diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 20f6ab6..110af6c 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,7 +19,7 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.5 + container: obolibrary/odkfull:v1.5.2 # Steps represent a sequence of tasks that will be executed as part of the job steps: diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 1868f0c..3bc6584 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -21,6 +21,7 @@ These are the current imports in APOLLO_SV | geo | http://purl.obolibrary.org/obo/geo/dev/geo.owl | mirror | | ido | http://purl.obolibrary.org/obo/ido.owl | slme | | mf | http://purl.obolibrary.org/obo/mf.owl | slme | +| go | http://purl.obolibrary.org/obo/go.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 4aeb2d3..450b672 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for apollo_sv # Generated using ontology-development-kit -# ODK Version: v1.5 +# ODK Version: v1.5.2 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use apollo_sv.Makefile instead @@ -16,7 +16,7 @@ # 3. [Update repo to latest ODK](update_repo) # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 8c83508f90aec6eebe48cba22814c2547bdf197ecf902ac8f55664f6ae708683 +CONFIG_HASH= c731446a515442f3b378e0f8803a2a533d775453ddcf1c23a26ddaed7564e0a1 # ---------------------------------------- @@ -52,7 +52,7 @@ REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range SPARQL_EXPORTS = basic-report -ODK_VERSION_MAKEFILE = v1.5 +ODK_VERSION_MAKEFILE = v1.5.2 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -165,7 +165,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = ro pno geo ido mf +IMPORTS = ro pno geo ido mf go IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -423,6 +423,14 @@ $(IMPORTDIR)/mf_import.owl: $(MIRRORDIR)/mf.owl $(IMPORTDIR)/mf_terms_combined.t query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ $(ANNOTATE_CONVERT_FILE); fi +## Module for ontology: go + +$(IMPORTDIR)/go_import.owl: $(MIRRORDIR)/go.owl $(IMPORTDIR)/go_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/go_terms_combined.txt --copy-ontology-annotations true --force true --individuals exclude --method BOT \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ + $(ANNOTATE_CONVERT_FILE); fi + .PHONY: refresh-imports refresh-imports: @@ -493,6 +501,14 @@ mirror-mf: | $(TMPDIR) $(ROBOT) convert -i $(TMPDIR)/mf-download.owl -o $(TMPDIR)/$@.owl +## ONTOLOGY: go +.PHONY: mirror-go +.PRECIOUS: $(MIRRORDIR)/go.owl +mirror-go: | $(TMPDIR) + curl -L $(OBOBASE)/go.owl --create-dirs -o $(TMPDIR)/go-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/go-download.owl -o $(TMPDIR)/$@.owl + + $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ cp $(TMPDIR)/mirror-$*.owl $@; fi; fi diff --git a/src/ontology/apollo_sv-edit.owl b/src/ontology/apollo_sv-edit.owl index 970c738..cbc23a9 100644 --- a/src/ontology/apollo_sv-edit.owl +++ b/src/ontology/apollo_sv-edit.owl @@ -2,6 +2,7 @@ + @@ -3983,7 +3985,7 @@ The concept derives from the epidemiological notion of ‘herd immunity,’ whic - + @@ -4001,7 +4003,7 @@ The concept derives from the epidemiological notion of ‘herd immunity,’ whic - + @@ -5181,26 +5183,19 @@ I checked because an infection and immunity census would involve two different c - + - + - - - - - - - - + - + @@ -5598,7 +5593,7 @@ The infectious disease scenario typically also includes a lot of additional data - + @@ -6460,7 +6455,7 @@ can't recall whether we should use process or processual_entity for future - + @@ -7634,7 +7629,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + @@ -7842,7 +7837,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + @@ -7862,7 +7857,7 @@ The constant rate may be zero. The period of an epidemic may be defined using s - + biological colonization a reproduction of a pathogen of a particular biological taxon inside a host organism of another taxon, without invasion of the tissues of the host. William R. Hogan @@ -13451,6 +13446,28 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + + + + + + + + + + organism reproduction + The process by which new organisms are created from existing ones. + William R. Hogan + Reproduction + reproduction + + + + @@ -14116,923 +14133,6 @@ By "similar vaccines" we typically mean same pathogen, but could be si - - - - - The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. - http://purl.org/obo/owl/gene_ontology - The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism. - Reproduction - GO:0019952 - GO:0050876 - biological_process - - - - - reproduction - - - - - - - - - Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). - http://purl.obolibrary.org/obo/go.owl - biological_process - response to abiotic stress - response to biotic stress - GO:0006950 - - - - - - - - - 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. - response to stress - - - - - - - - - Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. - http://purl.obolibrary.org/obo/go.owl - GO:0002217 - GO:0042829 - defence response - physiological defense response - biological_process - antimicrobial peptide activity - defense/immunity protein activity - GO:0006952 - - defense response - - - - - - - - - The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. - http://purl.obolibrary.org/obo/go.owl - Inflammation - Wikipedia:Inflammation - biological_process - GO:0006954 - This term was improved by GO_REF:0000022. It was moved. - inflammatory response - - - - - - - - - The emergence of an adult insect from a pupa case. - http://purl.org/obo/owl/gene_ontology - - - - - - - biological_process - eclose - eclosion - - - - - - - - - The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth. - http://purl.obolibrary.org/obo/go.owl - Wikipedia:Gestation - gestation - biological_process - carrying of young - GO:0007565 - - female pregnancy - - - - - - - - - The reproductive process in which the parent is separated from its offspring either by giving birth to live young or by laying eggs. - http://purl.obolibrary.org/obo/go.owl - giving birth - egg laying - biological_process - GO:0007567 - parturition - - - - - - - - - http://purl.org/obo/owl/gene_ontology - GO:0016280 - - - - - - - - - - - - - biological_process - - aging - - - - - - - - - The internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli. - http://purl.obolibrary.org/obo/go.owl - Behavior - Wikipedia:Behavior - behavioral response to stimulus - behaviour - behavioural response to stimulus - biological_process - GO:0007610 - - - - 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. - behavior - - - - - - - - - The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes. - http://purl.obolibrary.org/obo/go.owl - Wikipedia:Mating_behaviour - mating behaviour - biological_process - GO:0007617 - mating behavior - - - - - - - - - biological_process - Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. - http://purl.obolibrary.org/obo/ido.owl - biological process - - - - - - - - - An aging process that has as participant a whole multicellular organism. Multicellular organism aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Multicellular organisms aging includes processes like cellular senescence and organ senescence, but is more inclusive. May precede death (GO:0016265) of an organism and may succeed developmental maturation (GO:0021700). - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0010259 - multicellular organismal aging - - - - - - - - - Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0010941 - regulation of cell death - - - - - - - - - http://purl.org/obo/owl/gene_ontology - - - - - - - - - - - - - - - - - - - biological_process - oviposition - - - - - - - - - The process in which a virus effects a change in the structure or processes of its host organism. - http://purl.obolibrary.org/obo/go.owl - GO:0044792 - virus-host interaction - Reactome:REACT_6323 - VZ:886 - host-virus interaction - modulation by virus of host anatomical structure or process - modulation by virus of host anatomy or process - viral interaction with host - viral-host process - virus-host process - biological_process - GO:0019048 - - - modulation by virus of host morphology or physiology - - - - - - - - - The set of viral processes that induce an apoptotic process in infected host cells, facilitating release and spread of progeny virions. - http://purl.obolibrary.org/obo/go.owl - activation by virus of host apoptosis - activation by virus of host apoptotic programmed cell death - activation of apoptosis in host by virus - induction by virus of host apoptotic programmed cell death - induction of apoptosis in host by virus - induction by virus of host apoptosis - biological_process - GO:0019051 - induction by virus of host apoptotic process - - - - - - - - - The process in which a virus effects a change in the processes and activities of its host organism. - http://purl.obolibrary.org/obo/go.owl - Reactome:REACT_6222 - modification by virus of host cellular process - regulation by virus of host cellular process - regulation of cellular process in host by virus - regulation of host cellular process by virus - viral host cell process manipulation - biological_process - modulation of cellular process in host by virus - GO:0019054 - - modulation by virus of host process - - - - - - - - - - http://purl.org/obo/owl/gene_ontology - - - - - - - biological_process - reproductive behavior - - - - - - - - - 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. - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0022414 - - reproductive process - - - - - - - - - http://purl.org/obo/owl/gene_ontology - - - - - - - biological_process - - - - developmental process - - - - - - - - - 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. - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0032504 - multicellular organism reproduction - - - - - - - - - http://purl.org/obo/owl/gene_ontology - - - - - - - biological_process - multicellular organismal reproductive behavior - - - - - - - - - Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. - http://purl.obolibrary.org/obo/go.owl - Wikipedia:Social_behavior - social behaviour - biological_process - cooperative behavior - GO:0035176 - Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. - social behavior - - - - - - - - - The process in which an organism effects a change in the structure or processes of a second organism. - http://purl.obolibrary.org/obo/go.owl - rfoulger - 2011-04-21T01:31:51Z - regulation of morphology of other organism - regulation of physiological process of other organism - regulation of physiology of other organism - biological_process - regulation of morphology or physiology of other organism - GO:0035821 - modification of morphology or physiology of other organism - - - - - - - - - Any process in which a virus increases the frequency, rate or extent of host cysteine-type endopeptidase activity (also called caspase activity) which contributes to the apoptotic process. - http://purl.obolibrary.org/obo/go.owl - rfoulger - 2012-10-09T15:44:29Z - activation of host caspases by virus - induction by virus of host caspase activity - biological_process - GO:0039651 - induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process - - - - - - - - - Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes. - http://purl.obolibrary.org/obo/go.owl - GO:0043070 - regulation of non-apoptotic programmed cell death - biological_process - GO:0043067 - regulation of programmed cell death - - - - - - - - - The process in which a symbiont organism effects a change in the structure or processes of its host organism. - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0044003 - - modification by symbiont of host morphology or physiology - - - - - - - - - Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. - entry into host - - - - - - - - - Any process in which an organism has an effect on an organism of a different species. - interspecies interaction between organisms - - - - - - - - - A process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism. - http://purl.obolibrary.org/obo/go.owl - janelomax - 2012-03-20T04:48:41Z - biological_process - GO:0044531 - modulation of programmed cell death in other organism - - - - - - - - - A biological process that directly contributes to the process of producing new individuals, involving another organism. - http://purl.obolibrary.org/obo/go.owl - janelomax - 2012-09-19T15:56:30Z - biological_process - GO:0044703 - multi-organism reproductive process - - - - - - - - - The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species. - http://purl.obolibrary.org/obo/go.owl - janelomax - 2012-09-19T16:02:12Z - biological_process - GO:0044705 - multi-organism reproductive behavior - - - - - - - - - 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. - http://purl.obolibrary.org/obo/go.owl - organismal reproductive process - reproductive process in a multicellular organism - biological_process - GO:0048609 - multicellular organismal reproductive process - - - - - - - - - Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. - http://purl.obolibrary.org/obo/go.owl - GO:0050791 - regulation of physiological process - biological_process - GO:0050789 - - - - regulation of biological process - - - - - - - - - Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. - http://purl.obolibrary.org/obo/go.owl - GO:0051244 - regulation of cellular physiological process - biological_process - GO:0050794 - - regulation of cellular process - - - - - - - - - Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. - http://purl.obolibrary.org/obo/go.owl - GO:0051869 - physiological response to stimulus - biological_process - GO:0050896 - - - - 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. - response to stimulus - - - - - - - - - establishment of localization - The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location. - http://purl.obolibrary.org/obo/ido.owl - establishment of localization - establishment of localization - - - - - - - - - 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. - http://purl.obolibrary.org/obo/go.owl - biological_process - GO:0051701 - - interaction with host - - - - - - - - - A biological process which involves another organism of the same or different species. - multi-organism process - - - - - - - - - Any process in which an organism has a behavioral effect on another organism of the same or different species. - http://purl.obolibrary.org/obo/go/releases/2019-07-01/go.owl - GO:0023032 - GO:0044709 - GOC:ai - GOC:mah - behavioral interaction between organisms - behavioral interaction with other organism - behavioural interaction between organisms - behavioural interaction with other organism - behavioral signaling - behavioral signalling - biological_process - GO:0051705 - - multi-organism behavior - - - - - - - - - The process in which an organism effects a change in the structure or processes of a second organism, where the two organisms are in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - regulation of morphology of other organism during symbiotic interaction - regulation of physiological process in other organism during symbiotic interaction - regulation of physiology of other organism during symbiotic interaction - biological_process - modification of morphology or physiology of other organism during symbiotic interaction - modulation of morphology or physiology of other organism during symbiotic interaction - regulation of morphology or physiology of other organism during symbiotic interaction - GO:0051817 - - modification of morphology or physiology of other organism involved in symbiotic interaction - - - - - - - - - Any process in which an organism modulates the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - GO:0052152 - modulation of host PCD - modulation by symbiont of host non-apoptotic programmed cell death - biological_process - GO:0052040 - - modulation by symbiont of host programmed cell death - - - - - - - - - Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - GO:0012504 - GO:0052044 - GO:0052045 - GO:0052153 - GO:0052397 - GO:0052400 - activation by organism of host programmed cell death - activation by organism of programmed cell death in other organism during symbiotic interaction - enhancement of host programmed cell death - enhancement of host programmed cell death by organism - induction by organism of programmed cell death in other organism involved in symbiotic interaction - induction by symbiont of host programmed cell death - upregulation by symbiont of host programmed cell death - activation by organism of non-apoptotic programmed cell death in other organism - activation by symbiont of host programmed cell death - induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction - positive regulation by symbiont of host non-apoptotic programmed cell death - stimulation by symbiont of host programmed cell death - biological_process - induction by organism of programmed cell death in other organism during symbiotic interaction - induction of non-apoptotic programmed cell death by other organism - GO:0052042 - - positive regulation by symbiont of host programmed cell death - - - - - - - - - Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death in the host, where programmed cell death proceeds by apoptosis. The host is defined as the larger of the organisms involved in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - GO:0033669 - GO:0052030 - activation by organism of host apoptosis - activation by organism of host apoptotic programmed cell death - induction by organism of host apoptotic programmed cell death - induction by symbiont of host apoptosis - positive regulation by organism of host apoptotic programmed cell death - up regulation by organism of host apoptotic programmed cell death - up regulation by symbiont of host apoptosis - up-regulation by organism of host apoptotic programmed cell death - up-regulation by symbiont of host apoptosis - upregulation by organism of host apoptotic programmed cell death - upregulation by symbiont of host apoptosis - activation by symbiont of host apoptosis - positive regulation by symbiont of host apoptosis - stimulation by symbiont of host apoptosis - biological_process - GO:0052151 - - Note that term is to be used to annotate gene products in the symbiont. To annotate host gene products, consider the biological process term 'positive regulation of apoptosis ; GO:0043065'. - positive regulation by symbiont of host apoptotic process - - - - - - - - - Any process in which an organism modulates the frequency, rate or extent of programmed cell death in a second organism, where the two organisms are in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - GO:0052459 - modulation by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction - biological_process - modulation of programmed cell death in other organism during symbiotic interaction - GO:0052248 - - modulation of programmed cell death in other organism involved in symbiotic interaction - - - - - - - - - Any process in which an organism activates, maintains or increases the frequency, rate or extent of programmed cell death by apoptosis in a second organism, where the two organisms are in a symbiotic interaction. - http://purl.obolibrary.org/obo/go.owl - GO:0052388 - induction by organism of apoptosis in other organism involved in symbiotic interaction - activation by organism of apoptosis in other organism during symbiotic interaction - positive regulation by organism of apoptosis in other organism involved in symbiotic interaction - positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction - stimulation by organism of apoptosis in other organism during symbiotic interaction - biological_process - activation by organism of apoptotic programmed cell death in other organism during symbiotic interaction - induction by organism of apoptosis in other organism during symbiotic interaction - induction by organism of apoptotic programmed cell death in other organism during symbiotic interaction - positive regulation by organism of apoptosis in other organism during symbiotic interaction - positive regulation by organism of apoptotic programmed cell death in other organism during symbiotic interaction - up regulation by organism of apoptosis in other organism during symbiotic interaction - up-regulation by organism of apoptosis in other organism during symbiotic interaction - upregulation by organism of apoptosis in other organism during symbiotic interaction - GO:0052501 - - positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction - - - - - - - - - Any viral process that activates or increases the frequency, rate or extent of cell death by apoptotic process. - http://purl.obolibrary.org/obo/go.owl - positive regulation of apoptosis by virus - biological_process - GO:0060139 - positive regulation of apoptotic process by virus - - - - - - - - - Any viral process that modulates the rate or extent of progression through the cell cycle. - http://purl.obolibrary.org/obo/go.owl - VZ:1636 - modulation of host cell cycle by virus - regulation by virus of host cell cycle - regulation of host cell cycle by virus - viral process regulating host cell cycle - biological_process - GO:0060153 - - modulation by virus of host cell cycle - - - - - - - - - http://purl.org/obo/owl/gene_ontology - biological_process - post-mating oviposition - - - - - - - - - Any process that modulates a measurable attribute of any biological process, quality or function. - http://purl.obolibrary.org/obo/go.owl - regulation - biological_process - GO:0065007 - - - biological regulation - - - - - - - - - Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc. - http://purl.obolibrary.org/obo/go.owl - regulation of biological attribute - regulation of biological characteristic - biological_process - GO:0065008 - - regulation of biological quality - - - - - - - - - http://purl.org/obo/owl/gene_ontology - biological_process - organism emergence from protective structure - - - - diff --git a/src/ontology/apollo_sv-odk.yaml b/src/ontology/apollo_sv-odk.yaml index 236e2d1..3230def 100644 --- a/src/ontology/apollo_sv-odk.yaml +++ b/src/ontology/apollo_sv-odk.yaml @@ -36,6 +36,9 @@ import_group: - id: mf module_type: slme slme_individuals: exclude + - id: go + module_type: slme + slme_individuals: exclude use_custom_import_module: TRUE robot_java_args: '-Xmx8G' custom_makefile_header: | diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index c7adf53..92c6939 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -18,6 +18,8 @@ + + diff --git a/src/ontology/imports/geo_import.owl b/src/ontology/imports/geo_import.owl index 936a3f8..cad659b 100644 --- a/src/ontology/imports/geo_import.owl +++ b/src/ontology/imports/geo_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-04-19") + +Annotation(owl:versionInfo "2024-08-13") Declaration(Class()) Declaration(Class()) @@ -2690,7 +2690,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "geopolitical dependency"@en) SubClassOf( ) -# Class: (aggregate of major administrative subdivisions) +# Class: (group of major administrative subdivisions) AnnotationAssertion( "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common."@en) AnnotationAssertion( "Amanda Hicks"@en) 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/ontology/imports/ido_import.owl b/src/ontology/imports/ido_import.owl index 4932c20..ed30dde 100644 --- a/src/ontology/imports/ido_import.owl +++ b/src/ontology/imports/ido_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-19") +Annotation(owl:versionInfo "2024-08-13") Declaration(Class()) Declaration(Class()) @@ -37,14 +37,11 @@ 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()) @@ -1206,13 +1203,6 @@ AnnotationAssertion(rdfs:isDefinedBy "history"@en) SubClassOf( ) -# Class: (reproduction) - -AnnotationAssertion( "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "reproduction") -SubClassOf( ) - # Class: (immune response) AnnotationAssertion( "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.") @@ -1227,13 +1217,6 @@ AnnotationAssertion( "biological_process") SubClassOf( ) -# Class: (developmental process) - -AnnotationAssertion( "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "developmental process") -SubClassOf( ) - # Class: (entry into host) AnnotationAssertion( "Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.") @@ -1256,13 +1239,6 @@ AnnotationAssertion( "multi-organism process") SubClassOf( ) -# Class: (biological regulation) - -AnnotationAssertion( "Any process that modulates a measurable attribute of any biological process, quality or function.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "biological regulation") -SubClassOf( ) - # Class: (data item) AnnotationAssertion(rdfs:label "data item"@en) diff --git a/src/ontology/imports/mf_import.owl b/src/ontology/imports/mf_import.owl index 2038588..791f084 100644 --- a/src/ontology/imports/mf_import.owl +++ b/src/ontology/imports/mf_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-19") +Annotation(owl:versionInfo "2024-08-13") Declaration(Class()) Declaration(Class()) @@ -35,14 +35,7 @@ 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()) @@ -876,20 +869,6 @@ AnnotationAssertion( "behavior") SubClassOf( ) -# Class: (mating behavior) - -AnnotationAssertion( "The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "mating behavior") -SubClassOf( ) - -# Class: (oviposition) - -AnnotationAssertion( "The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "oviposition") -SubClassOf( ) - # Class: (reproductive behavior) AnnotationAssertion( "The specific behavior of an organism that is associated with reproduction.") @@ -897,43 +876,6 @@ AnnotationAssertion( "reproductive behavior") SubClassOf( ) -# Class: (social behavior) - -AnnotationAssertion( "Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "social behavior") -SubClassOf( ) - -# Class: (multi-organism reproductive behavior) - -AnnotationAssertion( "The specific behavior of an organism that is associated with reproduction involving another organism of the same or different species.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "multi-organism reproductive behavior") -SubClassOf( ) -SubClassOf( ) - -# Class: (post-mating behavior) - -AnnotationAssertion( "The specific behavior of an organism following mating.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "post-mating behavior") -SubClassOf( ) - -# Class: (multi-organism behavior) - -AnnotationAssertion( "Any process in which an organism has a behavioral effect on another organism of the same or different species.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "multi-organism behavior") -SubClassOf( ) - -# Class: (post-mating oviposition) - -AnnotationAssertion( "The deposition of eggs, either fertilized or not, upon a surface or into a medium, following mating.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "post-mating oviposition") -SubClassOf( ) -SubClassOf( ) - # Class: (data item) AnnotationAssertion( "data item"@en) diff --git a/src/ontology/imports/pno_import.owl b/src/ontology/imports/pno_import.owl index 23ac377..775d0dc 100644 --- a/src/ontology/imports/pno_import.owl +++ b/src/ontology/imports/pno_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - + Annotation( ) -Annotation(owl:versionInfo "2024-04-19") +Annotation(owl:versionInfo "2024-08-13") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index 82ab86b..acb2e78 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -7,9 +7,9 @@ Prefix(rdfs:=) Ontology( - -Annotation( ) -Annotation(owl:versionInfo "2024-04-19") + +Annotation( ) +Annotation(owl:versionInfo "2024-08-13") Declaration(Class()) Declaration(Class()) @@ -30,6 +30,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -95,6 +96,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -113,6 +115,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -154,6 +157,8 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -528,7 +533,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "part of"@en) -AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) @@ -555,7 +559,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has part"@en) -AnnotationAssertion(rdfs:label "has part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -628,11 +631,9 @@ AnnotationAssertion( "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) -AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) ObjectPropertyDomain( ) -ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (contains process) @@ -668,8 +669,6 @@ AnnotationAssertion( "is bearer of"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "has characteristic"@en) -AnnotationAssertion(rdfs:label "has characteristic") -AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -697,9 +696,7 @@ AnnotationAssertion( "has_participant"@en) AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion(rdfs:label "has participant"@en) -AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) -ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (is concretized as) @@ -1224,6 +1221,21 @@ SubObjectPropertyOf( ) ObjectPropertyDomain( ) +# Object Property: (has output) + +AnnotationAssertion( ) +AnnotationAssertion( "p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.") +AnnotationAssertion( ) +AnnotationAssertion( "produces") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has output"@en) +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + # Object Property: (acts upstream of) AnnotationAssertion( "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.") @@ -1349,7 +1361,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "enabled by"@en) -AnnotationAssertion(rdfs:label "enabled by") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1413,6 +1424,16 @@ AnnotationAssertion(rdfs:label "inpu SubObjectPropertyOf( ) SubObjectPropertyOf( ) +# Object Property: (output of) + +AnnotationAssertion( "inverse of has output") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "output of"@en) +SubObjectPropertyOf( ) +SubObjectPropertyOf( ) + # Object Property: (spatially coextensive with) AnnotationAssertion( "A lump of clay and a statue") @@ -1837,6 +1858,28 @@ AnnotationAssertion(rdfs:seeAlso "ht SubObjectPropertyOf( ) SubObjectPropertyOf( ) +# Object Property: (produces) + +AnnotationAssertion( ) +AnnotationAssertion( "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.") +AnnotationAssertion(rdfs:label "produces"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (produced by) + +AnnotationAssertion( ) +AnnotationAssertion( "a produced_by b iff some process that occurs_in b has_output a.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "produced by"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # 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.") @@ -1990,10 +2033,10 @@ SubObjectPropertyOf( "A diagnostic testing device utilizes a specimen.") AnnotationAssertion( "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion( "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.") AnnotationAssertion( "See github ticket https://github.com/oborel/obo-relations/issues/497") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "2021-11-08T12:00:00Z"^^xsd:dateTime) AnnotationAssertion( "utilizes") AnnotationAssertion(rdfs:label "device utilizes material"@en) @@ -2063,7 +2106,6 @@ AnnotationAssertion( "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t."@en) AnnotationAssertion(rdfs:label "process"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) # Class: (disposition) @@ -2096,7 +2138,6 @@ AnnotationAssertion(rdfs:seeAlso "h AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) # Class: (role) @@ -2161,7 +2202,7 @@ AnnotationAssertion(rdfs:comment "No AnnotationAssertion(rdfs:label "biological process"@en) AnnotationAssertion(rdfs:label "biological_process") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +DisjointClasses( ) # Class: (kinase activity) @@ -2193,6 +2234,21 @@ AnnotationAssertion( "curation status specification"@en) EquivalentClasses( ObjectOneOf( )) +# Class: (planned process) + +AnnotationAssertion( "planned process"@en) +AnnotationAssertion( "planned process") +AnnotationAssertion( "Injecting mice with a vaccine in order to test its efficacy") +AnnotationAssertion( ) +AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) +AnnotationAssertion( "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)") +AnnotationAssertion( "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some +objectives is a planned process.") +AnnotationAssertion( "Bjoern Peters") +AnnotationAssertion( "branch derived") +AnnotationAssertion(rdfs:label "planned process"@en) +SubClassOf( ) + # Class: (processed material) AnnotationAssertion( "processed material"@en) @@ -2459,6 +2515,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) @@ -2492,6 +2549,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) @@ -2505,19 +2563,19 @@ DLSafeRule(Body(ObjectPropertyAtom( V DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) AnnotationAssertion( "## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' diff --git a/src/ontology/imports/ro_terms.txt b/src/ontology/imports/ro_terms.txt index 8b13789..be36c9f 100644 --- a/src/ontology/imports/ro_terms.txt +++ b/src/ontology/imports/ro_terms.txt @@ -1 +1 @@ - +http://purl.obolibrary.org/obo/RO_0002234 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