PREFIX owl: PREFIX rdf: PREFIX rdfs: PREFIX xsd: PREFIX miiid: PREFIX linkml: PREFIX schema: PREFIX WIKIDATA_PROPERTY: PREFIX EDAM_TOPIC: PREFIX EDAM_DATA: PREFIX NCIT: PREFIX OBI: PREFIX GENEPIO: PREFIX dcterms: PREFIX skos: PREFIX pav: PREFIX sh: PREFIX vann: a owl:Ontology ; rdfs:label "miiid-schema" ; rdfs:comment "Minimal Information about Intermicrobial Interaction Data schema" ; rdfs:seeAlso ; dcterms:license "GNU GPL v3.0" ; pav:version "0.2.0" ; vann:preferredNamespacePrefix "miiid" ; vann:preferredNamespaceUri "https://w3id.org/FAIR-MI/miiid/"^^xsd:anyURI ; sh:declare [ sh:prefix "miiid" ; sh:namespace "https://w3id.org/FAIR-MI/miiid/"^^xsd:anyURI ] , [ sh:prefix "linkml" ; sh:namespace "https://w3id.org/linkml/"^^xsd:anyURI ] , [ sh:prefix "schema" ; sh:namespace "http://schema.org/"^^xsd:anyURI ] , [ sh:prefix "WIKIDATA_PROPERTY" ; sh:namespace "https://www.wikidata.org/prop/"^^xsd:anyURI ] , [ sh:prefix "EDAM_TOPIC" ; sh:namespace "http://edamontology.org/topic_"^^xsd:anyURI ] , [ sh:prefix "EDAM_DATA" ; sh:namespace "http://edamontology.org/data_"^^xsd:anyURI ] , [ sh:prefix "NCIT" ; sh:namespace "http://purl.obolibrary.org/obo/NCIT_"^^xsd:anyURI ] , [ sh:prefix "OBI" ; sh:namespace "http://purl.obolibrary.org/obo/OBI_"^^xsd:anyURI ] , [ sh:prefix "GENEPIO" ; sh:namespace "http://purl.obolibrary.org/obo/GENEPIO_"^^xsd:anyURI ] . schema:Thing a owl:Class ; rdfs:comment "A generic grouping for any identifiable entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty schema:name ; owl:allValuesFrom xsd:string ] , [ a owl:Restriction ; owl:onProperty schema:name ; owl:maxCardinality "1"^^xsd:nonNegativeInteger ] , [ a owl:Restriction ; owl:onProperty schema:description ; owl:allValuesFrom xsd:string ] , [ a owl:Restriction ; owl:onProperty schema:description ; owl:maxCardinality "1"^^xsd:nonNegativeInteger ] . miiid:IntermicrobialInteraction a owl:Class ; rdfs:comment "Represents an interaction between microbial entities" ; rdfs:subClassOf schema:Thing , [ a owl:Restriction ; owl:onProperty miiid:participants ; owl:allValuesFrom xsd:string ] , [ a owl:Restriction ; owl:onProperty miiid:participants ; owl:minCardinality "1"^^xsd:nonNegativeInteger ] , [ a owl:Restriction ; owl:onProperty miiid:tax_id ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:integer ; owl:withRestrictions ( _:o18 ) ] ] , [ a owl:Restriction ; owl:onProperty miiid:tax_id ; owl:minCardinality "1"^^xsd:nonNegativeInteger ] , [ a owl:Restriction ; owl:onProperty miiid:sequence_id ; owl:allValuesFrom xsd:string ] , [ a owl:Restriction ; owl:onProperty miiid:evidence_type ; owl:allValuesFrom [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( _:o23 ) ] ] , [ a owl:Restriction ; owl:onProperty miiid:evidence_type ; owl:cardinality "1"^^xsd:nonNegativeInteger ] , [ a owl:Restriction ; owl:onProperty miiid:method_type ; owl:allValuesFrom miiid:MethodType ] , [ a owl:Restriction ; owl:onProperty miiid:reference ; owl:allValuesFrom xsd:string ] , [ a owl:Restriction ; owl:onProperty miiid:reference ; owl:cardinality "1"^^xsd:nonNegativeInteger ] , [ a owl:Restriction ; owl:onProperty miiid:participant_outcomes ; owl:allValuesFrom miiid:ParticipantOutcome ] . _:o18 xsd:minInclusive 2 . _:o23 xsd:pattern ".*[^\\:\\n\\r]+\\:[^\\:\\n\\r]+.*" . miiid:IntermicrobialInteractionCollection a owl:Class ; rdfs:comment "A holder for IntermicrobialInteraction objects" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty miiid:entries ; owl:allValuesFrom miiid:IntermicrobialInteraction ] . schema:name a owl:DatatypeProperty ; rdfs:comment "A human-readable name for a thing" ; rdfs:range xsd:string ; a owl:FunctionalProperty . schema:description a owl:DatatypeProperty ; rdfs:comment "A human-readable description for a thing" ; rdfs:range xsd:string ; a owl:FunctionalProperty . miiid:participants a owl:DatatypeProperty ; rdfs:comment "Names of the microbial entities, with descriptions of any genetic manipulations performed." ; rdfs:range xsd:string . miiid:tax_id a owl:DatatypeProperty ; rdfs:comment "NCBI Taxonomy identifiers at the relevant taxonomic level. Novel taxa lacking identifiers are denoted by N/A." ; rdfs:range [ a rdfs:Datatype ; owl:onDatatype xsd:integer ; owl:withRestrictions ( _:o31 ) ] . _:o31 xsd:minInclusive 2 . miiid:sequence_id a owl:DatatypeProperty ; rdfs:comment "Accession to the matching sequence data (e.g., genome, marker gene sequence)." ; rdfs:range xsd:string . miiid:evidence_type a owl:DatatypeProperty ; rdfs:comment "Type of evidence used to determine the interaction using the Evidence and Conclusion Ontology." ; rdfs:range [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( _:o33 ) ] ; a owl:FunctionalProperty . _:o33 xsd:pattern ".*[^\\:\\n\\r]+\\:[^\\:\\n\\r]+.*" . miiid:method_type a owl:ObjectProperty ; rdfs:comment "One or several of the types of methods used to determine the interaction." ; rdfs:range miiid:MethodType . miiid:reference a owl:DatatypeProperty ; rdfs:comment "Persistent identifier (e.g. DOI or URL) to a resource, script, or article, documenting the method." ; skos:exactMatch schema:url ; rdfs:range xsd:string ; a owl:FunctionalProperty . miiid:env_exp a owl:DatatypeProperty ; rdfs:comment "Biome term (from the Environmental Ontology) used in the experiment. Engineered ecosystems such as bioreactors, agar plates or computational models use N/A." ; rdfs:range [ a rdfs:Datatype ; owl:onDatatype xsd:string ; owl:withRestrictions ( _:o35 ) ] ; a owl:FunctionalProperty . _:o35 xsd:pattern ".*[^\\:\\n\\r]+\\:[^\\:\\n\\r]+.*" . miiid:participant_outcomes a owl:ObjectProperty ; rdfs:comment "Outcomes of each of the participants described in the interaction when known." ; rdfs:range miiid:ParticipantOutcome . miiid:entries a owl:ObjectProperty ; rdfs:comment "An IntermicrobialInteraction object" ; rdfs:range miiid:IntermicrobialInteraction . miiid:MethodType a owl:Class ; rdfs:comment "List of methods used to determine interactions" ; owl:equivalentClass [ a owl:Class ; owl:oneOf ( EDAM_TOPIC:3524 EDAM_TOPIC:3382 NCIT:C25300 OBI:0000659 ) ] . EDAM_TOPIC:3524 a owl:NamedIndividual ; skos:notation "simulation" ; rdfs:comment "Any type of biological computational model experiments" ; skos:example "generalized Lotka-Volterra model" , "genome-scale metabolic model" ; a miiid:MethodType . EDAM_TOPIC:3382 a owl:NamedIndividual ; skos:notation "microscopy" ; rdfs:comment "Any type of imaging-related experiments" ; skos:example "co-localization with fluorescent markers" , "assisted motility" ; a miiid:MethodType . NCIT:C25300 a owl:NamedIndividual ; skos:notation "cultivation" ; rdfs:comment "Any laboratory procedure for growing microorganisms" ; skos:example "continuous co-culture in bioreactor" , "co-plating on solid media" ; a miiid:MethodType . OBI:0000659 a owl:NamedIndividual ; skos:notation "sample" ; rdfs:comment "Any type of experiments based on the analysis of a sample" ; skos:example "co-occurrences drawn from analyses of abundances obtained from in situ or in vivo sampling" ; a miiid:MethodType . miiid:ParticipantOutcome a owl:Class ; rdfs:comment "Outcome indicating how each participant was affected" ; owl:equivalentClass [ a owl:Class ; owl:oneOf ( miiid:ParticipantOutcome.NOT_AFFECTED miiid:ParticipantOutcome.POSITIVELY miiid:ParticipantOutcome.NEGATIVELY GENEPIO:0001619 ) ] . miiid:ParticipantOutcome.NOT_AFFECTED a owl:NamedIndividual ; skos:notation "not_affected" ; rdfs:comment "usually encoded with numerical 0" ; a miiid:ParticipantOutcome . miiid:ParticipantOutcome.POSITIVELY a owl:NamedIndividual ; skos:notation "positively" ; rdfs:comment "usually encoded with +1" ; a miiid:ParticipantOutcome . miiid:ParticipantOutcome.NEGATIVELY a owl:NamedIndividual ; skos:notation "negatively" ; rdfs:comment "usually encoded with -1" ; a miiid:ParticipantOutcome . GENEPIO:0001619 a owl:NamedIndividual ; skos:notation "not_applicable" ; rdfs:comment "The information is inappropriate to report, this can indicate that the standard itself fails to model or represent the information appropriately" ; a miiid:ParticipantOutcome . dcterms:license a owl:AnnotationProperty . pav:version a owl:AnnotationProperty . vann:preferredNamespacePrefix a owl:AnnotationProperty . vann:preferredNamespaceUri a owl:AnnotationProperty . skos:exactMatch a owl:AnnotationProperty . skos:notation a owl:AnnotationProperty . skos:example a owl:AnnotationProperty . sh:declare a owl:AnnotationProperty . sh:prefix a owl:AnnotationProperty . sh:namespace a owl:AnnotationProperty .