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agri-schemas-0.1.ttl
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agri-schemas-0.1.ttl
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@prefix : <http://agrischemas.org/ontology#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix oa: <http://www.w3.org/ns/oa#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix owl: <https://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix agri: <http://agrischemas.org/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix schema: <http://schema.org/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix bioschema: <http://bioschemas.org/> .
@prefix metaSchema: <https://meta.schema.org/> .
@base <http://agrischemas.org/ontology> .
<http://agrischemas.org/ontology> rdf:type owl:Ontology .
#################################################################
# Annotation properties
#################################################################
### http://agrischemas.org/BioSchemasNewPropertyProposal
agri:BioSchemasNewPropertyProposal rdf:type owl:AnnotationProperty ;
rdfs:seeAlso agri:SchemaNewClassProposal .
### http://agrischemas.org/SchemaNewPropertyProposal
agri:SchemaNewPropertyProposal rdf:type owl:AnnotationProperty ;
rdfs:seeAlso agri:SchemaNewClassProposal .
### http://agrischemas.org/Soil
agri:Soil rdf:type owl:AnnotationProperty .
### http://agrischemas.org/StudyObservedValue
agri:StudyObservedValue rdf:type owl:AnnotationProperty .
### http://agrischemas.org/authorsList
agri:authorsList rdf:type owl:AnnotationProperty;
rdfs:subPropertyOf dc:creator .
### http://agrischemas.org/evidence
agri:evidence rdf:type owl:AnnotationProperty ;
rdfs:subPropertyOf agri:SchemaNewPropertyProposal ,
oa:motivatedBy .
### http://agrischemas.org/hasGeneExpressionIn
agri:hasGeneExpressionIn rdf:type owl:AnnotationProperty ;
rdfs:comment "Associates an entity like a DNA sequence or protein to another entity like a sample or disease term, to tell that the former shows some (differential) gene expression upon the condition represented by the latter." ;
rdfs:seeAlso obo:GO_0010467 ;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal ,
agri:isBiologicallyRelatedTo .
### http://agrischemas.org/interactionHost
agri:interactionHost rdf:type owl:AnnotationProperty ;
schema:domainIncludes agri:HostPathogenInteraction ;
schema:rangeIncludes schema:Phenotype ;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal ,
schema:hasPart .
### http://agrischemas.org/interactionPathogen
agri:interactionPathogen rdf:type owl:AnnotationProperty ;
schema:domainIncludes agri:HostPathogenInteraction ;
schema:rangeIncludes schema:Phenotype ;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal ,
schema:hasPart .
### http://agrischemas.org/isBiologicallyRelatedTo
agri:isBiologicallyRelatedTo rdf:type owl:AnnotationProperty ;
rdfs:seeAlso sio:SIO_000897 ;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal ,
schema:Property .
### http://agrischemas.org/pmedId
agri:pmedId rdf:type owl:AnnotationProperty ;
rdfs:subPropertyOf agri:SchemaNewPropertyProposal ,
schema:identifier .
agri:doiId rdf:type owl:AnnotationProperty ;
rdfs:subPropertyOf agri:SchemaNewPropertyProposal ,
schema:identifier .
### http://agrischemas.org/pvalue
agri:pvalue rdf:type owl:AnnotationProperty ;
dc:type obo:OBI_0000175, sio:SIO_000765;
schema:rangeIncludes schema:Number ;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal ,
agri:score .
agri:tpmCount rdf:type owl:AnnotationProperty ;
schema:alternateName "Transcripts Per Million";
rdfs:comment "The transcripts per million count, as measured in RNA-Seq data. See: https://rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/";
dc:type obo:STATO_0000047, sio:SIO_000794;
schema:rangeIncludes schema:Number ;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal ,
agri:score .
agri:ordinalTpm rdf:type owl:AnnotationProperty ;
rdfs:label "TPM level";
rdfs:comment "The ordinal ('low', 'medium', 'high') level of TPM. This is established from the TPM count, using the EBI thresholds: [0.5-10]/low, [11-1000] med, >1000. See: See: https://rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/";
schema:rangeIncludes schema:Text ;
rdfs:seeAlso agri:tpmCount;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal ,
agri:score .
agri:foldChange rdf:type owl:AnnotationProperty ;
dc:type obo:STATO_0000169, sio:SIO_001078;
schema:rangeIncludes schema:Number ;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal ,
agri:score .
agri:log2FoldChange rdf:type owl:AnnotationProperty ;
dc:type obo:STATO_0000169, sio:SIO_001078;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal ,
agri:foldChange .
### http://agrischemas.org/score
agri:score rdf:type owl:AnnotationProperty ;
dc:type obo:OBI_0000071 ;
schema:rangeIncludes schema:Enumeration ,
schema:Number ,
schema:Text ;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal ,
<http://meta.schema.org/Property> .
agri:baseCondition rdf:type owl:AnnotationProperty ;
schema:rangeIncludes agri:StudyFactor;
rdfs:seeAlso obo:OBI_0000143 ;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal, schema:Property .
agri:timePoint rdf:type owl:AnnotationProperty ;
schema:rangeIncludes agri:StudyFactor;
rdfs:label "Time Point";
rdfs:seeAlso obo:OBI_0001508 ;
rdfs:subPropertyOf agri:BioSchemasNewPropertyProposal, schema:Property .
### http://meta.schema.org/Property
<http://meta.schema.org/Property> rdf:type owl:AnnotationProperty .
### http://schema.org/Property
schema:Property rdf:type owl:AnnotationProperty .
### http://schema.org/abstract
schema:abstract rdf:type owl:AnnotationProperty .
### http://schema.org/additionalType
dc:type rdf:type owl:AnnotationProperty .
### http://schema.org/alternateName
schema:alternateName rdf:type owl:AnnotationProperty ;
rdfs:seeAlso schema:name ;
rdfs:subPropertyOf skos:altLabel .
### http://schema.org/description
schema:description rdf:type owl:AnnotationProperty .
### http://schema.org/domainIncludes
schema:domainIncludes rdf:type owl:AnnotationProperty .
### http://schema.org/hasPart
schema:hasPart rdf:type owl:AnnotationProperty .
### http://schema.org/identifier
schema:identifier rdf:type owl:AnnotationProperty .
### http://schema.org/name
schema:name rdf:type owl:AnnotationProperty ;
rdfs:comment "schema:name is described and used as preferred name, so here we map to skos:prefLabel.";
rdfs:subPropertyOf skos:prefLabel .
### http://schema.org/rangeIncludes
schema:rangeIncludes rdf:type owl:AnnotationProperty .
### http://www.w3.org/2004/02/skos/core#altLabel
skos:altLabel rdf:type owl:AnnotationProperty .
### http://www.w3.org/2004/02/skos/core#prefLabel
skos:prefLabel rdf:type owl:AnnotationProperty .
### http://www.w3.org/ns/oa#motivatedBy
oa:motivatedBy rdf:type owl:AnnotationProperty .
#################################################################
# Classes
#################################################################
### http://agrischemas.org/BioPathway
agri:BioPathway rdf:type owl:Class ;
rdfs:subClassOf agri:BioSchemasNewClassProposal ,
agri:BiologicalAssociation .
### http://agrischemas.org/BioSchemasNewClassProposal
agri:BioSchemasNewClassProposal rdf:type owl:Class ;
rdfs:seeAlso agri:BioSchemasNewClassProposal .
### http://agrischemas.org/BiologicalAssociation
agri:BiologicalAssociation rdf:type owl:Class ;
rdfs:subClassOf agri:BioSchemasNewClassProposal ,
schema:Intangible .
### http://agrischemas.org/HostPathogenInteraction
agri:HostPathogenInteraction rdf:type owl:Class ;
rdfs:subClassOf agri:BioSchemasNewClassProposal ,
agri:BiologicalAssociation .
### http://agrischemas.org/SchemaNewClassProposal
agri:SchemaNewClassProposal rdf:type owl:Class ;
schema:description "Top-level containers named *New*Proposal are markers to track actions needed for new terms (eg, propose to schema/bioschemas)." .
### http://agrischemas.org/ScholarlyPublication
agri:ScholarlyPublication rdf:type owl:Class ;
rdfs:subClassOf agri:BioSchemasNewClassProposal ,
schema:CreativeWork .
### http://agrischemas.org/Soil
agri:Soil rdf:type owl:Class ;
rdfs:subClassOf bioschema:BioChemEntity .
### http://agrischemas.org/StudyDesign
agri:StudyDesign rdf:type owl:Class ;
rdfs:subClassOf agri:BioSchemasNewClassProposal ,
agri:StudyItemEvent .
### http://agrischemas.org/StudyFactor
agri:StudyFactor rdf:type owl:Class ;
owl:equivalentClass obo:OBI_0000750 ,
<http://www.ebi.ac.uk/efo/EFO_0000001> ;
rdfs:subClassOf agri:BioSchemasNewClassProposal ,
schema:PropertyValue .
### http://agrischemas.org/StudyItemEvent
agri:StudyItemEvent rdf:type owl:Class ;
rdfs:subClassOf agri:BioSchemasNewClassProposal ,
schema:Action ;
schema:description """An event that occurs to a sample or a data set/file, which yields another item,
knowlingly or potentially affecting the characteristics such new item has.
This might be an on-purpose action (ie, a bioschema:LabProtocol), or a tracked event that
might have affected an experiment step (eg, a weather change on a field location).
Events can also be used to represent data extraction from samples (what is considered an
assaying procedure in ISA-Tab), or data transformations (eg, normalisation, computation
of differentially expressed genes, gene enrichment). This might also represent a plan or potential
event""" .
### http://agrischemas.org/StudyObservedValue
agri:StudyObservedValue rdf:type owl:Class ;
owl:equivalentClass <http://purl.org/ppeo/PPEO.owl#observed_variable> ;
rdfs:subClassOf agri:BioSchemasNewClassProposal ,
schema:PropertyValue .
### http://bioschemas.org/BioChemEntity
bioschema:BioChemEntity rdf:type owl:Class .
### http://bioschemas.org/LabProtocol
bioschema:LabProtocol rdf:type owl:Class ;
rdfs:subClassOf agri:StudyItemEvent .
### http://purl.obolibrary.org/obo/OBI_0000750
obo:OBI_0000750 rdf:type owl:Class .
### http://purl.org/ppeo/PPEO.owl#observed_variable
<http://purl.org/ppeo/PPEO.owl#observed_variable> rdf:type owl:Class .
### http://schema.org/Action
schema:Action rdf:type owl:Class .
### http://schema.org/CreativeWork
schema:CreativeWork rdf:type owl:Class .
### http://schema.org/Intangible
schema:Intangible rdf:type owl:Class .
### http://schema.org/PropertyValue
schema:PropertyValue rdf:type owl:Class .
### http://schema.org/ScholarlyArticle
schema:ScholarlyArticle rdf:type owl:Class ;
rdfs:subClassOf agri:ScholarlyPublication .
### http://www.ebi.ac.uk/efo/EFO_0000001
<http://www.ebi.ac.uk/efo/EFO_0000001> rdf:type owl:Class .
### Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi