 + @@ -2905,7 +2946,12 @@ - + + + + + + @@ -2918,14 +2964,6 @@ https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 - - - - - - - - @@ -2934,12 +2972,6 @@ quality characteristic - - - - - We should name the inverse in COB and avoid the confusing inverse(..) construct - @@ -2972,23 +3004,23 @@ 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. + 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. +Example of use: A whole device like an engine; a component like a bolt is also a device. + + 2023-03-24T16:04:27Z device - + - + @@ -3082,17 +3114,17 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + chromosome - + - + min 2 @@ -3134,6 +3166,16 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + + + + + + @@ -3169,6 +3211,15 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + + + + + @@ -3190,7 +3241,6 @@ Example of use: A whole device like an engine; a component like a bolt is also a - @@ -3208,7 +3258,6 @@ Example of use: A whole device like an engine; a component like a bolt is also a - @@ -3261,6 +3310,15 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + + + + + @@ -3311,6 +3369,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a + @@ -3767,5 +3826,5 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + diff --git a/cob-full.owl b/cob-full.owl index fa13eb3..f29dcdc 100644 --- a/cob-full.owl +++ b/cob-full.owl @@ -11,11 +11,11 @@ xmlns:skos="http://www.w3.org/2004/02/skos/core#" 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 + + COB brings together key terms from a wide range of OBO projects to improve interoperability. - 2023-11-16 + Core Ontology for Biology and Biomedicine + 2024-09-20 @@ -77,12 +77,30 @@ + + + + + + + + + + + + + + + + + + @@ -306,7 +324,7 @@ - Anything can have a characteristic + Anything can have a characteristic @@ -314,7 +332,6 @@ - http://purl.obolibrary.org/obo/IAO_0000136 is about @@ -335,7 +352,7 @@ - The range of this property should be a user-defined unit datatype, e.g 182^:cm + 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 @@ -348,7 +365,7 @@ 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 + 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 @@ -499,7 +516,7 @@ 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. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. atom @@ -510,8 +527,8 @@ http://purl.obolibrary.org/obo/CHEBI_33252 - Some people may be uncomfortable calling every proton an atomic nucleus - This is equivalent to CHEBI:33252 + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 atomic nucleus @@ -529,8 +546,8 @@ 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. + 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 @@ -540,7 +557,7 @@ 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 + Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 obsolete macromolecular entity true @@ -564,8 +581,8 @@ 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. + 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 @@ -602,8 +619,8 @@ 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 + 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 @@ -615,7 +632,7 @@ 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. + 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 @@ -625,11 +642,10 @@ - http://purl.obolibrary.org/obo/CARO_0001010 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. + "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 @@ -640,7 +656,7 @@ http://purl.obolibrary.org/obo/OBI_0000245 - Should revisit if we can place outside of material entity - a collection of roles. + Should revisit if we can place outside of material entity - a collection of roles. organization @@ -651,7 +667,7 @@ http://purl.obolibrary.org/obo/OBI_0000047 - A material entity processed by human activity with an intent to produce + A material entity that is created or changed during material processing. processed material entity @@ -755,7 +771,7 @@ 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 + A biological process is an evolved process biological process @@ -781,7 +797,7 @@ http://purl.obolibrary.org/obo/GO_0003674 - This is the same as GO molecular function + This is the same as GO molecular function gene product or complex activity @@ -862,22 +878,18 @@ - - + + - - - - - - + + http://purl.obolibrary.org/obo/IAO_0000030 - Pier: 'data, information or knowledge'. OR 'representation + Pier: 'data, information or knowledge'. OR 'representation information @@ -929,7 +941,7 @@ http://purl.obolibrary.org/obo/MOP_0000543 - This is meant to capture processes that are more fundamental than macromolecular activities + This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process @@ -985,7 +997,7 @@ http://purl.obolibrary.org/obo/GO_0032991 - This is not covalently bonded, which conflicts with changes to the parent definition. + This is not covalently bonded, which conflicts with changes to the parent definition. protein-containing macromolecular complex @@ -1048,20 +1060,16 @@ - + + + + + + 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 - - - - - - - - - >=2 parts (not we cannot use cardinality with transitive properties) - @@ -1100,8 +1108,7 @@ - - http://purl.obolibrary.org/obo/DRON_0000005 + 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 @@ -1253,11 +1260,7 @@ - - - - - + @@ -1301,7 +1304,7 @@ - OBI:0000067 + http://purl.obolibrary.org/obo/OBI_0000067 evaluant role @@ -1324,8 +1327,8 @@ 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 + Pier 'representational entity' + This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc information representation @@ -1386,7 +1389,12 @@ - + + + + + + @@ -1399,20 +1407,6 @@ https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 - - - - - - - - - - - - - We should name the inverse in COB and avoid the confusing inverse(..) construct - @@ -1443,20 +1437,20 @@ 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. + 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. +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-native.owl b/cob-native.owl index 47d334e..58f78c5 100644 --- a/cob-native.owl +++ b/cob-native.owl @@ -11,11 +11,11 @@ xmlns:skos="http://www.w3.org/2004/02/skos/core#" 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 + + COB brings together key terms from a wide range of OBO projects to improve interoperability. - 2023-11-16 + Core Ontology for Biology and Biomedicine + 2024-09-20 @@ -31,12 +31,6 @@ - - - - - - @@ -75,12 +69,30 @@ + + + + + + + + + + + + + + + + + + @@ -304,7 +316,7 @@ - Anything can have a characteristic + Anything can have a characteristic @@ -312,7 +324,6 @@ - http://purl.obolibrary.org/obo/IAO_0000136 is about @@ -333,7 +344,7 @@ - The range of this property should be a user-defined unit datatype, e.g 182^:cm + 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 @@ -346,7 +357,7 @@ 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 + 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 @@ -492,7 +503,7 @@ 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. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. atom @@ -502,8 +513,8 @@ - Some people may be uncomfortable calling every proton an atomic nucleus - This is equivalent to CHEBI:33252 + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 atomic nucleus @@ -521,8 +532,8 @@ 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. + 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 @@ -533,7 +544,7 @@ 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 + Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 obsolete macromolecular entity true @@ -554,8 +565,8 @@ 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. + 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 @@ -590,8 +601,8 @@ 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 + 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 @@ -602,7 +613,7 @@ 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. + 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 @@ -613,8 +624,8 @@ 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. + "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 @@ -624,7 +635,7 @@ - Should revisit if we can place outside of material entity - a collection of roles. + Should revisit if we can place outside of material entity - a collection of roles. organization @@ -634,7 +645,7 @@ - A material entity processed by human activity with an intent to produce + A material entity that is created or changed during material processing. processed material entity @@ -735,7 +746,7 @@ 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 + A biological process is an evolved process biological process @@ -760,7 +771,7 @@ - This is the same as GO molecular function + This is the same as GO molecular function gene product or complex activity @@ -836,21 +847,17 @@ - - + + - - - - - - + + - Pier: 'data, information or knowledge'. OR 'representation + Pier: 'data, information or knowledge'. OR 'representation information @@ -897,7 +904,7 @@ - This is meant to capture processes that are more fundamental than macromolecular activities + This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process @@ -949,7 +956,7 @@ - This is not covalently bonded, which conflicts with changes to the parent definition. + This is not covalently bonded, which conflicts with changes to the parent definition. protein-containing macromolecular complex @@ -1010,20 +1017,16 @@ - + + + + + + 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 - - - - - - - - - >=2 parts (not we cannot use cardinality with transitive properties) - @@ -1062,7 +1065,6 @@ - A processed material entity created to be administered to an individual with the intent to improve health. drug product @@ -1205,11 +1207,7 @@ - - - - - + @@ -1249,7 +1247,6 @@ - OBI:0000067 evaluant role @@ -1265,9 +1262,8 @@ - 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 + Pier 'representational entity' + This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc information representation @@ -1277,7 +1273,6 @@ - http://purl.obolibrary.org/obo/IAO_0000109 measurement datum @@ -1317,7 +1312,12 @@ - + + + + + + @@ -1328,20 +1328,6 @@ https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 - - - - - - - - - - - - - We should name the inverse in COB and avoid the confusing inverse(..) construct - @@ -1372,20 +1358,20 @@ 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. + 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. +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.owl b/cob.owl index a0b1599..f21dc97 100644 --- a/cob.owl +++ b/cob.owl @@ -11,12 +11,12 @@ xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:dcterms="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 + + 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. - 2023-11-16 + 2024-09-20 @@ -32,12 +32,6 @@ - - - - - - @@ -76,12 +70,30 @@ + + + + + + + + + + + + + + + + + + @@ -120,12 +132,22 @@ - + realized in + + + + + + realizes + + + + @@ -153,15 +175,6 @@ - - - - - concretizes - - - - @@ -186,20 +199,9 @@ - - - - - - realizes - - - - - http://purl.obolibrary.org/obo/IAO_0000136 is about @@ -267,7 +269,7 @@ - Anything can have a characteristic + Anything can have a characteristic @@ -293,11 +295,20 @@ + is concretized as + + + + concretizes + + + + @@ -311,8 +322,8 @@ - - + + executes @@ -334,7 +345,7 @@ - The range of this property should be a user-defined unit datatype, e.g 182^:cm + 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 @@ -347,7 +358,7 @@ 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 + 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 @@ -420,7 +431,12 @@ - + + + + + + @@ -431,20 +447,6 @@ https://github.com/OBOFoundry/COB/issues/65 https://github.com/oborel/obo-relations/pull/284 - - - - - - - - - - - - - We should name the inverse in COB and avoid the confusing inverse(..) construct - @@ -498,28 +500,16 @@ 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. + 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 - - - - - + cellular organism @@ -581,8 +571,8 @@ - Some people may be uncomfortable calling every proton an atomic nucleus - This is equivalent to CHEBI:33252 + Some people may be uncomfortable calling every proton an atomic nucleus + This is equivalent to CHEBI:33252 atomic nucleus @@ -611,8 +601,8 @@ 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. + 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 @@ -665,7 +655,7 @@ 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. + This atom is closely related to ChEBI's atom, but not exactly equivalent to. atom @@ -683,8 +673,8 @@ 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. + 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 @@ -695,7 +685,7 @@ 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 + Terms moved to 'molecular entity', see https://github.com/OBOFoundry/Experimental-OBO-Core/issues/33 obsolete macromolecular entity true @@ -713,8 +703,8 @@ 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 + 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 @@ -772,20 +762,16 @@ - + + + + + + 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 - - - - - - - - - >=2 parts (not we cannot use cardinality with transitive properties) - @@ -795,14 +781,14 @@ - - + + - - + + 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. @@ -830,44 +816,6 @@ - - - - - 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 - - - - @@ -876,7 +824,7 @@ - + @@ -915,25 +863,24 @@ A processed material entity which is designed to perform a function. - - 2023-03-24T16:04:27+00:00 - 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. + 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. +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 @@ -989,7 +936,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - This is the same as GO molecular function + This is the same as GO molecular function gene product or complex activity @@ -1013,18 +960,18 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + - + - + @@ -1039,7 +986,7 @@ 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 + A biological process is an evolved process biological process @@ -1055,7 +1002,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - This is not covalently bonded, which conflicts with changes to the parent definition. + This is not covalently bonded, which conflicts with changes to the parent definition. protein-containing macromolecular complex @@ -1070,6 +1017,23 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + + + + + + + Pier 'representational entity' + This captures: pattern of writing in a book; neural state in the brain, electronic charges in computer memory etc + information representation + + + + @@ -1091,15 +1055,11 @@ Example of use: A whole device like an engine; a component like a bolt is also a - - - - - - + + - Pier: 'data, information or knowledge'. OR 'representation + Pier: 'data, information or knowledge'. OR 'representation information @@ -1135,6 +1095,15 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + measurement datum + + + + @@ -1148,7 +1117,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - This is meant to capture processes that are more fundamental than macromolecular activities + This is meant to capture processes that are more fundamental than macromolecular activities physico-chemical process @@ -1160,7 +1129,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + @@ -1173,7 +1142,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - A material entity processed by human activity with an intent to produce + A material entity that is created or changed during material processing. processed material entity @@ -1188,6 +1157,15 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + evaluant role + + + + @@ -1201,7 +1179,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + @@ -1214,7 +1192,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + @@ -1223,7 +1201,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + @@ -1252,7 +1230,7 @@ Example of use: A whole device like an engine; a component like a bolt is also a - Should revisit if we can place outside of material entity - a collection of roles. + Should revisit if we can place outside of material entity - a collection of roles. organization @@ -1262,20 +1240,16 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + - + - - - - - + @@ -1293,6 +1267,18 @@ Example of use: A whole device like an engine; a component like a bolt is also a + + + + + 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 + + + + @@ -1388,5 +1374,5 @@ Example of use: A whole device like an engine; a component like a bolt is also a - + diff --git a/cob.tsv b/cob.tsv index 9cbefb2..1093964 100644 --- a/cob.tsv +++ b/cob.tsv @@ -2,15 +2,14 @@ ID ID [LABEL] definition subClassOf [ID NAMED] subClassOf [LABEL NAMED] subClass 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 inverse (RO:0000053) some owl:Thing|BFO:0000051 only BFO:0000020 inverse (has characteristic) some |has part only 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: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:0001010 organism A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. BFO:0000040 material entity -CARO:0010004 cellular organism CARO:0001010 organism +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 @@ -32,38 +31,39 @@ 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 COB:0000081 some OBI:0000260|COB:0000087 some SEPIO:0000048 intended to realize some plan|realizes some agent role +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:0000083 failed planned process COB:0000082 planned process COB:0000116 cellular membrane COB:0000020 subcellular structure -COB:0000119 evaluant role BFO:0000023 role -COB:0000120 information representation BFO:0000020 characteristic -COB:0000121 measurement datum IAO:0000027 data item 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:0000005 drug product A processed material entity created to be administered to an individual with the intent to improve health. OBI:0000047 processed material entity +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 CARO:0001010) or (RO:0000057 some CARO:0001010) or (RO:0000057 some (BFO:0000050 some CARO:0001010))|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: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 inverse (COB:0000078) some COB:0000120|IAO:0000136 some owl:Thing inverse (concretizes) some information representation|is about some +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 COB:0000087 some OBI:0000260 realizes some plan -OBI:0000047 processed material entity A material entity processed by human activity with an intent to produce BFO:0000040 material entity +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:0000070 assay OBI:0000011 completely executed planned process OBI:0000293 some (BFO:0000040 and (RO:0000053 some COB:0000119))|OBI:0000299 some (COB:0000121 and (IAO:0000136 some (BFO:0000040 and (RO:0000053 some COB:0000119)))) 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: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|COB:0000120 information representation|realizable inverse (COB:0000087) only COB:0000082|COB:0000078 some IAO:0000104 inverse (realizes) only planned process|concretizes some plan specification +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 diff --git a/src/ontology/components/cob-annotations.owl b/src/ontology/components/cob-annotations.owl index 61150b7..315e89c 100644 --- a/src/ontology/components/cob-annotations.owl +++ b/src/ontology/components/cob-annotations.owl @@ -9,11 +9,218 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - 2024-08-20 + 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 + - +