Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
432 lines (355 sloc) 18.1 KB
@prefix : <http://www.w3.org/2002/07/owl#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@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 prov: <http://www.w3.org/ns/prov#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <http://schema.org/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix biosdterms: <http://rdf.ebi.ac.uk/terms/biosd/> .
<http://rdf.ebi.ac.uk/terms/biosd/> a :Ontology ;
:imports <http://semanticscience.org/ontology/sio-v1.0.10-release.owl> , <http://www.openannotation.org/ns/> , <http://topbraid.org/schema/> , <http://purl.obolibrary.org/obo/ro/releases/2015-04-12/ro.owl> , <http://purl.obolibrary.org/obo/iao/2011-05-09/iao-main.owl> , <http://purl.org/ontology/bibo/> , <http://purl.org/spar/fabio/> , <http://www.w3.org/ns/prov-o-20130430> , <http://purl.obolibrary.org/obo/obi/2015-03-17/obi.owl> , <http://xmlns.com/foaf/0.1/> .
#
#
# #################################################################
# #
# # Annotation properties
# #
# #################################################################
#
#
# http://rdf.ebi.ac.uk/terms/biosd/has-address-line
biosdterms:has-address-line a :AnnotationProperty ;
rdfs:subPropertyOf rdfs:comment ;
rdfs:range xsd:string .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-affiliation-line
biosdterms:has-affiliation-line a :AnnotationProperty ;
rdfs:subPropertyOf rdfs:comment ;
rdfs:range xsd:string .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-authors-list
biosdterms:has-authors-list a :AnnotationProperty ;
rdfs:subPropertyOf rdfs:comment ;
rdfs:range xsd:string .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-knowledgeable-organization
biosdterms:has-knowledgeable-organization a :AnnotationProperty .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-knowledgeable-person
biosdterms:has-knowledgeable-person a :AnnotationProperty .
#
#
#
# #################################################################
# #
# # Object Properties
# #
# #################################################################
#
#
# http://purl.obolibrary.org/obo/RO_0000086
obo:RO_0000086 a :ObjectProperty .
#
# http://rdf.ebi.ac.uk/terms/biosd/child-of
biosdterms:child-of a :ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002202 ;
:inverseOf biosdterms:parent-of ;
rdfs:domain obo:OBI_0100026 , sio:SIO_010000 ;
rdfs:range obo:OBI_0100026 , sio:SIO_010000 ;
obo:IAO_0000115 "x child-of y iff the organism x is the biological direct offspring of y. " ;
rdfs:label "child of" .
#
# http://rdf.ebi.ac.uk/terms/biosd/computed-from
biosdterms:computed-from a :ObjectProperty ;
rdfs:subPropertyOf sio:SIO_000244 , prov:wasDerivedFrom ;
obo:IAO_0000115 "The current entity (usually some data, a document, or other information item) was computed using another one. For instance, an ontology term annotation was computed starting from some free text." ;
rdfs:label "is computed from" .
#
# http://rdf.ebi.ac.uk/terms/biosd/derived-from-organism
biosdterms:derived-from-organism a :ObjectProperty ;
rdfs:subPropertyOf sio:SIO_000244 , prov:wasDerivedFrom ;
rdfs:domain biosdterms:Sample ;
rdfs:range obo:OBI_0100026 , sio:SIO_010000 ;
obo:IAO_0000115 "a sample directly taken from an organism, or from another sample, which is taken from an organism." ;
rdfs:label "derived from organism" .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-address-line
biosdterms:has-address-line a :ObjectProperty ;
rdfs:subPropertyOf schema:description .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-affiliation-line
biosdterms:has-affiliation-line a :ObjectProperty ;
rdfs:subPropertyOf schema:description .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-authors-list
biosdterms:has-authors-list a :ObjectProperty ;
rdfs:subPropertyOf schema:description ;
rdfs:domain obo:IAO_0000311 , <http://purl.org/ontology/bibo/Document> , <http://purl.org/spar/fabio/Work> , <http://xmlns.com/foaf/0.1/Document> .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-bio-characteristic
biosdterms:has-bio-characteristic a :ObjectProperty ;
rdfs:subPropertyOf biosdterms:has-sample-attribute ;
obo:IAO_0000115 "Relates a biological sample to a biological property that it has, such as the disease state or the organism it derives from. This correponds to the characteristic column in formats such as SampleTab or MAGE-TAB. As such, this relation might establish a not-too-formal associatios. For instance, an association to mus-musculus might mean either that the samle is a mouse, or that it is a part of a mouse."@en ;
rdfs:label "biological characteristic"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-bio-characteristic-type
biosdterms:has-bio-characteristic-type a :ObjectProperty ;
rdfs:subPropertyOf sio:SIO_000332 ;
obo:IAO_0000115 "The type of a biological characteristic. This usually comes from data file annotations, for instance, one has a '10C' attribute value, of type x, where x is an instance of 'temperature', or 'mus-musculus 123' attribute value, of type x, where x is an instance of the class mus-musculus."@en ;
obo:IAO_0000116 "PLEASE NOTE: This cannot be iao:is about, since that assumes the domain is an ICE, which is not always true in BioSD."@en , "This was used in an initial version of BioSD Linked Data model. Now an attribute/characteristic value can be instance of an ontology class if known, in addition to having the attributes rdfs:label + dcterms:title for the value, and dc:type + atlas:propertyType for the type. See http://www.ebi.ac.uk/rdf/biosd/newschema16 for details."@en ;
rdfs:label "biological characteristic type"@en ;
:deprecated "true"^^xsd:boolean .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-knowledgeable-organization
biosdterms:has-knowledgeable-organization a :ObjectProperty ;
rdfs:subPropertyOf dcterms:contributor , schema:contributor .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-knowledgeable-person
biosdterms:has-knowledgeable-person a :ObjectProperty ;
rdfs:subPropertyOf dcterms:contributor , schema:contributor .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-sample-attribute
biosdterms:has-sample-attribute a :ObjectProperty ;
rdfs:subPropertyOf obo:RO_0000086 , sio:SIO_000008 ;
rdfs:domain _:genid1 .
_:genid1 a :Class ;
:unionOf _:genid3 .
_:genid3 a rdf:List ;
rdf:first biosdterms:Sample ;
rdf:rest _:genid2 .
_:genid2 a rdf:List ;
rdf:first biosdterms:SampleGroup ;
rdf:rest rdf:nil .
biosdterms:has-sample-attribute obo:IAO_0000115 "Relates a sample or sample group to one of its attributes, not necessarily an attributes that is strictly related to biological qualities. For instance: provider name, identification code. This corresponds to attribute columns from formats like SampleTab or MAGE-TAB, such that the column header doesn't necessarily refer to a biological characteristic explicitly,e.g., 'Comment[Sample Provider]'. This relation might establish a not-too-formal associatios. For instance, an association from sample group to 'sample provider' might mean the group contains some samples coming from that provider."@en ;
rdfs:label "sample attribute"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/parent-of
biosdterms:parent-of a :ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002226 ;
rdfs:domain obo:OBI_0100026 , sio:SIO_010000 ;
rdfs:range obo:OBI_0100026 , sio:SIO_010000 ;
obo:IAO_0000115 "x parent-of y iff the organism x is the biological parent of y. " ;
rdfs:label "parent of" .
#
# http://rdf.ebi.ac.uk/terms/biosd/sample-child
biosdterms:sample-child a :ObjectProperty ;
rdfs:subPropertyOf sio:SIO_000244 , prov:wasDerivedFrom ;
:inverseOf biosdterms:sample-parent-of ;
rdfs:domain biosdterms:Sample ;
rdfs:range biosdterms:Sample ;
:propertyChainAxiom _:genid7 .
_:genid7 a rdf:List ;
rdf:first biosdterms:derived-from-organism ;
rdf:rest _:genid6 .
_:genid6 a rdf:List ;
rdf:first biosdterms:child-of ;
rdf:rest _:genid4 .
_:genid4 a rdf:List ;
rdf:first _:genid5 .
_:genid5 :inverseOf biosdterms:derived-from-organism .
_:genid4 rdf:rest rdf:nil .
biosdterms:sample-child obo:IAO_0000115 "A sample x is sample-child-of y iff x derives from organism xo, y derives from organism yo and xo is the biological child of yo. In other words, the two samples are taken from two orgranisms having a biological parentage relationship. We have used OWL-2 chain axioms, PROV-O, RO to formalise this relationship." ;
rdfs:label "sample-child of" .
#
# http://rdf.ebi.ac.uk/terms/biosd/sample-parent-of
biosdterms:sample-parent-of a :ObjectProperty ;
rdfs:subPropertyOf sio:SIO_000245 , prov:hadDerivation ;
rdfs:domain biosdterms:Sample ;
rdfs:range biosdterms:Sample ;
:propertyChainAxiom _:genid11 .
_:genid11 a rdf:List ;
rdf:first biosdterms:derived-from-organism ;
rdf:rest _:genid10 .
_:genid10 a rdf:List ;
rdf:first biosdterms:parent-of ;
rdf:rest _:genid8 .
_:genid8 a rdf:List ;
rdf:first _:genid9 .
_:genid9 :inverseOf biosdterms:derived-from-organism .
_:genid8 rdf:rest rdf:nil .
biosdterms:sample-parent-of obo:IAO_0000115 "A sample x is sample-parent-of y iff x derives from organism xo, y derives from organism yo and xo is the biological parent of yo. In other words, the two samples are taken from two organisms having a biological parentage relationship. We have used OWL-2 chain axioms, PROV-O, RO to formalise this relationship." ;
rdfs:label "sample-parent of" .
#
# http://schema.org/contributor
schema:contributor a :ObjectProperty .
#
# http://schema.org/description
schema:description a :ObjectProperty .
#
# http://schema.org/sameAs
schema:sameAs a :ObjectProperty , :SymmetricProperty , :TransitiveProperty , :ReflexiveProperty ;
rdfs:comment "We change schema:sameAs to be reflexive/symmetric/transitive, since it's pretty clear the semantics of this property implies that, it's practical to change it this way and it doesn't hurt to make this minimal changes to a third-party ontology (we make them in our files anyway)." .
#
# http://semanticscience.org/resource/SIO_000008
sio:SIO_000008 a :ObjectProperty .
#
# http://semanticscience.org/resource/SIO_000244
sio:SIO_000244 a :ObjectProperty .
#
# http://semanticscience.org/resource/SIO_000245
sio:SIO_000245 a :ObjectProperty .
#
# http://semanticscience.org/resource/SIO_000332
sio:SIO_000332 a :ObjectProperty .
#
# http://www.w3.org/ns/prov#hadDerivation
prov:hadDerivation a :ObjectProperty .
#
# http://www.w3.org/ns/prov#wasDerivedFrom
prov:wasDerivedFrom a :ObjectProperty .
#
#
#
# #################################################################
# #
# # Data properties
# #
# #################################################################
#
#
# http://rdf.ebi.ac.uk/terms/biosd/has-address-line
biosdterms:has-address-line a :DatatypeProperty ;
rdfs:subPropertyOf dcterms:description .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-affiliation-line
biosdterms:has-affiliation-line a :DatatypeProperty ;
rdfs:subPropertyOf dcterms:description .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-authors-list
biosdterms:has-authors-list a :DatatypeProperty ;
rdfs:subPropertyOf dcterms:description .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-high-value
biosdterms:has-high-value a :DatatypeProperty , :FunctionalProperty ;
obo:IAO_0000115 "A high end value for those structures that admit one, such as intervals (eg, SIO_000944)."@en ;
rdfs:label "has high value"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-low-value
biosdterms:has-low-value a :DatatypeProperty , :FunctionalProperty ;
obo:IAO_0000115 "A low end value for those structures that admit one, such as intervals (eg, SIO_000944)."@en ;
rdfs:label "has low value"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/has-percent-score
biosdterms:has-percent-score a :DatatypeProperty ;
rdfs:subPropertyOf sio:SIO_000300 ;
obo:IAO_0000115 "A score ranging from 0 to 100, representing the confidence we have that the element bearing this property (e.g. estimate, ontology mapping) is true/valid/significant/etc" ;
sio:narrowerThan obo:OBI_0000071 , sio:SIO_000257 ;
rdfs:label "has percent score" .
#
# http://schema.org/description
schema:description a :DatatypeProperty .
#
#
#
# #################################################################
# #
# # Classes
# #
# #################################################################
#
#
# http://purl.obolibrary.org/obo/IAO_0000311
obo:IAO_0000311 rdfs:subClassOf <http://purl.org/ontology/bibo/Document> , <http://purl.org/spar/fabio/Work> , <http://xmlns.com/foaf/0.1/Document> .
#
# http://purl.org/spar/fabio/Work
<http://purl.org/spar/fabio/Work> a :Class .
#
# http://rdf.ebi.ac.uk/terms/biosd/BiosamplesSubmission
biosdterms:BiosamplesSubmission a :Class ;
rdfs:subClassOf obo:IAO_0000310 , <http://purl.org/ontology/bibo/Document> , <http://purl.org/spar/fabio/Work> , <http://xmlns.com/foaf/0.1/Document> ;
obo:IAO_0000115 "A chunk of data that is submitted into the Biosamples Database, typically defined in a single document, such as a SampleTab file."@en ;
rdfs:label "Biosamples Database submission"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/ContactOrganization
biosdterms:ContactOrganization a :Class ;
rdfs:subClassOf schema:Organization , <http://xmlns.com/foaf/0.1/Organization> , _:genid12 .
_:genid12 a :Restriction ;
:onProperty obo:BFO_0000053 ;
:someValuesFrom obo:BFO_0000023 .
biosdterms:ContactOrganization obo:IAO_0000115 "An organization having some role, such as being a reference organization for the submission of an experimental data-set."@en ;
rdfs:label "contact organization"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/ContactPerson
biosdterms:ContactPerson a :Class ;
rdfs:subClassOf schema:Person , <http://xmlns.com/foaf/0.1/Person> , _:genid13 .
_:genid13 a :Restriction ;
:onProperty obo:BFO_0000053 ;
:someValuesFrom obo:OBI_0001687 .
biosdterms:ContactPerson obo:IAO_0000115 "A person that is a reference contact for some entity, such as an experimental data-set."@en ;
rdfs:label "contact person"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/OntologyMappingAnnotation
biosdterms:OntologyMappingAnnotation a :Class ;
rdfs:subClassOf <http://www.openannotation.org/ns/Annotation> ;
obo:IAO_0000115 "A subclass from the Open Annotation Model, to track the provenance of a mapping between two ontology terms. For instance, a term might have been passed as input to the Bioportal Mapping service and terms mapped from the input might have been returned. In such a case, for each returned term an OntologyMappingAnnotation is created, where the initial term is the annotation target and returned term is the annotation body."@en ;
rdfs:label "Ontology Mapping Annotation"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/RepositoryWebRecord
biosdterms:RepositoryWebRecord a :Class ;
rdfs:subClassOf obo:IAO_0000310 , <http://purl.org/ontology/bibo/Document> , <http://purl.org/spar/fabio/Work> , sio:SIO_000088 , <http://xmlns.com/foaf/0.1/Document> ;
obo:IAO_0000115 "A web page in a repository that represents a record about an entity, such as a biological sample or an experiment."@en ;
rdfs:label "Repository Web Record"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/Sample
biosdterms:Sample a :Class ;
rdfs:subClassOf obo:OBI_0000747 ;
obo:IAO_0000115 "A biological sample, for which a record exists (or potentially exists) in the EBI Biosamples database."@en ;
rdfs:comment "TODO: an axiom to state that the origin of a biosample is BioSD (use the same individual used in Void)."@en ;
rdfs:label "Biosample"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/SampleAttributeOntologyAnnotation
biosdterms:SampleAttributeOntologyAnnotation a :Class ;
rdfs:subClassOf <http://www.openannotation.org/ns/Annotation> ;
obo:IAO_0000115 "A subclass from the Open Annotation Model, to track the provenance of an ontology term annotation (body) regarding a BioSD sample attribute (target)."@en ;
rdfs:label "Sample Attribute Annotation"@en .
#
# http://rdf.ebi.ac.uk/terms/biosd/SampleGroup
biosdterms:SampleGroup a :Class ;
rdfs:subClassOf obo:IAO_0000314 , sio:SIO_000616 ;
obo:IAO_0000115 "A collection of biological samples stored in the EBI Biosamples database. Sample membership to a group is assigned by submitters or via automatic tools (i.e., it's a fiat relationship)."@en ;
rdfs:comment "TODO: an axiom to state that the origin of a biosample group is BioSD (use the same individual used in Void)."@en ;
rdfs:label "biosample group"@en .
#
# http://schema.org/Organization
schema:Organization a :Class .
#
# http://schema.org/Person
schema:Person a :Class .
#
# http://semanticscience.org/resource/SIO_000088
sio:SIO_000088 a :Class .
#
# http://semanticscience.org/resource/SIO_000616
sio:SIO_000616 a :Class .
#
# http://semanticscience.org/resource/SIO_010000
sio:SIO_010000 a :Class .
#
#
#
# #################################################################
# #
# # Annotations
# #
# #################################################################
#
#
biosdterms:has-address-line obo:IAO_0000115 "A postal address in the form of simple text (i.e., string). This can be used for those cases where it's too complicated to achieve a proper structure for an address."@en ;
rdfs:label "postal address"@en .
#
biosdterms:has-affiliation-line obo:IAO_0000115 "An affiliation description for a person (e.g., department+university), in the form of simple text (i.e., string). This can be used for those cases where it's too complicated to achieve a proper structure for an affiliation."@en ;
rdfs:label "affiliation"@en .
#
biosdterms:has-authors-list obo:IAO_0000115 "The list of authors of a publication or document, in the form of a simple text (i.e., a string). This can be used for those cases where extracting a proper list of authors (e.g., from a database record) is too complicated."@en ;
rdfs:label "authors list"@en .
#
biosdterms:has-knowledgeable-organization obo:IAO_0000115 "An organization that is somehow involved with the subject of this relation, for example because it is its creator, or the maintainer, or alike."@en ;
rdfs:label "has knowledgeable organization"@en .
#
biosdterms:has-knowledgeable-person obo:IAO_0000115 "A person that is somehow involved with the subject of this relation, for example because he/she is its creator, or the maintainer, or alike."@en ;
rdfs:label "has knowledgeable person"@en .
#
# Generated by the OWL API (version 4.1.3.20151118-2017) https://github.com/owlcs/owlapi
You can’t perform that action at this time.