Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) Prefix(xsd:=) Prefix(rdfs:=) Ontology( Annotation(owl:versionInfo "2023-05-19") 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()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty(rdfs:label)) ############################ # Annotation Properties ############################ # Annotation Property: (definition) AnnotationAssertion(rdfs:label "definition") # Annotation Property: () SubAnnotationPropertyOf( ) # Annotation Property: (has_alternative_id) AnnotationAssertion(rdfs:label "has_alternative_id") # Annotation Property: (database_cross_reference) AnnotationAssertion(rdfs:label "database_cross_reference") # Annotation Property: (has_exact_synonym) AnnotationAssertion(rdfs:label "has_exact_synonym") # Annotation Property: (has_narrow_synonym) AnnotationAssertion(rdfs:label "has_narrow_synonym") # Annotation Property: (has_obo_namespace) AnnotationAssertion(rdfs:label "has_obo_namespace") # Annotation Property: (has_related_synonym) AnnotationAssertion(rdfs:label "has_related_synonym") # Annotation Property: (shorthand) AnnotationAssertion(rdfs:label "shorthand") ############################ # Object Properties ############################ # Object Property: (part_of) AnnotationAssertion( "BFO:0000050") AnnotationAssertion( "protein") AnnotationAssertion( "part_of") AnnotationAssertion( "part_of") AnnotationAssertion(rdfs:label "part_of") TransitiveObjectProperty() # Object Property: (has_part) AnnotationAssertion( "BFO:0000051") AnnotationAssertion( "protein") AnnotationAssertion( "has_part") AnnotationAssertion( "has_part") AnnotationAssertion(rdfs:label "has_part") TransitiveObjectProperty() # Object Property: (participates_in) AnnotationAssertion( "RO:0000056") AnnotationAssertion( "protein") AnnotationAssertion( "participates_in") AnnotationAssertion( "false"^^xsd:boolean) AnnotationAssertion( "participates_in") AnnotationAssertion(rdfs:label "participates_in") # Object Property: (has_component) AnnotationAssertion( "RO:0002180") AnnotationAssertion( "protein") AnnotationAssertion( "has_component") AnnotationAssertion( "false"^^xsd:boolean) AnnotationAssertion( "has_component") AnnotationAssertion(rdfs:label "has_component") # Object Property: (output_of) AnnotationAssertion( "RO:0002353") AnnotationAssertion( "protein") AnnotationAssertion( "output_of") AnnotationAssertion( "false"^^xsd:boolean) AnnotationAssertion( "output_of") AnnotationAssertion(rdfs:label "output_of") # Object Property: (has_constituent_monomer) AnnotationAssertion(Annotation( "PRO:DAN") "A relation that holds between a polymer and its constituent monomers. P has_constituent_monomer c if and only if P has_component multiple instances of c and each instance of c is covalently attached to another instance of c.") AnnotationAssertion( "protein") AnnotationAssertion( "has_constituent_monomer") AnnotationAssertion( "false"^^xsd:boolean) AnnotationAssertion(rdfs:comment "The constituent monomers need not be covalently attached in an end-to-end manner; that is, polymers with internal connections (e.g., polyubiquitin) can use this relation, as can circular polymers (e.g., plasmids) and multi-branched polymers (e.g., glycans). This relation, as non-transitive, allows one to indicate the number of instances of c.") AnnotationAssertion(rdfs:label "has_constituent_monomer") SubObjectPropertyOf( ) # Object Property: (has_gene_template) AnnotationAssertion(Annotation( "PRO:DAN") "See document https://docs.google.com/document/d/15iVMtMyYbQSlvUDgn2XUaDzpwkB0USZI for full definition.") AnnotationAssertion( "protein") AnnotationAssertion( "has_gene_template") AnnotationAssertion( "false"^^xsd:boolean) AnnotationAssertion(rdfs:label "has_gene_template") SubObjectPropertyOf( ) ############################ # Classes ############################ # Class: (process) AnnotationAssertion( "bfo") AnnotationAssertion( "BFO:0000015") AnnotationAssertion(rdfs:label "process") # Class: (object) AnnotationAssertion( "bfo") AnnotationAssertion( "BFO:0000030") AnnotationAssertion(rdfs:label "object") SubClassOf( ) # Class: (material entity) AnnotationAssertion( "bfo") AnnotationAssertion( "BFO:0000040") AnnotationAssertion(rdfs:label "material entity") # Class: (molecular entity) AnnotationAssertion(Annotation( "fake:2") "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.") AnnotationAssertion( "chebi_ontology") AnnotationAssertion( "CHEBI:23367") AnnotationAssertion(rdfs:label "molecular entity") SubClassOf( ) # Class: (chemical entity) AnnotationAssertion( "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.") AnnotationAssertion( "chebi_ontology") AnnotationAssertion( "CHEBI:24431") AnnotationAssertion(rdfs:label "chemical entity") SubClassOf( ) # Class: (organic group) AnnotationAssertion( "Any substituent group or skeleton containing carbon.") AnnotationAssertion( "chebi_ontology") AnnotationAssertion( "CHEBI:33247") AnnotationAssertion(rdfs:label "organic group") SubClassOf( ) # Class: (amino-acid residue) AnnotationAssertion(Annotation( "Dummy:dummy") "When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.") AnnotationAssertion( "amino acid residue") AnnotationAssertion(Annotation( "PRO:DAN") "protein residue") AnnotationAssertion( "chebi_ontology") AnnotationAssertion( "CHEBI:33708") AnnotationAssertion(rdfs:label "amino-acid residue") SubClassOf( ) # Class: (organic amino compound) AnnotationAssertion( "A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.") AnnotationAssertion( "chebi_ontology") AnnotationAssertion( "CHEBI:50047") AnnotationAssertion(rdfs:label "organic amino compound") SubClassOf( ) # Class: (translation) AnnotationAssertion(Annotation( "GOC:go_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( "protein anabolism") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0006412") AnnotationAssertion(rdfs:label "translation") SubClassOf( ) # Class: (biological_process) AnnotationAssertion(Annotation( "GOC:pdt") "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. 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( "biological process") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0008150") AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.") AnnotationAssertion(rdfs:label "biological_process") # Class: (Eukaryota) AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion(Annotation( "PRO:DAN") Annotation( ) "euk-") AnnotationAssertion( "NCBITaxon:2759") AnnotationAssertion(rdfs:label "Eukaryota") SubClassOf( ) # Class: (Schizosaccharomyces pombe) AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:4896") AnnotationAssertion(rdfs:label "Schizosaccharomyces pombe") SubClassOf( ) # Class: (Saccharomyces cerevisiae) AnnotationAssertion( "ncbi_taxonomy") AnnotationAssertion( "NCBITaxon:4932") AnnotationAssertion(rdfs:label "Saccharomyces cerevisiae") SubClassOf( ) # Class: (organism) AnnotationAssertion( "obi") AnnotationAssertion( "OBI:0100026") AnnotationAssertion(rdfs:comment "Category=external.") AnnotationAssertion(rdfs:label "organism") SubClassOf( ) # Class: (protein) AnnotationAssertion(Annotation( "PRO:DAN") Annotation( "PRO:WCB") "An amino acid chain that is 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:comment "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].") AnnotationAssertion(rdfs:label "protein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (amino acid chain) AnnotationAssertion(Annotation( "PRO:DAN") Annotation( "PRO:JSG") "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.") AnnotationAssertion(Annotation( "PRO:DAN") "peptide") AnnotationAssertion(Annotation( "PRO:DAN") "polypeptide") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000018263") AnnotationAssertion(rdfs:comment "Category=polymer.") AnnotationAssertion(rdfs:label "amino acid chain") SubClassOf( ) SubClassOf( ObjectMinCardinality(2 )) # Class: (protein-containing material entity) AnnotationAssertion(Annotation( "PRO:DAN") "A material entity that minimally consists of a protein.") AnnotationAssertion(Annotation( "PRO:DAN") "protein") AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000050567") AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).") AnnotationAssertion(rdfs:label "protein-containing material entity") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sequence_feature) AnnotationAssertion(Annotation( "SO:ke") "An extent of biological sequence.") AnnotationAssertion( "located_sequence_feature") AnnotationAssertion( "sequence feature") AnnotationAssertion( "sequence") AnnotationAssertion( "located sequence feature") AnnotationAssertion( "SO:0000110") AnnotationAssertion(rdfs:label "sequence_feature") # Class: (gene) AnnotationAssertion(Annotation( "SO:immuno_workshop") "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.") AnnotationAssertion( "sequence") AnnotationAssertion( "SO:0000704") AnnotationAssertion(rdfs:label "gene") SubClassOf( ) )