From 0309dbf77a7359cd5f9ffa3f21a5067fcab63df7 Mon Sep 17 00:00:00 2001 From: jamesaoverton Date: Thu, 23 Jan 2025 16:10:57 +0000 Subject: [PATCH 1/2] Update release files --- cob-base.owl | 4 +- cob-root.owl | 4 +- cob.owl | 4 +- src/ontology/cob-edit.owl | 1369 +++++++++++++++++++++++++++++++++++++ src/ontology/cob.tsv | 69 ++ 5 files changed, 1444 insertions(+), 6 deletions(-) create mode 100644 src/ontology/cob-edit.owl create mode 100644 src/ontology/cob.tsv diff --git a/cob-base.owl b/cob-base.owl index 59b959f..c66f067 100644 --- a/cob-base.owl +++ b/cob-base.owl @@ -10,12 +10,12 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" 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 - 2024-12-12 + 2025-01-23 diff --git a/cob-root.owl b/cob-root.owl index b2730fa..f971e8d 100644 --- a/cob-root.owl +++ b/cob-root.owl @@ -9,11 +9,11 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" 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 - 2024-12-12 + 2025-01-23 diff --git a/cob.owl b/cob.owl index 9e4005c..5ebae71 100644 --- a/cob.owl +++ b/cob.owl @@ -9,11 +9,11 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" 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 - 2024-12-12 + 2025-01-23 diff --git a/src/ontology/cob-edit.owl b/src/ontology/cob-edit.owl new file mode 100644 index 0000000..ead0a98 --- /dev/null +++ b/src/ontology/cob-edit.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 + 2025-01-23 + + + + + + + + + + + + + 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/src/ontology/cob.tsv b/src/ontology/cob.tsv new file mode 100644 index 0000000..cc64a53 --- /dev/null +++ b/src/ontology/cob.tsv @@ -0,0 +1,69 @@ +ID ID [LABEL] definition subClassOf [ID NAMED] subClassOf [LABEL NAMED] subClassOf [ID ANON] subClassOf [LABEL ANON] +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 +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 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: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. From a91255bbf9667478b8ca98aa986e76b4f3b83e1c Mon Sep 17 00:00:00 2001 From: "James A. Overton" Date: Thu, 23 Jan 2025 14:18:52 -0500 Subject: [PATCH 2/2] Remove and ignore files that are now generated --- .gitignore | 2 + src/ontology/cob-edit.owl | 1369 ------------------------------------- src/ontology/cob.tsv | 69 -- 3 files changed, 2 insertions(+), 1438 deletions(-) delete mode 100644 src/ontology/cob-edit.owl delete mode 100644 src/ontology/cob.tsv diff --git a/.gitignore b/.gitignore index 9939507..6ef5778 100644 --- a/.gitignore +++ b/.gitignore @@ -22,8 +22,10 @@ src/ontology/reports/* src/ontology/cob.owl src/ontology/cob.obo src/ontology/cob.json +src/ontology/cob.tsv src/ontology/cob-base.* src/ontology/cob-basic.* +src/ontology/cob-edit.owl src/ontology/cob-full.* src/ontology/cob-simple.* src/ontology/cob-simple-non-classified.* diff --git a/src/ontology/cob-edit.owl b/src/ontology/cob-edit.owl deleted file mode 100644 index ead0a98..0000000 --- a/src/ontology/cob-edit.owl +++ /dev/null @@ -1,1369 +0,0 @@ - - - - - COB brings together key terms from a wide range of OBO projects to improve interoperability. - - Core Ontology for Biology and Biomedicine - 2025-01-23 - - - - - - - - - - - - - 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/src/ontology/cob.tsv b/src/ontology/cob.tsv deleted file mode 100644 index cc64a53..0000000 --- a/src/ontology/cob.tsv +++ /dev/null @@ -1,69 +0,0 @@ -ID ID [LABEL] definition subClassOf [ID NAMED] subClassOf [LABEL NAMED] subClassOf [ID ANON] subClassOf [LABEL ANON] -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 -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 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: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.