diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl new file mode 100644 index 0000000..70fcb13 --- /dev/null +++ b/src/ontology/imports/go_import.owl @@ -0,0 +1,558 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-08-13") + +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(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()) +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:comment)) +Declaration(AnnotationProperty(rdfs:label)) +############################ +# Annotation Properties +############################ + +# Annotation Property: (definition) + +AnnotationAssertion(rdfs:label "definition") + +# Annotation Property: (term replaced by) + +AnnotationAssertion(rdfs:label "term replaced by") + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: (has_alternative_id) + +AnnotationAssertion(rdfs:label "has_alternative_id") + +# Annotation Property: (has_broad_synonym) + +AnnotationAssertion(rdfs:label "has_broad_synonym") + +# 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: (has_synonym_type) + +AnnotationAssertion(rdfs:label "has_synonym_type") + +# Annotation Property: (in_subset) + +AnnotationAssertion(rdfs:label "in_subset") + +# Annotation Property: (shorthand) + +AnnotationAssertion(rdfs:label "shorthand") + + +############################ +# Object Properties +############################ + +# Object Property: (part of) + +AnnotationAssertion( "BFO:0000050") +AnnotationAssertion( "external") +AnnotationAssertion( "part_of") +AnnotationAssertion( "part_of") +AnnotationAssertion(rdfs:label "part of") +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (has part) + +AnnotationAssertion( "BFO:0000051") +AnnotationAssertion( "external") +AnnotationAssertion( "has_part") +AnnotationAssertion( "has_part") +AnnotationAssertion(rdfs:label "has part") +TransitiveObjectProperty() + +# Object Property: (occurs in) + +AnnotationAssertion( "BFO:0000066") +AnnotationAssertion( "external") +AnnotationAssertion( "occurs_in") +AnnotationAssertion( "occurs_in") +AnnotationAssertion(rdfs:label "occurs in") + +# Object Property: (ends during) + +AnnotationAssertion( "RO:0002093") +AnnotationAssertion( "external") +AnnotationAssertion( "ends_during") +AnnotationAssertion( "ends_during") +AnnotationAssertion(rdfs:label "ends during") + +# Object Property: (regulates) + +AnnotationAssertion( "RO:0002211") +AnnotationAssertion( "external") +AnnotationAssertion( "regulates") +AnnotationAssertion( "regulates") +AnnotationAssertion(rdfs:label "regulates") +TransitiveObjectProperty() + +# Object Property: (negatively regulates) + +AnnotationAssertion( "RO:0002212") +AnnotationAssertion( "external") +AnnotationAssertion( "negatively_regulates") +AnnotationAssertion( "negatively_regulates") +AnnotationAssertion(rdfs:label "negatively regulates") +SubObjectPropertyOf( ) + +# Object Property: (positively regulates) + +AnnotationAssertion( "RO:0002213") +AnnotationAssertion( "external") +AnnotationAssertion( "positively_regulates") +AnnotationAssertion( "positively_regulates") +AnnotationAssertion(rdfs:label "positively regulates") +SubObjectPropertyOf( ) + + + +############################ +# Classes +############################ + +# Class: (behavior) + +AnnotationAssertion(Annotation( "GOC:ems") Annotation( "GOC:jl") Annotation( "ISBN:0395448956") Annotation( "PMID:20160973") "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.") +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-20T14:06:08Z") +AnnotationAssertion( "GO:0023032") +AnnotationAssertion( "GO:0044708") +AnnotationAssertion( "GO:0044709") +AnnotationAssertion( "Wikipedia:Behavior") +AnnotationAssertion( "behavioral response to stimulus") +AnnotationAssertion( "behaviour") +AnnotationAssertion( "behavioural response to stimulus") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "single-organism behavior") +AnnotationAssertion( "GO:0007610") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. +2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis).") +AnnotationAssertion(rdfs:label "behavior") +SubClassOf( ) + +# 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( "https://github.com/geneontology/go-ontology/issues/24968"^^xsd:anyURI) +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-19T15:05:24Z") +AnnotationAssertion( "GO:0000004") +AnnotationAssertion( "GO:0007582") +AnnotationAssertion( "GO:0044699") +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( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that, in addition to forming the root of the biological process ontology, this term is recommended 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: (viral process) + +AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:jl") Annotation( "GOC:mah") "A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.") +AnnotationAssertion( ) +AnnotationAssertion( "GO:0022415") +AnnotationAssertion( "Wikipedia:Viral_life_cycle") +AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:jl") "virus process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "viral infection") +AnnotationAssertion( "virulence") +AnnotationAssertion( "GO:0016032") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "See also the biological process terms 'viral infectious cycle ; GO:0019058' and 'lysogeny ; GO:0030069'.") +AnnotationAssertion(rdfs:label "viral process") +SubClassOf( ) + +# Class: (viral life cycle) + +AnnotationAssertion(Annotation( "ISBN:1555811272") "A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.") +AnnotationAssertion( "GO:0019067") +AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:jl") "viral assembly, maturation, egress, and release") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "lytic viral life cycle") +AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:jl") "viral infectious cycle") +AnnotationAssertion(Annotation( "GOC:bf") Annotation( "GOC:jl") "viral replication") +AnnotationAssertion( "GO:0019058") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "viral life cycle") +SubClassOf( ) + +# Class: (reproductive behavior) + +AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:pr") "The specific behavior of an organism that is associated with reproduction.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/23491"^^xsd:anyURI) +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-19T16:01:37Z") +AnnotationAssertion( "GO:0033057") +AnnotationAssertion( "GO:0044704") +AnnotationAssertion( "GO:0044705") +AnnotationAssertion( "reproductive behavior in a multicellular organism") +AnnotationAssertion( "reproductive behaviour") +AnnotationAssertion( "multi-organism reproductive behavior") +AnnotationAssertion( "multicellular organism reproductive behavior") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "single-organism reproductive behavior") +AnnotationAssertion( "GO:0019098") +AnnotationAssertion(rdfs:label "reproductive behavior") +EquivalentClasses( ObjectIntersectionOf( )) +SubClassOf( ) +SubClassOf( ) + +# Class: (sexual reproduction) + +AnnotationAssertion(Annotation( "Wikipedia:Sexual_reproduction") "A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid).") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22929"^^xsd:anyURI) +AnnotationAssertion( "Wikipedia:Sexual_reproduction") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0019953") +AnnotationAssertion(rdfs:comment "Note that gametes may come from two organisms or from a single organism in the case of self-fertilizing hermaphrodites, e.g. C. elegans, or self-fertilization in plants. Note also that sexual reproduction may be seen as the regular alternation, in the life cycle of haplontic, diplontic and diplohaplontic organisms, of meiosis and fertilization which provides for the production offspring. In diplontic organisms there is a life cycle in which the products of meiosis behave directly as gametes, fusing to form a zygote from which the diploid, or sexually reproductive polyploid, adult organism will develop. In diplohaplontic organisms a haploid phase (gametophyte) exists in the life cycle between meiosis and fertilization (e.g. higher plants, many algae and Fungi); the products of meiosis are spores that develop as haploid individuals from which haploid gametes develop to form a diploid zygote; diplohaplontic organisms show an alternation of haploid and diploid generations. In haplontic organisms meiosis occurs in the zygote, giving rise to four haploid cells (e.g. many algae and protozoa), only the zygote is diploid and this may form a resistant spore, tiding organisms over hard times.") +AnnotationAssertion(rdfs:label "sexual reproduction") +SubClassOf( ) + +# Class: (asexual reproduction) + +AnnotationAssertion(Annotation( "ISBN:0387520546") Annotation( "PMID:22977071") Annotation( "PMID:28779329") Annotation( "PMID:29559496") "A type of reproduction in which new individuals are produced from a single organism, either from an unfertilized egg or from a single cell or group of cells.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/22929"^^xsd:anyURI) +AnnotationAssertion( "Wikipedia:Asexual_reproduction") +AnnotationAssertion( "biological_process") +AnnotationAssertion(Annotation( "Wikipedia:Parthenogenesis") "parthenogenesis") +AnnotationAssertion( "GO:0019954") +AnnotationAssertion(rdfs:label "asexual reproduction") +SubClassOf( ) + +# Class: (reproductive process) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:isa_complete") "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27054"^^xsd:anyURI) +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-19T15:56:06Z") +AnnotationAssertion( "GO:0044702") +AnnotationAssertion( "Wikipedia:Reproduction") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "single organism reproductive process") +AnnotationAssertion( "GO:0022414") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "reproductive process") +SubClassOf( ) + +# Class: (multicellular organismal process) + +AnnotationAssertion(Annotation( "GOC:curators") Annotation( "GOC:dph") Annotation( "GOC:isa_complete") Annotation( "GOC:tb") "Any biological process, occurring at the level of a multicellular organism, pertinent to its function.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27189"^^xsd:anyURI) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "jl") +AnnotationAssertion( "2012-09-19T16:07:47Z") +AnnotationAssertion( "GO:0044707") +AnnotationAssertion( "GO:0050874") +AnnotationAssertion( "organismal physiological process") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "single-multicellular organism process") +AnnotationAssertion( "GO:0032501") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.") +AnnotationAssertion(rdfs:label "multicellular organismal process") +SubClassOf( ) + +# Class: (obsolete multicellular organism reproduction) + +AnnotationAssertion(Annotation( "GOC:isa_complete") Annotation( "GOC:jid") "OBSOLETE. The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27054"^^xsd:anyURI) +AnnotationAssertion( "GO:0048609") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0032504") +AnnotationAssertion(rdfs:comment "The reason for obsoletion is that this term is equivalent to multicellular organismal reproductive process.") +AnnotationAssertion(rdfs:label "obsolete multicellular organism reproduction") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) + +# Class: (biological process involved in symbiotic interaction) + +AnnotationAssertion(Annotation( "GOC:cc") Annotation( "PMID:31257129") "A process carried out by gene products in an organism that enable the organism to engage in a symbiotic relationship, a more or less intimate association, with another organism. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/14807"^^xsd:anyURI) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20191"^^xsd:anyURI) +AnnotationAssertion( "GO:0043298") +AnnotationAssertion( "GO:0044404") +AnnotationAssertion( "GO:0072519") +AnnotationAssertion( "GO:0085031") +AnnotationAssertion( "commensalism") +AnnotationAssertion( "host-pathogen interaction") +AnnotationAssertion( "parasitism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "symbiosis") +AnnotationAssertion( "symbiosis, encompassing mutualism through parasitism") +AnnotationAssertion( "symbiotic interaction") +AnnotationAssertion( "symbiotic interaction between host and organism") +AnnotationAssertion( "symbiotic interaction between organisms") +AnnotationAssertion( "symbiotic interaction between species") +AnnotationAssertion( "symbiotic process") +AnnotationAssertion( "GO:0044403") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "biological process involved in symbiotic interaction") +SubClassOf( ) + +# Class: (symbiont entry into host) + +AnnotationAssertion(Annotation( "GOC:vw") "Entry of a symbiont into the body, tissues, or cells of a host organism as part of the symbiont life cycle. The host is defined as the larger of the organisms involved in a symbiotic interaction.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18563"^^xsd:anyURI) +AnnotationAssertion( "GO:0030260") +AnnotationAssertion( "GO:0044411") +AnnotationAssertion( "GO:0051806") +AnnotationAssertion( "GO:0051828") +AnnotationAssertion( "GO:0051830") +AnnotationAssertion( "GO:0075052") +AnnotationAssertion( "GO:0085027") +AnnotationAssertion( "GO:0085028") +AnnotationAssertion( "entry into host") +AnnotationAssertion( "host invasion") +AnnotationAssertion(Annotation( "GOC:vw") "host penetration") +AnnotationAssertion( "invasion into host") +AnnotationAssertion( "invasion of host") +AnnotationAssertion(Annotation( "GOC:vw") "penetration into host") +AnnotationAssertion(Annotation( "GOC:tb") "entry into cell of other organism during symbiotic interaction") +AnnotationAssertion( "entry into host cell via penetration peg") +AnnotationAssertion( "entry into host via a specialized structure during symbiotic interaction") +AnnotationAssertion( "entry into host via enzymatic degradation of host anatomical structure") +AnnotationAssertion( "entry into host via enzymatic degradation of host cuticle") +AnnotationAssertion(Annotation( "GOC:vw") "penetration into host via a specialized structure") +AnnotationAssertion(Annotation( "GOC:vw") "penetration into host via a specialized structure during symbiotic interaction") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "entry into cell of other organism involved in symbiotic interaction") +AnnotationAssertion( "entry into host through host barriers") +AnnotationAssertion(Annotation( "GOC:tb") "entry into other organism during symbiotic interaction") +AnnotationAssertion( "entry into other organism involved in symbiotic interaction") +AnnotationAssertion( "invasion into other organism") +AnnotationAssertion( "invasion of other organism") +AnnotationAssertion( "invasive growth") +AnnotationAssertion( "other organism invasion") +AnnotationAssertion( "GO:0044409") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "symbiont entry into host") +SubClassOf( ) + +# Class: (biological process involved in interspecies interaction between organisms) + +AnnotationAssertion(Annotation( "GOC:cc") "Any process evolved to enable an interaction with an organism of a different species.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20191"^^xsd:anyURI) +AnnotationAssertion( ) +AnnotationAssertion( "interaction with another species") +AnnotationAssertion( "interspecies interaction") +AnnotationAssertion( "interspecies interaction between organisms") +AnnotationAssertion( "interspecies interaction with other organisms") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0044419") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "biological process involved in interspecies interaction between organisms") +SubClassOf( ) + +# Class: (multicellular organismal reproductive process) + +AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jid") Annotation( "GOC:tb") "The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/27054"^^xsd:anyURI) +AnnotationAssertion( "organismal reproductive process") +AnnotationAssertion( "reproductive process in a multicellular organism") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0048609") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "multicellular organismal reproductive process") +SubClassOf( ) + +# Class: (biological process involved in interaction with host) + +AnnotationAssertion(Annotation( "GOC:cc") "An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/20191"^^xsd:anyURI) +AnnotationAssertion( "GO:0044112") +AnnotationAssertion( "GO:0044116") +AnnotationAssertion( "GO:0044117") +AnnotationAssertion( "GO:0044119") +AnnotationAssertion( "GO:0044121") +AnnotationAssertion( "GO:0044123") +AnnotationAssertion( "GO:0044125") +AnnotationAssertion( "interaction with host") +AnnotationAssertion( "growth of symbiont in host") +AnnotationAssertion( "growth of symbiont in host cell") +AnnotationAssertion( "growth of symbiont in host organelle") +AnnotationAssertion( "growth of symbiont in host vacuole") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0051701") +AnnotationAssertion(rdfs:label "biological process involved in interaction with host") +SubClassOf( ) + + +SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) +) \ No newline at end of file diff --git a/src/ontology/imports/go_terms.txt b/src/ontology/imports/go_terms.txt new file mode 100644 index 0000000..8cd41af --- /dev/null +++ b/src/ontology/imports/go_terms.txt @@ -0,0 +1,56 @@ +GO_0000003 +GO_0006950 +GO_0006952 +GO_0006954 +GO_0007562 +GO_0007565 +GO_0007567 +GO_0007568 +GO_0007610 +GO_0007617 +GO_0008150 +GO_0010259 +GO_0010941 +GO_0018991 +GO_0019048 +GO_0019051 +GO_0019054 +GO_0019098 +GO_0022414 +GO_0022414 +GO_0032502 +GO_0032504 +GO_0033057 +GO_0035176 +GO_0035821 +GO_0039651 +GO_0043067 +GO_0044003 +GO_0044409 +GO_0044419 +GO_0044531 +GO_0044703 +GO_0044705 +GO_0048609 +GO_0050789 +GO_0050794 +GO_0050896 +GO_0051234 +GO_0051701 +GO_0051704 +GO_0051705 +GO_0051817 +GO_0052040 +GO_0052042 +GO_0052151 +GO_0052248 +GO_0052501 +GO_0060139 +GO_0060153 +GO_0060403 +GO_0065007 +GO_0065008 +GO_0071684 +GO:0019058 +GO:0019954 +GO:0019953 diff --git a/src/scripts/run-command.sh b/src/scripts/run-command.sh new file mode 100755 index 0000000..45d431d --- /dev/null +++ b/src/scripts/run-command.sh @@ -0,0 +1,4 @@ +#!/bin/sh +ODK_DEBUG_FILE=${ODK_DEBUG_FILE:-debug.log} +echo "Command: sh $@" >> $ODK_DEBUG_FILE +/usr/bin/time -a -o $ODK_DEBUG_FILE -f "Elapsed time: %E\nPeak memory: %M kb" /bin/sh "$@" diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql new file mode 100644 index 0000000..a6a4851 --- /dev/null +++ b/src/sparql/class-count-by-prefix.sparql @@ -0,0 +1,10 @@ +prefix owl: +prefix obo: + +SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE +{ + ?cls a owl:Class . + FILTER (!isBlank(?cls)) + BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix) +} +GROUP BY ?prefix \ No newline at end of file