From 74fbe3ce21ae7e8ca100e180af8faebb0d73e5b7 Mon Sep 17 00:00:00 2001 From: Ximeaixa Date: Fri, 18 Sep 2026 10:32:49 +0200 Subject: [PATCH 1/6] import PR:000000001 and parents from PR and COB, update repo and refresh imports --- docs/odk-workflows/RepositoryFileStructure.md | 2 + src/ontology/Makefile | 27 +- src/ontology/idpo-odk.yaml | 12 + src/ontology/imports/cob_terms.txt | 1 + src/ontology/imports/merged_import.owl | 877 +++++++++++++++++- src/ontology/imports/pr_terms.txt | 2 + 6 files changed, 917 insertions(+), 4 deletions(-) create mode 100644 src/ontology/imports/cob_terms.txt create mode 100644 src/ontology/imports/pr_terms.txt diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 5c34042..96e6a67 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -21,6 +21,8 @@ These are the current imports in IDPO | bfo | http://purl.obolibrary.org/obo/bfo.owl | slme | | go | http://purl.obolibrary.org/obo/go.owl | slme | | iao | http://purl.obolibrary.org/obo/iao.owl | slme | +| pr | http://purl.obolibrary.org/obo/pr.owl | slme | +| cob | http://purl.obolibrary.org/obo/cob.owl | slme | ## Components Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases: diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 38c93ce..24628d6 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 98b52c17665ae96ff0faa9ab8d0db7ef77748df8fe2cf20122e9cab3604e090b +CONFIG_HASH= 7b81db2dfb9d6b1b60d5081ec9ff3101008a1dd872d7573a3fac3c2821f98c57 # ---------------------------------------- @@ -188,7 +188,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = ro omo bfo go iao +IMPORTS = ro omo bfo go iao pr cob IMPORT_ROOTS = $(IMPORTDIR)/merged_import IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -408,6 +408,11 @@ ALL_TERMS = $(foreach imp, $(IMPORTS), $(IMPORTDIR)/$(imp)_terms.txt) $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(ALL_TERMS) \ $(IMPORTSEED) | all_robot_plugins $(ROBOT) merge --input $< \ + remove --select "" \ + remove --select "" \ + remove --select "" \ + remove --select "" \ + remove --select "" \ extract $(foreach f, $(ALL_TERMS), --term-file $(f)) $(T_IMPORTSEED) \ --force true --copy-ontology-annotations false \ --individuals exclude \ @@ -492,6 +497,24 @@ mirror-iao: | $(TMPDIR) curl -L $(OBOBASE)/iao.owl --create-dirs -o $(TMPDIR)/iao-download.owl --retry 4 --max-time 200 && \ $(ROBOT) convert -i $(TMPDIR)/iao-download.owl -o $(TMPDIR)/$@.owl + +## ONTOLOGY: pr +.PHONY: mirror-pr +.PRECIOUS: $(MIRRORDIR)/pr.owl +ifeq ($(IMP_LARGE),true) +mirror-pr: | $(TMPDIR) + curl -L $(OBOBASE)/pr.owl.gz --create-dirs -o $(MIRRORDIR)/pr.owl.gz --retry 4 --max-time 200 && \ + $(ROBOT) remove -i $(MIRRORDIR)/pr.owl.gz --base-iri http://purl.obolibrary.org/obo/PR --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl +endif + + +## ONTOLOGY: cob +.PHONY: mirror-cob +.PRECIOUS: $(MIRRORDIR)/cob.owl +mirror-cob: | $(TMPDIR) + curl -L $(OBOBASE)/cob/cob-base.owl --create-dirs -o $(TMPDIR)/cob-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/cob-download.owl -o $(TMPDIR)/$@.owl + ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS)) MERGE_MIRRORS = true diff --git a/src/ontology/idpo-odk.yaml b/src/ontology/idpo-odk.yaml index 1a84cb3..c7b989e 100644 --- a/src/ontology/idpo-odk.yaml +++ b/src/ontology/idpo-odk.yaml @@ -15,6 +15,12 @@ export_formats: import_group: use_base_merging: TRUE slme_individuals: exclude + exclude_iri_patterns: + - + - + - + - + - products: - id: ro use_base: TRUE @@ -23,6 +29,12 @@ import_group: - id: go use_base: TRUE - id: iao + - id: pr + use_gzipped: TRUE + is_large: TRUE + make_base: TRUE + - id: cob + use_base: TRUE documentation: documentation_system: mkdocs robot_java_args: "-Xmx8G" diff --git a/src/ontology/imports/cob_terms.txt b/src/ontology/imports/cob_terms.txt new file mode 100644 index 0000000..8226923 --- /dev/null +++ b/src/ontology/imports/cob_terms.txt @@ -0,0 +1 @@ +COB:0000013 \ No newline at end of file diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 131641d..a36ce93 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2026-09-14") + +Annotation(owl:versionInfo "2026-09-17") Declaration(Class()) Declaration(Class()) @@ -26,17 +26,73 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -61,13 +117,21 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -83,9 +147,17 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -409,6 +481,40 @@ AnnotationAssertion(rdfs:label "temp ObjectPropertyDomain( ) ObjectPropertyRange( ) +# Object Property: (starts) + +AnnotationAssertion( "inverse of starts with") +AnnotationAssertion( "Allen") +AnnotationAssertion(rdfs:label "starts"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (starts with) + +AnnotationAssertion( "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor") +AnnotationAssertion( "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") +AnnotationAssertion(rdfs:label "starts with"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + +# Object Property: (ends) + +AnnotationAssertion( "inverse of ends with") +AnnotationAssertion(rdfs:label "ends"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (ends with) + +AnnotationAssertion( "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.") +AnnotationAssertion(rdfs:label "ends with"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +TransitiveObjectProperty() + # Object Property: (has input) AnnotationAssertion( "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.") @@ -424,6 +530,23 @@ AnnotationAssertion(rdfs:label "has SubObjectPropertyOf( ) InverseObjectProperties( ) +# Object Property: (results in developmental progression of) + +AnnotationAssertion( "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).") +AnnotationAssertion(rdfs:label "results in developmental progression of"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) + +# Object Property: (results in formation of anatomical entity) + +AnnotationAssertion( "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.") +AnnotationAssertion( "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) +AnnotationAssertion( "GOC:mtg_berkeley_2013") +AnnotationAssertion(rdfs:label "results in formation of anatomical entity"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + # Object Property: (characteristic of part of) AnnotationAssertion( "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w.") @@ -436,6 +559,11 @@ SubObjectPropertyOf( "A mereological relationship or a topological relationship") AnnotationAssertion(rdfs:label "mereotopologically related to"@en) +# Object Property: (developmentally related to) + +AnnotationAssertion( "A relationship that holds between entities participating in some developmental process (GO:0032502)") +AnnotationAssertion(rdfs:label "developmentally related to"@en) + # Object Property: (functionally related to) AnnotationAssertion( "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.") @@ -455,6 +583,11 @@ AnnotationAssertion(rdfs:label "outp SubObjectPropertyOf( ) SubObjectPropertyOf( ) +# Object Property: (formed as result of) + +AnnotationAssertion(rdfs:label "formed as result of"@en) +SubObjectPropertyOf( ) + # Object Property: (causally downstream of) AnnotationAssertion( "inverse of upstream of") @@ -556,6 +689,48 @@ SubObjectPropertyOf( "molecular interaction relation helper property") SubObjectPropertyOf( ) +# Object Property: (results in breakdown of) + +AnnotationAssertion( "p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p") +AnnotationAssertion(rdfs:label "results in breakdown of") +SubObjectPropertyOf( ) + +# Object Property: (results in assembly of) + +AnnotationAssertion(rdfs:label "results in assembly of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (results in disassembly of) + +AnnotationAssertion(rdfs:label "results in disassembly of") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (results in organization of) + +AnnotationAssertion( "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c") +AnnotationAssertion(rdfs:label "results in organization of") +SubObjectPropertyOf( ) + +# Object Property: (has primary input or output) + +AnnotationAssertion( "p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.") +AnnotationAssertion(rdfs:label "has primary input or output") +SubObjectPropertyOf( ) + +# Object Property: (has primary output) + +AnnotationAssertion(rdfs:label "has primary output") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + +# Object Property: (has primary input) + +AnnotationAssertion(rdfs:label "has primary input") +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + # Object Property: (realized in response to stimulus) AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") @@ -585,6 +760,12 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) +# Object Property: (results in changes to anatomical or cellular structure) + +AnnotationAssertion( "p has anatomical participant c iff p has participant c, and c is an anatomical entity") +AnnotationAssertion(rdfs:label "results in changes to anatomical or cellular structure") +SubObjectPropertyOf( ) + ############################ @@ -793,6 +974,52 @@ AnnotationAssertion( "material entity"@en) SubClassOf( ) +# Class: (atom) + +AnnotationAssertion( "A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it."@en) +AnnotationAssertion(rdfs:label "atom"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (molecule) + +AnnotationAssertion( "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."@en) +AnnotationAssertion(rdfs:label "molecule"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (complex of molecules) + +AnnotationAssertion( "A complex of two or more molecules that are not covalently bound."@en) +AnnotationAssertion(rdfs:label "complex of molecules"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (peptidyltransferase activity) + +AnnotationAssertion(Annotation( "EC:2.3.2.12") Annotation( "PMID:11433365") Annotation( "PMID:9242921") "Catalysis of the reaction: peptidyl-tRNA(1) + aminoacyl-tRNA(2) = tRNA(1) + peptidylaminoacyl-tRNA(2). This reaction is catalyzed by a ribozyme.") +AnnotationAssertion( "EC:2.3.2.12") +AnnotationAssertion( "MetaCyc:PEPTIDYLTRANSFERASE-RXN") +AnnotationAssertion(Annotation(rdfs:label "Peptide transfer from P-site tRNA to the A-site tRNA") "Reactome:R-HSA-156912") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0000048") +AnnotationAssertion(rdfs:label "peptidyltransferase activity") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) + +# Class: (formation of translation initiation ternary complex) + +AnnotationAssertion(Annotation( "GOC:hjd") "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).") +AnnotationAssertion( "translation initiation ternary complex assembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0001677") +AnnotationAssertion(rdfs:label "formation of translation initiation ternary complex") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (molecular_function) AnnotationAssertion(Annotation( "GOC:pdt") "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.") @@ -801,6 +1028,8 @@ AnnotationAssertion( "GO:0003674") AnnotationAssertion(rdfs:label "molecular_function") SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) # Class: (catalytic activity) @@ -812,6 +1041,251 @@ AnnotationAssertion( "catalytic activity") SubClassOf( ) +# Class: (cellular_component) + +AnnotationAssertion(Annotation( "GOC:pdt") "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).") +AnnotationAssertion( "NIF_Subcellular:sao1337158144") +AnnotationAssertion( "cell or subcellular entity") +AnnotationAssertion( "cellular component") +AnnotationAssertion( "cellular_component") +AnnotationAssertion(Annotation( "NIF_Subcellular:nlx_subcell_100315") "subcellular entity") +AnnotationAssertion( "GO:0005575") +AnnotationAssertion(rdfs:label "cellular_component") +EquivalentClasses( ObjectUnionOf( )) +SubClassOf( ) +DisjointClasses( ) +DisjointUnion( ) + +# Class: (intracellular anatomical structure) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.") +AnnotationAssertion( "Wikipedia:Intracellular") +AnnotationAssertion( "internal to cell") +AnnotationAssertion( "intracellular") +AnnotationAssertion( "protoplasm") +AnnotationAssertion( "cellular_component") +AnnotationAssertion(Annotation( "GOC:mah") "nucleocytoplasm") +AnnotationAssertion(Annotation( "GOC:mah") "protoplast") +AnnotationAssertion( "GO:0005622") +AnnotationAssertion(rdfs:label "intracellular anatomical structure") +SubClassOf( ) + +# Class: (cytoplasm) + +AnnotationAssertion(Annotation( "ISBN:0198547684") "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.") +AnnotationAssertion( "Wikipedia:Cytoplasm") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0005737") +AnnotationAssertion(rdfs:label "cytoplasm") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (nucleobase-containing compound metabolic process) + +AnnotationAssertion(Annotation( "GOC:ai") "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.") +AnnotationAssertion( "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process") +AnnotationAssertion( "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism") +AnnotationAssertion( "nucleobase, nucleoside, nucleotide and nucleic acid metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "nucleobase, nucleoside and nucleotide metabolic process") +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process") +AnnotationAssertion( "GO:0006139") +AnnotationAssertion(rdfs:label "nucleobase-containing compound metabolic process") +SubClassOf( ) + +# Class: (tRNA metabolic process) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.") +AnnotationAssertion( "tRNA metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006399") +AnnotationAssertion(rdfs:label "tRNA metabolic process") +SubClassOf( ) + +# Class: (translation) + +AnnotationAssertion(Annotation( "GOC:curators") "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.") +AnnotationAssertion(Annotation(rdfs:label "Translation") "Reactome:R-HSA-72766") +AnnotationAssertion( "Wikipedia:Translation_(genetics)") +AnnotationAssertion( "protein translation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006412") +AnnotationAssertion(rdfs:label "translation") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (translational initiation) + +AnnotationAssertion(Annotation( "ISBN:019879276X") "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.") +AnnotationAssertion( "biopolymerisation") +AnnotationAssertion( "biopolymerization") +AnnotationAssertion( "protein synthesis initiation") +AnnotationAssertion(Annotation(rdfs:label "Eukaryotic Translation Initiation") "Reactome:R-HSA-72613") +AnnotationAssertion( "translation initiation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006413") +AnnotationAssertion(rdfs:label "translational initiation") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (translational elongation) + +AnnotationAssertion(Annotation( "GOC:ems") "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.") +AnnotationAssertion( "protein synthesis elongation") +AnnotationAssertion(Annotation(rdfs:label "Eukaryotic Translation Elongation") "Reactome:R-HSA-156842") +AnnotationAssertion( "translation elongation") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006414") +AnnotationAssertion(rdfs:label "translational elongation") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (translational termination) + +AnnotationAssertion(Annotation( "GOC:hjd") Annotation( "ISBN:019879276X") "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).") +AnnotationAssertion( "protein synthesis termination") +AnnotationAssertion(Annotation(rdfs:label "Eukaryotic Translation Termination") "Reactome:R-HSA-72764") +AnnotationAssertion( "translation termination") +AnnotationAssertion( "translational complex disassembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0006415") +AnnotationAssertion(rdfs:label "translational termination") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amino acid metabolic process) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.") +AnnotationAssertion( "cellular amino acid metabolic process") +AnnotationAssertion( "cellular amino acid metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "amino acid and derivative metabolism") +AnnotationAssertion( "cellular amino acid and derivative metabolic process") +AnnotationAssertion( "GO:0006520") +AnnotationAssertion(rdfs:label "amino acid metabolic process") +SubClassOf( ) + +# Class: (cytoplasm organization) + +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:dph") Annotation( "GOC:jl") Annotation( "GOC:mah") "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.") +AnnotationAssertion( "cytoplasm organisation") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:mah") "cytoplasm organization and biogenesis") +AnnotationAssertion( "GO:0007028") +AnnotationAssertion(rdfs:label "cytoplasm organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (biological_process) + +AnnotationAssertion(Annotation( "GOC:pdt") "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.") +AnnotationAssertion( "Wikipedia:Biological_process") +AnnotationAssertion( "biological process") +AnnotationAssertion( "physiological process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "single organism process") +AnnotationAssertion( "single-organism process") +AnnotationAssertion( "GO:0008150") +AnnotationAssertion(rdfs:label "biological_process") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (metabolic process) + +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism transforms chemical substances. This includes including anabolism (biosynthetic process) and catabolism (catabolic process). Metabolic processes includes the transformation of small molecules, as well macromolecular processes such as DNA repair and replication, protein synthesis and degradation.") +AnnotationAssertion(Annotation(rdfs:label "Metabolism") "Reactome:R-HSA-1430728") +AnnotationAssertion( "Wikipedia:Metabolism") +AnnotationAssertion( "metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0008152") +AnnotationAssertion(rdfs:label "metabolic process") +SubClassOf( ) + +# Class: (biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "ISBN:0198547684") "A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.") +AnnotationAssertion( "formation") +AnnotationAssertion( "Wikipedia:Anabolism") +AnnotationAssertion( "anabolism") +AnnotationAssertion( "biosynthesis") +AnnotationAssertion( "synthesis") +AnnotationAssertion( "multicellular organismal biosynthetic process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "single-organism biosynthetic process") +AnnotationAssertion( "GO:0009058") +AnnotationAssertion(rdfs:label "biosynthetic process") +SubClassOf( ) + +# Class: (macromolecule biosynthetic process) + +AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") +AnnotationAssertion(Annotation( "GOC:mtg_chebi_dec09") "biopolymer biosynthetic process") +AnnotationAssertion( "macromolecule anabolism") +AnnotationAssertion( "macromolecule biosynthesis") +AnnotationAssertion( "macromolecule formation") +AnnotationAssertion( "macromolecule synthesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0009059") +AnnotationAssertion(rdfs:label "macromolecule biosynthetic process") +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular process) + +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:isa_complete") "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.") +AnnotationAssertion( "cell physiology") +AnnotationAssertion( "cellular physiological process") +AnnotationAssertion( "cell growth and/or maintenance") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "single-organism cellular process") +AnnotationAssertion( "GO:0009987") +AnnotationAssertion(rdfs:label "cellular process") +SubClassOf( ) + +# Class: (gene expression) + +AnnotationAssertion(Annotation( "GOC:txnOH-2018") Annotation( "PMID:25934543") Annotation( "PMID:31580950") "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.") +AnnotationAssertion( "Wikipedia:Gene_expression") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0010467") +AnnotationAssertion(rdfs:label "gene expression") +SubClassOf( ) + +# Class: (cellular component organization) + +AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:jl") Annotation( "GOC:mah") "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.") +AnnotationAssertion( "cell organisation") +AnnotationAssertion(Annotation( "GOC:mah") "cellular component organisation at cellular level") +AnnotationAssertion(Annotation( "GOC:mah") "cellular component organisation in other organism") +AnnotationAssertion( "cellular component organization at cellular level") +AnnotationAssertion( "cellular component organization in other organism") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "GOC:mah") "cell organization and biogenesis") +AnnotationAssertion( "GO:0016043") +AnnotationAssertion(rdfs:label "cellular component organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (RNA metabolic process) + +AnnotationAssertion(Annotation( "ISBN:0198506732") "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.") +AnnotationAssertion(Annotation(rdfs:label "Metabolism of RNA") "Reactome:R-HSA-8953854") +AnnotationAssertion( "RNA metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0016070") +AnnotationAssertion(rdfs:label "RNA metabolic process") +SubClassOf( ) + # Class: (kinase activity) AnnotationAssertion(Annotation( "ISBN:0198506732") "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.") @@ -838,6 +1312,30 @@ AnnotationAssertion( "transferase activity") SubClassOf( ) +# Class: (acyltransferase activity) + +AnnotationAssertion(Annotation( "EC:2.3.-.-") "Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).") +AnnotationAssertion( "EC:2.3.-.-") +AnnotationAssertion(Annotation(rdfs:label "Cytosolic chenodeoxycholoyl-CoA or choloyl-CoA are conjugated with glycine or taurine") "Reactome:R-HSA-159431") +AnnotationAssertion(Annotation(rdfs:label "Choloyl CoA reacts with glycine or taurine to form glycocholate or taurocholate") "Reactome:R-HSA-192312") +AnnotationAssertion(Annotation(rdfs:label "Chenodeoxycholoyl CoA reacts with glycine or taurine to form glycochenodeoxycholate or taurochenodeoxycholate") "Reactome:R-HSA-193491") +AnnotationAssertion(Annotation(rdfs:label "HRASLS transfer acyl group from PC to PE to form NAPE") "Reactome:R-HSA-8858298") +AnnotationAssertion( "transferase activity, transferring acyl groups") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0016746") +AnnotationAssertion(rdfs:label "acyltransferase activity") +SubClassOf( ) + +# Class: (aminoacyltransferase activity) + +AnnotationAssertion(Annotation( "GOC:jl") "Catalysis of the transfer of an amino-acyl group from one compound (donor) to another (acceptor).") +AnnotationAssertion( "EC:2.3.2.-") +AnnotationAssertion( "transferase activity, transferring amino-acyl groups") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0016755") +AnnotationAssertion(rdfs:label "aminoacyltransferase activity") +SubClassOf( ) + # Class: (transferase activity, transferring phosphorus-containing groups) AnnotationAssertion(Annotation( "EC:2.7.-.-") "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).") @@ -848,6 +1346,345 @@ AnnotationAssertion( "transferase activity, transferring phosphorus-containing groups") SubClassOf( ) +# Class: (protein metabolic process) + +AnnotationAssertion(Annotation( "GOC:ma") "The chemical reactions and pathways involving a protein. Includes protein modification.") +AnnotationAssertion(Annotation(rdfs:label "Metabolism of proteins") "Reactome:R-HSA-392499") +AnnotationAssertion( "Wikipedia:Protein_metabolism") +AnnotationAssertion( "cellular protein metabolic process") +AnnotationAssertion( "cellular protein metabolism") +AnnotationAssertion( "protein metabolic process and modification") +AnnotationAssertion( "protein metabolism") +AnnotationAssertion( "protein metabolism and modification") +AnnotationAssertion( "multicellular organismal protein metabolic process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0019538") +AnnotationAssertion(rdfs:label "protein metabolic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular component disassembly) + +AnnotationAssertion(Annotation( "GOC:isa_complete") "A cellular process that results in the breakdown of a cellular component.") +AnnotationAssertion( "cell structure disassembly") +AnnotationAssertion( "cellular component disassembly at cellular level") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0022411") +AnnotationAssertion(rdfs:label "cellular component disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) + +# Class: (cellular component assembly) + +AnnotationAssertion(Annotation( "GOC:isa_complete") "The aggregation, arrangement and bonding together of a cellular component.") +AnnotationAssertion( "cell structure assembly") +AnnotationAssertion( "cellular component assembly at cellular level") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0022607") +AnnotationAssertion(rdfs:label "cellular component assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ribonucleoprotein complex biogenesis) + +AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:mah") "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex.") +AnnotationAssertion(Annotation( "GOC:mah") "RNA-protein complex biogenesis") +AnnotationAssertion(Annotation( "GOC:mah") "ribonucleoprotein complex biogenesis and assembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0022613") +AnnotationAssertion(rdfs:label "ribonucleoprotein complex biogenesis") +SubClassOf( ) + +# Class: (protein-RNA complex assembly) + +AnnotationAssertion(Annotation( "GOC:jl") "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.") +AnnotationAssertion( "RNA-protein complex assembly") +AnnotationAssertion( "RNP complex assembly") +AnnotationAssertion( "ribonucleoprotein complex assembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0022618") +AnnotationAssertion(rdfs:label "protein-RNA complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein-containing complex disassembly) + +AnnotationAssertion(Annotation( "GOC:mah") "The disaggregation of a protein-containing macromolecular complex into its constituent components.") +AnnotationAssertion( "protein complex disassembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "cellular macromolecule complex disassembly") +AnnotationAssertion( "cellular protein complex disassembly") +AnnotationAssertion( "macromolecule complex disassembly") +AnnotationAssertion( "GO:0032984") +AnnotationAssertion(rdfs:label "protein-containing complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein-RNA complex disassembly) + +AnnotationAssertion(Annotation( "GOC:mah") "The disaggregation of a protein-RNA complex into its constituent components.") +AnnotationAssertion( "RNA-protein complex disassembly") +AnnotationAssertion( "RNP complex disassembly") +AnnotationAssertion( "ribonucleoprotein complex disassembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032988") +AnnotationAssertion(rdfs:label "protein-RNA complex disassembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein-containing complex) + +AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:mah") "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.") +AnnotationAssertion( "macromolecular complex") +AnnotationAssertion( "macromolecule complex") +AnnotationAssertion( "protein containing complex") +AnnotationAssertion( "protein complex") +AnnotationAssertion( "protein-protein complex") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0032991") +AnnotationAssertion(rdfs:label "protein-containing complex") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (amino acid activation) + +AnnotationAssertion(Annotation( "GOC:jl") "The modification of an amino acid to an active form, for incorporation into a peptide, protein or other macromolecule.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0043038") +AnnotationAssertion(rdfs:label "amino acid activation") +SubClassOf( ) + +# Class: (tRNA aminoacylation) + +AnnotationAssertion(Annotation( "GOC:ma") Annotation( "GOC:mah") "The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.") +AnnotationAssertion(Annotation( "GOC:mah") "aminoacyl-tRNA biosynthesis") +AnnotationAssertion(Annotation( "GOC:mah") "aminoacyl-tRNA biosynthetic process") +AnnotationAssertion( "tRNA charging") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "amino acid activation") +AnnotationAssertion( "GO:0043039") +AnnotationAssertion(rdfs:label "tRNA aminoacylation") +SubClassOf( ) +SubClassOf( ) + +# Class: (macromolecule metabolic process) + +AnnotationAssertion(Annotation( "GOC:mah") "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.") +AnnotationAssertion(Annotation( "GOC:mtg_chebi_dec09") "biopolymer metabolic process") +AnnotationAssertion( "macromolecule metabolism") +AnnotationAssertion( "organismal macromolecule metabolism") +AnnotationAssertion( "multicellular organismal macromolecule metabolic process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0043170") +AnnotationAssertion(rdfs:label "macromolecule metabolic process") +SubClassOf( ) + +# Class: (protein-containing complex organization) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex.") +AnnotationAssertion(Annotation( "GOC:mah") "protein complex subunit organisation") +AnnotationAssertion( "protein complex subunit organization") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "cellular macromolecular complex organization") +AnnotationAssertion( "cellular macromolecular complex subunit organisation") +AnnotationAssertion( "cellular macromolecular complex subunit organization") +AnnotationAssertion( "macromolecular complex organization") +AnnotationAssertion( "macromolecular complex subunit organisation") +AnnotationAssertion( "macromolecular complex subunit organization") +AnnotationAssertion( "protein-containing complex subunit organization") +AnnotationAssertion( "GO:0043933") +AnnotationAssertion(rdfs:label "protein-containing complex organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular component biogenesis) + +AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:mah") "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.") +AnnotationAssertion( "cellular component biogenesis at cellular level") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0044085") +AnnotationAssertion(rdfs:label "cellular component biogenesis") +SubClassOf( ) + +# Class: (translation initiation ternary complex) + +AnnotationAssertion(Annotation( "GOC:jl") "A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator).") +AnnotationAssertion( "translation initiation (ternary) complex") +AnnotationAssertion( "Met-tRNA/eIF2.GTP ternary complex") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0044207") +AnnotationAssertion(rdfs:label "translation initiation ternary complex") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (primary metabolic process) + +AnnotationAssertion(Annotation( "GOC:curators") "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.") +AnnotationAssertion(Annotation(rdfs:label "Metabolism of amino acids and derivatives") "Reactome:R-HSA-71291") +AnnotationAssertion( "Wikipedia:Primary_metabolite") +AnnotationAssertion( "primary metabolism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0044238") +AnnotationAssertion(rdfs:label "primary metabolic process") +SubClassOf( ) + +# Class: (virion component) + +AnnotationAssertion(Annotation( "GOC:jl") "Any constituent part of a virion, a complete fully infectious extracellular virus particle.") +AnnotationAssertion( "Wikipedia:Virus") +AnnotationAssertion( "virion part") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "complete virus particle") +AnnotationAssertion( "virion") +AnnotationAssertion( "GO:0044423") +AnnotationAssertion(rdfs:label "virion component") +SubClassOf( ) +DisjointClasses( ) + +# Class: (protein-containing complex assembly) + +AnnotationAssertion(Annotation( "GOC:jl") "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.") +AnnotationAssertion( "cellular protein complex assembly") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "cellular macromolecule complex assembly") +AnnotationAssertion( "cellular protein-containing complex assembly") +AnnotationAssertion( "chaperone activity") +AnnotationAssertion( "macromolecular complex assembly") +AnnotationAssertion( "macromolecule complex assembly") +AnnotationAssertion( "protein complex assembly") +AnnotationAssertion( "protein complex formation") +AnnotationAssertion( "GO:0065003") +AnnotationAssertion(rdfs:label "protein-containing complex assembly") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (protein-RNA complex organization) + +AnnotationAssertion(Annotation( "GOC:mah") "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex.") +AnnotationAssertion(Annotation( "GOC:mah") "RNA-protein complex subunit organization") +AnnotationAssertion(Annotation( "GOC:mah") "protein-RNA complex subunit organization") +AnnotationAssertion(Annotation( "GOC:mah") "ribonucleoprotein complex subunit organisation") +AnnotationAssertion( "ribonucleoprotein complex subunit organization") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0071826") +AnnotationAssertion(rdfs:label "protein-RNA complex organization") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (cellular component organization or biogenesis) + +AnnotationAssertion(Annotation( "GOC:mah") "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.") +AnnotationAssertion(Annotation( "GOC:mah") "cellular component organisation or biogenesis") +AnnotationAssertion(Annotation( "GOC:mah") "cellular component organisation or biogenesis at cellular level") +AnnotationAssertion( "cellular component organization or biogenesis at cellular level") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0071840") +AnnotationAssertion(rdfs:label "cellular component organization or biogenesis") +SubClassOf( ) + +# Class: (nucleic acid metabolic process) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:tb") "Any cellular metabolic process involving nucleic acids.") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0090304") +AnnotationAssertion(rdfs:label "nucleic acid metabolic process") +SubClassOf( ) +SubClassOf( ) + +# Class: (cellular anatomical structure) + +AnnotationAssertion(Annotation( "GOC:kmv") "A part of a cellular organism consisting of a material entity with granularity above the level of a protein complex but below that of an anatomical system. Note that cellular organisms exclude viruses.") +AnnotationAssertion( "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.") +AnnotationAssertion( "cellular anatomical entity") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:0110165") +AnnotationAssertion(rdfs:label "cellular anatomical structure") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (catalytic activity, acting on a protein) + +AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify a protein.") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0140096") +AnnotationAssertion(rdfs:label "catalytic activity, acting on a protein") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (catalytic activity, acting on RNA) + +AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify RNA.") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0140098") +AnnotationAssertion(rdfs:label "catalytic activity, acting on RNA") +SubClassOf( ) + +# Class: (catalytic activity, acting on a tRNA) + +AnnotationAssertion(Annotation( "GOC:molecular_function_refactoring") Annotation( "GOC:pdt") "Catalytic activity that acts to modify a tRNA.") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0140101") +AnnotationAssertion(rdfs:label "catalytic activity, acting on a tRNA") +SubClassOf( ) + +# Class: (catalytic activity, acting on a nucleic acid) + +AnnotationAssertion(Annotation( "GOC:pg") "Catalytic activity that acts to modify a nucleic acid.") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0140640") +AnnotationAssertion(rdfs:label "catalytic activity, acting on a nucleic acid") +SubClassOf( ) + +# Class: (protein biosynthetic process) + +AnnotationAssertion(Annotation( "Wikipedia:Protein_biosynthesis") "The chemical reactions and pathways resulting in the formation of protein.") +AnnotationAssertion( "protein biosynthesis") +AnnotationAssertion( "protein synthesis") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0160307") +AnnotationAssertion(rdfs:label "protein biosynthetic process") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (ribonucleoprotein complex) + +AnnotationAssertion(Annotation( "GOC:krc") Annotation( "GOC:vesicles") "A macromolecular complex that contains both RNA and protein molecules.") +AnnotationAssertion( "Wikipedia:Ribonucleoprotein") +AnnotationAssertion( "RNA-protein complex") +AnnotationAssertion( "RNP") +AnnotationAssertion( "protein-RNA complex") +AnnotationAssertion( "extracellular ribonucleoprotein complex") +AnnotationAssertion( "intracellular ribonucleoprotein complex") +AnnotationAssertion( "cellular_component") +AnnotationAssertion( "GO:1990904") +AnnotationAssertion(rdfs:label "ribonucleoprotein complex") +SubClassOf( ) + # Class: (data entity) AnnotationAssertion( "Data items include counts of things, analyte concentrations, and statistical summaries."@en) @@ -895,6 +1732,38 @@ AnnotationAssertion(rdfs:label "den EquivalentClasses( ObjectOneOf( )) SubClassOf( ) +# Class: (protein) + +AnnotationAssertion(Annotation( "PRO:DAN") Annotation( "PRO:WCB") "An amino acid chain that is canonically produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.") +AnnotationAssertion(Annotation( "PRO:DAN") "natural protein") +AnnotationAssertion(Annotation( "IEDB:BP") "native protein") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000000001") +AnnotationAssertion(rdfs:label "protein") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amino acid chain) + +AnnotationAssertion(Annotation( "PRO:DAN") Annotation( "PRO:JSG") "A molecule 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.") +AnnotationAssertion(Annotation( "PRO:DAN") "peptide") +AnnotationAssertion(Annotation( "PRO:DAN") "polypeptide") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000018263") +AnnotationAssertion(rdfs:label "amino acid chain") +SubClassOf( ) + +# Class: (protein aggregate) + +AnnotationAssertion(Annotation( "GOC:add") Annotation( "PRO:ADD") Annotation( "PRO:DAN") Annotation( "PRO:LW") "An object aggregate that is composed primarily of protein constituents whereby gain or loss of an individual constituent will typically not have biological impact (unlike protein-containing complexes).") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000050565") +AnnotationAssertion(rdfs:label "protein aggregate") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + ############################ # Named Individuals @@ -1000,6 +1869,10 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) diff --git a/src/ontology/imports/pr_terms.txt b/src/ontology/imports/pr_terms.txt new file mode 100644 index 0000000..577dca2 --- /dev/null +++ b/src/ontology/imports/pr_terms.txt @@ -0,0 +1,2 @@ +PR:000000001 +PR:000018263 \ No newline at end of file From 82a9be9dc5962c0515eceab199bf15de06094bfd Mon Sep 17 00:00:00 2001 From: Ximeaixa Date: Fri, 18 Sep 2026 11:41:30 +0200 Subject: [PATCH 2/6] replace IDPO protein term with PR, obsolete IDPO protein and compound --- src/ontology/idpo-edit.owl | 36 +++++++++++++++++++----------------- 1 file changed, 19 insertions(+), 17 deletions(-) diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 562b51b..90116c0 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -13,9 +13,7 @@ Annotation( ) Annotation( ) Annotation( ) -Annotation( ) Annotation( ) -Annotation( ) Annotation( ) Annotation( ) Annotation( "It describes structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state.") @@ -181,7 +179,7 @@ AnnotationAssertion( "IDPO:0000001") AnnotationAssertion(rdfs:label "protein structural state") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) # Class: (disorder state) @@ -870,6 +868,7 @@ SubClassOf( "OBSOLETE. A temporally extended process in which a protein or protein region changes from one state to another, under specific conditions.") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( "IDPO:0000080") AnnotationAssertion(rdfs:comment "Obsolete due to semantic ambiguity and excessive generality.") AnnotationAssertion(rdfs:label "obsolete transition") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -934,17 +933,19 @@ SubClassOf( "OBSOLETE. A quality of a protein or protein region that describes its organization, conformation, or material properties at a given time, under specific conditions, and that can change dynamically.") AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( "IDPO:0000089") AnnotationAssertion(rdfs:comment "The term was originally introduced as a high-level grouping class but is now obsolete because it is overly general and semantically ambiguous.") AnnotationAssertion(rdfs:label "obsolete state") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -# Class: (compound) +# Class: (obsolete compound) -AnnotationAssertion( "An object composed of two or more distinct chemical constituents.") -AnnotationAssertion( "material_entity") +AnnotationAssertion( "OBSOLETE. An object composed of two or more distinct chemical constituents.") +AnnotationAssertion( ) AnnotationAssertion( "IDPO:0000091") -AnnotationAssertion(rdfs:label "compound") -SubClassOf( ) +AnnotationAssertion(rdfs:comment "Obsolete because the term is no longer used in IDPO.") +AnnotationAssertion(rdfs:label "obsolete compound") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Class: (condensate) @@ -963,13 +964,14 @@ AnnotationAssertion(rdfs:label "bi SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (protein) +# Class: (obsolete protein) -AnnotationAssertion( "An object composed of one or more polypeptide chains.") -AnnotationAssertion( "material_entity") +AnnotationAssertion( "OBSOLETE. An object composed of one or more polypeptide chains.") +AnnotationAssertion( ) AnnotationAssertion( "IDPO:0000094") -AnnotationAssertion(rdfs:label "protein") -SubClassOf( ) +AnnotationAssertion(rdfs:comment "Obsolete because the term duplicates PR:000000001, which is reused directly.") +AnnotationAssertion(rdfs:label "obsolete protein") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) # Class: (protein region) @@ -978,7 +980,7 @@ AnnotationAssertion( "IDPO:0000095") AnnotationAssertion(rdfs:label "protein region") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (intrinsically disordered protein) @@ -987,8 +989,8 @@ AnnotationAssertion( "material_entity") AnnotationAssertion( "IDPO:0000096") AnnotationAssertion(rdfs:label "intrinsically disordered protein") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (intrinsically disordered region) @@ -1025,7 +1027,7 @@ AnnotationAssertion( "IDPO:0000100") AnnotationAssertion(rdfs:label "disorder role") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectSomeValuesFrom( ObjectUnionOf( ))) # Class: (N-glycosylation target role) From fe946284608bd129ef7ab62de07d19ee58276788 Mon Sep 17 00:00:00 2001 From: Ximeaixa Date: Fri, 18 Sep 2026 12:01:14 +0200 Subject: [PATCH 3/6] protein region definition fix --- src/ontology/idpo-edit.owl | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 90116c0..a0b7c6a 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -822,7 +822,6 @@ AnnotationAssertion( "IDPO:0000075") AnnotationAssertion(rdfs:label "condensate material state") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (liquid-like condensate state) @@ -975,7 +974,7 @@ AnnotationAssertion(owl:deprecated # Class: (protein region) -AnnotationAssertion( "A fiat object part that is a contiguous portion of a protein distinguishable by its structural, functional, or sequence properties.") +AnnotationAssertion( "A fiat object part that is a contiguous portion of a protein.") AnnotationAssertion( "material_entity") AnnotationAssertion( "IDPO:0000095") AnnotationAssertion(rdfs:label "protein region") From 3e3a9126c6539e22f40c86f5edf78ddbac92468b Mon Sep 17 00:00:00 2001 From: Ximeaixa Date: Fri, 18 Sep 2026 12:02:25 +0200 Subject: [PATCH 4/6] ontology root added for idp --- src/ontology/idpo-edit.owl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index a0b7c6a..7373539 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -15,6 +15,7 @@ Annotation( ) Annotation( ) Annotation( ) +Annotation( ) Annotation( ) Annotation( "It describes structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state.") Annotation( ) From 8c732c31d52a6313794ce7ac7e3273bf19caf385 Mon Sep 17 00:00:00 2001 From: Ximeaixa Date: Fri, 18 Sep 2026 14:00:34 +0200 Subject: [PATCH 5/6] remove LLPS axioms --- src/ontology/idpo-edit.owl | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 7373539..8843875 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -419,8 +419,6 @@ AnnotationAssertion( "IDPO:0000025") AnnotationAssertion(rdfs:label "liquid-liquid phase separation") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (condensate ageing) From a5906cf4eec54274d9b351255fe0bbcc51645aed Mon Sep 17 00:00:00 2001 From: Ximeaixa Date: Wed, 23 Sep 2026 09:46:10 +0200 Subject: [PATCH 6/6] refresh imports --- src/ontology/imports/merged_import.owl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index a36ce93..956512d 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2026-09-17") + +Annotation(owl:versionInfo "2026-09-23") Declaration(Class()) Declaration(Class())