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genex_with_import_v0_2.owl
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genex_with_import_v0_2.owl
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@prefix : <http://purl.org/genex#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix pav: <http://purl.org/pav/> .
@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 orth: <http://purl.org/net/orth#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix swrl: <http://www.w3.org/2003/11/swrl#> .
@prefix swrla: <http://swrl.stanford.edu/ontologies/3.3/swrla.owl#> .
@prefix swrlb: <http://www.w3.org/2003/11/swrlb#> .
@prefix terms: <http://purl.org/dc/terms/> .
@prefix uberon: <http://purl.obolibrary.org/obo/uberon#> .
@prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> .
@prefix vann: <http://purl.org/vocab/vann/> .
@prefix schema: <http://schema.org/> .
@prefix voaf: <http://purl.org/vocommons/voaf#> .
@prefix widoco: <https://w3id.org/widoco/vocab#> .
@prefix bibo: <http://purl.org/ontology/bibo/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix org: <http://www.w3.org/ns/org#> .
@base <http://purl.org/genex> .
<http://purl.org/genex> rdf:type owl:Ontology ;
owl:imports obo:caro.owl ,
<http://purl.org/net/orth/2.0> ,
obo:iao.owl ,
efo:efo.owl ,
obo:ro.owl ,
<http://www.w3.org/2004/02/skos/core>,
<http://purl.org/lscr> ;
terms:modified "2024-04-30"^^xsd:date ;
owl:versionInfo "0.2" ;
vann:preferredNamespacePrefix "genex" ;
terms:abstract "Expression patterns are a major feature of gene description, and are captured in many expression related databases (e.g., Bgee, Expression Atlas, GENEVESTIGATOR, or Tissue). Yet comparison and interoperability among these heterogeneous data sources or providers is limited by a lack of agreement for describing knowledge of gene expression. Ontologies are recognized as an interesting approach to achieve a consensus for knowledge representation, and allow to leverage semantic interoperability, but are lacking for the domain of gene expression. The Relational Ontology (RO) contains preliminary efforts to define terms for describing this domain. Notably, it contains `expressed in` and `expresses` properties (i.e., relations). Nonetheless, further work was necessary to address the following issue: the representation of additional information related to gene expression, such as developmental stages, as well as absent in and highly expressed relations. Furthermore, we reuse parts of the data schemas of the ORTH and UniProt core ontologies to provide the capacity to interoperate with other biological databases from different knowledge domains which are still relevant to the gene expression domain. Moreover, different gene expression databases use distinct confidence scores to assert expressed in or absent in relations. Finally, the GenEx ontology is fully adopted by Bgee, a gene expression database, as its core data schema to structure the Bgee RDF data accessible via its SPARQL endpoint at [https://www.bgee.org/sparql/](https://www.bgee.org/sparql/)."@en ;
terms:bibliographicCitation '''Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz, Enabling semantic queries across federated bioinformatics databases, Database, Volume 2019, 2019, baz106, <a href="https://doi.org/10.1093/database/baz106">https://doi.org/10.1093/database/baz106</a>''' ;
terms:license <https://creativecommons.org/publicdomain/zero/1.0/> ;
schema:image <http://biosoda.expasy.org/genex/images/Picture1.png> ;
schema:codeRepository "https://github.com/biosoda/genex"^^xsd:anyURI ;
terms:contributor <https://orcid.org/0000-0002-3175-5372>, <https://orcid.org/0000-0002-9415-5104>, <https://orcid.org/0000-0002-3099-3117>, <https://orcid.org/0000-0002-2170-853X>, <https://orcid.org/0000-0002-3437-3329> ;
terms:created "2019-01-25"^^xsd:date ;
terms:creator <https://orcid.org/0000-0002-3175-5372> ;
terms:description "The GenEx ontology is designed to capture and structure gene expression information provided by databases such as Bgee."@en ;
voaf:extends <http://purl.obolibrary.org/obo/ro.owl> ;
terms:issue "2019-11-07"^^xsd:date ;
vann:preferredNamespaceUri <http://purl.org/genex#> ;
terms:title "Gene expression (GenEx) ontology"@en ;
owl:versionIRI <http://purl.org/genex/0.2> ;
owl:previousVersion <http://purl.org/genex/0.1> ;
terms:publisher <https://www.sib.swiss> ;
bibo:status <http://purl.org/ontology/bibo/status/accepted> ;
rdfs:seeAlso <http://purl.obolibrary.org/obo/ro.owl>, <https://bioschemas.org>, <https://schema.org> ;
widoco:introduction '''There is a general lack of a comprehensive ontology to serve as a data schema for describing knowledge in the field of gene expression. This may seem surprising, considering the ubiquity of gene expression analyses in molecular biology and the existence of multiple well-established resources for gene expression, such as Bgee, Expression Atlas (EA), GENEVESTIGATOR, RefEx (Reference Expression dataset) or the Tissue Expression database. We note here that different gene expression databases often use distinct criteria to assert expressed in or absent in relations.
To the best of our knowledge, at least 3 semantic models currently exist as initial attempts to structure gene expression related data: the Relation Ontology (RO), the Expression Atlas semantic model (discontinued) and Bioschema.org / Schema.org. The Relation Ontology and Schema.org define only a few terms within the domain of gene expression and is not uniquely designed for this knowledge domain. Notably, they contain an 'expressed in' relation. The Expression Atlas defines a semantic model related to gene expression that mainly focuses on modelling the Expression Atlas data itself and not the domain of gene expression generally. In this EA model, additional data interpretations (i.e., semantics) are not explicitly represented, such as a given gene is expressed or lowly expressed in some sample relative to others. Although it would be possible to obtain this information through a more complex query on the Expression Atlas SPARQL endpoint (currently discontinued), we lack an explicit representation, which would allow us to compare gene expression data from these different databases.
To provide a first step toward a general-purpose gene expression ontology, we defined a semantic model called GenEx. GenEx is aligned with the Relation Ontology and Expression Atlas models to facilitate interoperability with existing RDF stores. Furthermore, we reuse parts of the data schemas of the ORTH and UniProtKB core ontologies to provide an easy way to interoperate with other biological databases from different knowledge domains that are relevant to the gene expression domain. For example, integrating orthology and gene expression data are relevant since we might want to predict gene expression conservation for orthologous genes.
GenEx is designed to capture and structure gene expression information at a higher level relative to others.
By doing so, we intend to model the data meanings which are expected by the end-users such as biologists. For example, often biologists are not interested in knowing expression scores, that depend on the method used or data transformations. Rather, for instance, they might look for an interpretation of expression scores, such as whether a gene is highly expressed.
GenEx was defined by using the [OWL 2 Description Logics (DL)](https://www.w3.org/TR/owl2-overview/).
The methodology to develop GenEx was inspired by the Simplified Agile Methodology for Ontology Development [SAMOD](http://essepuntato.github.io/samod/).
We defined a concept for describing absence of gene expression so-called [genex:AbsenceExpression](#AbsenceExpression). The [genex:AbsenceExpression](#AbsenceExpression) class is a subclass of the complement of [genex:Expression](#Expression) class (i.e., [genex:AbsenceExpression](#AbsenceExpression) ⊑ ¬[genex:Expression](#Expression). [genex:Expression](#Expression) is the concept for representing gene expression according to a given experimental condition (e.g. sex and anatomical entity). [genex:AbsenceExpression](#AbsenceExpression) is not equivalent to the negation of the [genex:Expression](#Expression) because it may lack experiments to conclude that a gene is expressed (i.e., missing gene expression information). Therefore, solely data processed from experiments which confirm no presence of expression are described by using the [genex:AbsenceExpression](#AbsenceExpression) class. We highlight that the [Bgee database](https://bgee.org) provides absence of expression, Bastian et al. in [(1)](https://doi.org/10.1093/nar/gkaa793) describe how the absence of expression information is computed in the Bgee database by also discussing about expression calls.
We mostly considered to reuse the following ontologies:
- The [Relation Ontology (RO)](http://www.obofoundry.org/ontology/ro.html). For example, we reuse ro:RO_0002245 OWL object property labelled as “over-expressed in” or “highly expressed”. In DL, we can formalise as follows: ∃[ro:RO_0002245](#http://purl.obolibrary.org/obo/RO_0002245).⊤ ⊑ [orth:SequenceUnit](#http://purl.org/net/orth#SequenceUnit) where [orth:SequenceUnit](#http://purl.org/net/orth#SequenceUnit) is the inferred domain of [ro:RO_0002245](#http://purl.obolibrary.org/obo/RO_0002245) and ⊤ is the top concept (i.e., [owl:Thing](https://www.w3.org/TR/2004/REC-owl-semantics-20040210/#owl_Thing) term).
- The [Orthology (ORTH) ontology](http://qfo.github.io/OrthologyOntology/). For example, we reuse the [orth:SequenceUnit](#http://purl.org/net/orth#SequenceUnit) class (i.e., [orth:SequenceUnit](#http://purl.org/net/orth#SequenceUnit) ⊑ ⊤). The reuse of terms and a part of the data schema of ORTH ontology significantly facilitate the integration with orthology databases (e.g. OMA). In doing so, we address the use case of predicting presence or absence of expression for orthologous genes.
- The [Experimental Factor Ontology (EFO)](https://www.ebi.ac.uk/efo/). This ontology provides a description of various experimental variables (e.g., organism part, material entity and developmental stage) available in EBI databases such as EA. In GenEx, we mainly reuse classes such as [efo:EFO_0000635](#http://www.ebi.ac.uk/efo/EFO_0000635) (labelled “organism part”), [efo:EFO_0005135](#http://www.ebi.ac.uk/efo/EFO_0005135) (labelled “strain”), and [efo:EFO_0000399](#http://www.ebi.ac.uk/efo/EFO_0000399) (labelled “developmental stage”).
- The [Confidence Information Ontology (CIO)](http://www.obofoundry.org/ontology/cio.html) classes as instance values of the [genex:hasConfidenceLevel](#hasConfidenceLevel) OWL object property. In the GenEx context, CIO classes are individuals to represent the confidence levels of gene expression predictions. This is possible in OWL 2 thanks to [punning](https://www.w3.org/TR/owl2-new-features/#F12:_Punning) . The following DL constraint is stated ⊤ ⊑∀[genex:hasConfidenceLevel](#hasConfidenceLevel).{[cio:0000029](#http://purl.obolibrary.org/obo/CIO_0000029), [cio:0000030](#http://purl.obolibrary.org/obo/CIO_0000030), [cio:0000031](#http://purl.obolibrary.org/obo/CIO_0000031)}. This means that the [genex:hasConfidenceLevel](#hasConfidenceLevel) property values (i.e., property range) can only be “high confidence level”', “medium confidence level”, or “low confidence level”.
- The Uber-anatomy (UBERON) ontology. In the GenEx context, UBERON classes are considered as individuals
of genex:AnatomicalEntity or [efo:EFO_0000399](#http://www.ebi.ac.uk/efo/EFO_0000399) (i.e., developmental stage) classes. The classes of the developmental stage per species ontologies in the [wiki](#https://github.com/obophenotype/developmental-stage-ontologies/wiki) developmental-stage-ontologies wiki</a> are also considered as individuals of [efo:EFO_0000399](#http://www.ebi.ac.uk/efo/EFO_0000399) class. Therefore, for GenEx, these ontologies are controlled vocabularies assigned as values of [genex:hasDevelopmentalStage](#hasDevelopmentalStage) and genex:hasAnatomicalEntity OWL object properties. These properties describe gene expression experimental conditions. In UBERON, despite the “life cycle stage” term is a synonym of “developmental stage” EFO term, we decided to reuse EFO “developmental stage” term in GenEx rather than UBERON one. This is because we want to separate the UBERON terms which are considered as OWL individuals in the GenEx context (by applying [OWL 2 punning](https://www.w3.org/TR/owl2-new-features/#F12:_Punning) feature) and the “developmental stage” class from EFO.
One of the main semantic modelling issues GenEx addresses is to provide terms and a data schema for explicitly describing and structuring multiple combined conditions for gene expression. For example, the HBB human gene is highly expressed in the cerebellum of 6-12 year-old child stage. Thus, experiments to derive this conclusion were mainly performed under two conditions: a human developmental stage and the cerebellum anatomical entity.
In GenEx, we explicitly define a relation for each experimental condition such as the [genex:hasAnatomicalEntity](#hasAnatomicalEntity) property assigned with an [Uber-anatomy (UBERON)](http://uberon.github.io/) class as value by [punning](https://www.w3.org/TR/owl2-new-features/#F12:_Punning). We reuse [Experimental Factor Ontology (EFO)](https://www.ebi.ac.uk/efo/) classes instead of defining literals.
As a limitation, at present, GenEx does not support differential expression analysis such as included in the Expression Atlas RDF schema (that is discontinued). This is because we mostly focus on describing information that may be extracted from the present state of the Bgee database. GenEx can be viewed as a start point towards an ontology to structure gene expression information. We consider GenEx a semantic model rather than an ontology. This is because, currently, it is not necessarily a shared conceptualisation among all stakeholders of interest, which include but not only the following gene expression database teams Bgee, Expression Atlas, GENEVESTIGATOR, and Tissue, and others (e.g., the Model Organisms Databases).
'''.
<https://orcid.org/0000-0002-3175-5372> foaf:name "Tarcisio Mendes de Farias"@en ;
org:memberOf <https://www.sib.swiss> .
<https://orcid.org/0000-0002-9415-5104> foaf:name "Frederic Bastian"@en ;
org:memberOf <https://www.sib.swiss> .
<https://orcid.org/0000-0002-3099-3117> foaf:name "Julien Wollbrett"@en ;
org:memberOf <https://www.sib.swiss> .
<https://orcid.org/0000-0002-2170-853X> foaf:name "Christophe Dessimoz"@en ;
org:memberOf <https://www.sib.swiss> .
<https://orcid.org/0000-0002-3437-3329> foaf:name "Marc Robinson-Rechavi"@en ;
org:memberOf <https://www.unil.ch> .
<https://www.sib.swiss> rdf:type owl:NamedIndividual ,
foaf:Organization ;
foaf:homepage "https://www.sib.swiss" ;
foaf:name "SIB Swiss Institute of Bioinformatics"@en .
<https://www.unil.ch> rdf:type owl:NamedIndividual ,
foaf:Organization ;
foaf:homepage "https://www.unil.ch" ;
foaf:name "University of Lausanne"@en .
<http://purl.uniprot.org/core/Taxon> vann:example
'''@prefix up: <http://purl.uniprot.org/core/> .
@prefix up-taxon: <http://purl.uniprot.org/taxonomy/> .
up-taxon:10090 rdf:type up:Taxon ;
up:rank up:Species . '''.
<http://purl.uniprot.org/core/scientificName> vann:example
'''@prefix up: <http://purl.uniprot.org/core/> .
@prefix up-taxon: <http://purl.uniprot.org/taxonomy/> .
up-taxon:10090 rdf:type up:Taxon ;
up:scientificName "Mus musculus". '''.
<http://purl.uniprot.org/core/commonName> vann:example
'''@prefix up: <http://purl.uniprot.org/core/> .
@prefix up-taxon: <http://purl.uniprot.org/taxonomy/> .
up-taxon:10090 rdf:type up:Taxon ;
up:commonName "mouse" . '''.
<http://www.ebi.ac.uk/efo/EFO_0000399> vann:example
'''@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .
obo:BtauDv_0000007 rdf:type efo:EFO_0000399 ;
dcterms:description "Embryo development period during the first 3 months of gestation, up to day 90 of development." ;
rdfs:label "first trimester of gestation (cow)". '''.
orth:Gene vann:example
'''@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
@prefix orth: <http://purl.org/net/orth#> .
oma:ENSG00000130208 rdf:type orth:Gene ;
dcterms:description "apolipoprotein C1 [Source:HGNC Symbol;Acc:HGNC:607]" ;
rdfs:label "first trimester of gestation (cow)";
dcterms:identifier "ENSG00000130208" . '''.
:AnatomicalEntity vann:example
'''@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
obo:UBERON_0000310 rdf:type genex:AnatomicalEntity ;
dcterms:description "The upper ventral region of the torso of an organism." ;
rdfs:label "breast" . '''.
:isExpressedIn vann:example
'''@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
obo:UBERON_0000310 rdf:type genex:AnatomicalEntity .
oma:ENSMUSG00000002396 rdf:type orth:Gene ;
genex:isExpressedIn obo:UBERON_0000310 .'''.
obo:RO_0002292 vann:example
'''@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
obo:UBERON_0000310 rdf:type genex:AnatomicalEntity ;
obo:RO_0002292 oma:ENSMUSG00000002396 .
oma:ENSMUSG00000002396 rdf:type orth:Gene . '''.
obo:RO_0002206 vann:example
'''@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix obo: <ttp://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
obo:UBERON_0000310 rdf:type genex:AnatomicalEntity .
oma:ENSMUSG00000002396 rdf:type orth:Gene ;
obo:RO_0002206 obo:UBERON_0000310 .'''.
orth:organism vann:example
'''@prefix bgee-species: <https://bgee.org/species/> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
oma:ENSMUSG00000002396 rdf:type orth:Gene ;
orth:organism bgee-species:10090 .'''.
obo:RO_0002162 vann:example
'''@prefix bgee-species: <https://bgee.org/species/> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
@prefix up: <http://purl.uniprot.org/core/> .
@prefix up-taxon: <http://purl.uniprot.org/taxonomy/> .
bgee-species:10090 rdf:type orth:Organism ;
obo:RO_0002162 up-taxon:10090 .
up-taxon:10090 rdf:type up:Taxon ;
up:scientificName "Mus musculus". '''.
:Expression vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix genex: <http://purl.org/genex#> .
bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
genex:hasExpressionLevel 83.9292 ;
genex:hasConfidenceLevel obo:CIO_0000029 ;
genex:hasFDRpvalue 0.00188199 ;
genex:hasSequenceUnit oma:ENSMUSG00000022751 ;
genex:hasExpressionCondition bgee:EXPRESSION_CONDITION_354899 . '''.
:hasExpressionCharacteristic vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix genex: <http://purl.org/genex#> .
bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
genex:hasExpressionCharacteristic genex:AVERAGE_EXPRESSED . '''.
:hasExpressionLevel vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix genex: <http://purl.org/genex#> .
bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
genex:hasExpressionLevel 83.9292 . '''.
:hasConfidenceLevel vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix genex: <http://purl.org/genex#> .
bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
genex:hasConfidenceLevel obo:CIO_0000029 . '''.
:hasFDRpvalue vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix genex: <http://purl.org/genex#> .
bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
genex:hasFDRpvalue 0.00188199 . '''.
:hasSequenceUnit vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix genex: <http://purl.org/genex#> .
bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
genex:hasSequenceUnit oma:ENSMUSG00000022751 .
oma:ENSMUSG00000022751 a orth:Gene . '''.
:hasExpressionCondition vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix genex: <http://purl.org/genex#> .
bgee:EXPRESSION_546588859 rdf:type genex:Expression ;
genex:hasExpressionCondition bgee:EXPRESSION_CONDITION_354899 .
bgee:EXPRESSION_CONDITION_354899 rdf:type genex:ExpressionCondition . '''.
:AbsenceExpression vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix oma: <http://omabrowser.org/ontology/oma#GENE_> .
@prefix orth: <http://purl.org/net/orth#> .
@prefix genex: <http://purl.org/genex#> .
bgee:NOT_EXPRESSED_310632766 rdf:type genex:AbsenceExpression ;
genex:hasExpressionLevel 6.44034 ;
genex:hasConfidenceLevel obo:CIO_0000029 ;
genex:hasFDRpvalue 1.0 ;
genex:hasSequenceUnit oma:ENSXETG00000010593 ;
genex:hasExpressionCondition bgee:EXPRESSION_CONDITION_134065 . '''.
:ExpressionCondition vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ;
genex:hasSex "any";
genex:hasStrain bgee:STRAIN_3d4eba69908860b0d838be983fd7f9c8 ;
genex:hasAnatomicalEntity obo:UBERON_0000080 ;
genex:hasDevelopmentalStage obo:UBERON_0000113 . '''.
:hasSex vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ;
genex:hasSex "any" . '''.
:hasStrain vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .
bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ;
genex:hasStrain bgee:STRAIN_3d4eba69908860b0d838be983fd7f9c8 .
bgee:STRAIN_3d4eba69908860b0d838be983fd7f9c8 rdf:type efo:EFO_0005135 ;
rdfs:label "wild-type" '''.
:hasAnatomicalEntity vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .
bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ;
genex:hasAnatomicalEntity obo:UBERON_0000080 .
obo:UBERON_0000080 rdf:type genex:AnatomicalEntity. '''.
:hasDevelopmentalStage vann:example
'''@prefix bgee: <http://bgee.org/#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix genex: <http://purl.org/genex#> .
@prefix efo: <http://www.ebi.ac.uk/efo/> .
bgee:EXPRESSION_CONDITION_134065 rdf:type genex:ExpressionCondition ;
genex:hasDevelopmentalStage obo:UBERON_0000113 .
obo:UBERON_0000113 rdf:type efo:EFO_0000399 . '''.
#################################################################
# Annotation properties
#################################################################
### http://purl.obolibrary.org/obo/IAO_0000112
obo:IAO_0000112 rdf:type owl:AnnotationProperty ;
rdfs:label "example of usage" .
### http://purl.obolibrary.org/obo/IAO_0000115
obo:IAO_0000115 rdf:type owl:AnnotationProperty ;
rdfs:label "definition"^^xsd:string .
### http://purl.obolibrary.org/obo/IAO_0000116
obo:IAO_0000116 rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy obo:iao.owl ;
rdfs:label "editor note"@en .
### http://purl.obolibrary.org/obo/IAO_0000232
obo:IAO_0000232 rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy obo:iao.owl ;
rdfs:label "curator note"@en .
### http://purl.obolibrary.org/obo/IAO_0000600
obo:IAO_0000600 rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy obo:iao.owl ;
rdfs:label "elucidation"@en .
### http://purl.org/dc/terms/description
terms:description rdf:type owl:AnnotationProperty ;
terms:description "Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource."@en ;
rdfs:comment "An account of the resource."@en ;
rdfs:isDefinedBy terms: ;
rdfs:label "Description"@en .
### http://purl.org/dc/terms/modified
terms:modified rdf:type owl:AnnotationProperty .
### http://purl.org/net/orth#inDatabase
orth:inDatabase rdf:type owl:AnnotationProperty ;
rdfs:comment "A property to define the database an orthology dataset belongs to."@en ;
rdfs:label "in database"@en ;
rdfs:domain orth:OrthologyDataset .
### http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation
efo:NCI_Thesaurus_definition_citation rdf:type owl:AnnotationProperty ;
obo:IAO_0000115 "http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation is an annotation property that is drawn from NCI_Thesaurus"^^xsd:string ;
efo:NCI_Thesaurus_definition_citation "http://www.ebi.ac.uk/efo/NCI_Thesaurus_definition_citation is an annotation property that is drawn from NCI_Thesaurus"^^xsd:string ;
rdfs:subPropertyOf efo:definition_citation .
### http://www.ebi.ac.uk/efo/alternative_term
efo:alternative_term rdf:type owl:AnnotationProperty ;
obo:IAO_0000115 "An alternative label for a given entity such as a commonly used abbreviation or synonym. " ;
rdfs:label "alternative_term"^^xsd:string .
### http://www.ebi.ac.uk/efo/definition_citation
efo:definition_citation rdf:type owl:AnnotationProperty ;
obo:IAO_0000115 "A definition citation is a document, ontology class, person or organization from which the definition of the class is derived. It is used in the same sense as a citation in literature, in that the definition may have been derived from these sources or that this definition is related to these source." .
### http://www.ebi.ac.uk/efo/source_definition
efo:source_definition rdf:type owl:AnnotationProperty .
### http://www.geneontology.org/formats/oboInOwl#id
oboInOwl:id rdf:type owl:AnnotationProperty .
### http://www.geneontology.org/formats/oboInOwl#inSubset
oboInOwl:inSubset rdf:type owl:AnnotationProperty .
### http://www.w3.org/2004/02/skos/core#altLabel
skos:altLabel rdf:type owl:AnnotationProperty ;
rdfs:comment "The range of skos:altLabel is the class of RDF plain literals."@en ,
"skos:prefLabel, skos:altLabel and skos:hiddenLabel are pairwise disjoint properties."@en ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "alternative label"@en ;
skos:definition "An alternative lexical label for a resource."@en ;
skos:example "Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel)."@en ;
rdfs:subPropertyOf rdfs:label .
### http://www.w3.org/2004/02/skos/core#changeNote
skos:changeNote rdf:type owl:AnnotationProperty .
### http://www.w3.org/2004/02/skos/core#definition
skos:definition rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "definition"@en ;
skos:definition "A statement or formal explanation of the meaning of a concept."@en ;
rdfs:subPropertyOf skos:note .
### http://www.w3.org/2004/02/skos/core#example
skos:example rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "example"@en ;
skos:definition "An example of the use of a concept."@en ;
rdfs:subPropertyOf skos:note .
### http://www.w3.org/2004/02/skos/core#note
skos:note rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "note"@en ;
skos:definition "A general note, for any purpose."@en ;
skos:scopeNote "This property may be used directly, or as a super-property for more specific note types."@en .
### http://www.w3.org/2004/02/skos/core#scopeNote
skos:scopeNote rdf:type owl:AnnotationProperty ;
rdfs:isDefinedBy <http://www.w3.org/2004/02/skos/core> ;
rdfs:label "scope note"@en ;
skos:definition "A note that helps to clarify the meaning and/or the use of a concept."@en ;
rdfs:subPropertyOf skos:note .
#################################################################
# Datatypes
#################################################################
### http://www.w3.org/2001/XMLSchema#date
xsd:date rdf:type rdfs:Datatype .
#################################################################
# Object Properties
#################################################################
### http://purl.obolibrary.org/obo/CDAO_0000194
obo:CDAO_0000194 rdf:type owl:ObjectProperty ;
rdfs:label "part_of"^^xsd:string .
### http://purl.obolibrary.org/obo/RO_0001018
obo:RO_0001018 rdf:type owl:ObjectProperty ;
rdfs:label "contained in"@en .
### http://purl.obolibrary.org/obo/RO_0002162
obo:RO_0002162 rdf:type owl:ObjectProperty ;
rdfs:comment "Connects a biological entity to its taxon of origin."@en ;
rdfs:label "in taxon"@en .
### http://purl.obolibrary.org/obo/RO_0002206
obo:RO_0002206 rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002330 ;
owl:inverseOf obo:RO_0002292 ;
rdfs:domain obo:BFO_0000002 ;
rdfs:range obo:BFO_0000004 ;
obo:IAO_0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" ;
obo:IAO_0000115 "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" ;
rdfs:label "expressed in"@en .
### http://purl.obolibrary.org/obo/RO_0002245
obo:RO_0002245 rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf :isExpressedIn ;
obo:IAO_0000115 "g is over-expressed in t iff g is expressed in t, and the expression level of g is increased relative to some background." ;
rdfs:label "over-expressed in" ;
skos:altLabel "highly expressed in"@en .
### http://purl.obolibrary.org/obo/RO_0002246
obo:RO_0002246 rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf :isExpressedIn ;
obo:IAO_0000115 "g is under-expressed in t iff g is expressed in t, and the expression level of g is decreased relative to some background." ;
rdfs:label "under-expressed in" .
### http://purl.obolibrary.org/obo/RO_0002291
obo:RO_0002291 rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf :isExpressedIn ;
owl:inverseOf obo:RO_0002293 ;
obo:IAO_0000115 "x is ubiquitously expressed in y if and only if x is expressed in y, and the majority of cells in y express x" ;
obo:IAO_0000116 "Revisit this term after coordinating with SO/SOM. The domain of this relation should be a sequence, as an instance of a DNA molecule is only expressed in the cell of which it is a part." ;
rdfs:label "ubiquitously expressed in"@en .
### http://purl.obolibrary.org/obo/RO_0002292
obo:RO_0002292 rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002330 ;
obo:IAO_0000115 "Inverse of 'expressed in'" ;
rdfs:label "expresses"@en .
### http://purl.obolibrary.org/obo/RO_0002293
obo:RO_0002293 rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002292 ;
obo:IAO_0000115 "inverse of ubiquiotously expressed in" ;
oboInOwl:inSubset obo:RO_0002259 ;
rdfs:label "ubiquitously expresses"@en .
### http://purl.obolibrary.org/obo/RO_0002330
obo:RO_0002330 rdf:type owl:ObjectProperty ;
rdfs:domain obo:BFO_0000002 ;
rdfs:range obo:BFO_0000002 ;
obo:IAO_0000115 "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." ;
obo:IAO_0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" ;
rdfs:label "genomically related to"@en .
### http://purl.org/genex#hasAnatomicalEntity
:hasAnatomicalEntity rdf:type owl:ObjectProperty ,
owl:FunctionalProperty ;
rdfs:domain :ExpressionCondition ;
rdfs:range :AnatomicalEntity ;
rdfs:label "has anatomical entity"@en .
### http://purl.org/genex#hasConfidenceLevel
:hasConfidenceLevel rdf:type owl:ObjectProperty ,
owl:FunctionalProperty ;
rdfs:domain [ rdf:type owl:Class ;
owl:unionOf ( :AbsenceExpression
:Expression
)
] ;
rdfs:range [ rdf:type owl:Class ;
owl:oneOf ( obo:CIO_0000029
obo:CIO_0000030
obo:CIO_0000031
)
] ;
rdfs:label "has expression or absence confidence level"@en .
### http://purl.org/genex#hasDevelopmentalStage
:hasDevelopmentalStage rdf:type owl:ObjectProperty ,
owl:FunctionalProperty ;
rdfs:domain :ExpressionCondition ;
rdfs:range efo:EFO_0000399 ;
rdfs:label "has a developmental stage"@en .
### http://purl.org/genex#hasExpressionCharacteristic
:hasExpressionCharacteristic rdf:type owl:ObjectProperty ,
owl:FunctionalProperty ;
rdfs:domain :Expression ;
rdfs:range [ rdf:type owl:Class ;
owl:oneOf ( :AVERAGE_EXPRESSED
:HIGHLY_EXPRESSED
:HIGH_EXPRESSED
:LOWLY_EXPRESSED
:LOW_EXPRESSED
:UBIQUITOUSLY_EXPRESSED
)
] ;
rdfs:label "has expression level characteristic"@en .
### http://purl.org/genex#hasExpressionCondition
:hasExpressionCondition rdf:type owl:ObjectProperty ;
rdfs:domain [ rdf:type owl:Class ;
owl:unionOf ( :AbsenceExpression
:Expression
)
] ;
rdfs:range :ExpressionCondition ;
rdfs:label "has an expression condition"@en ;
skos:altLabel "has an experimental condition"@en .
### http://purl.org/genex#hasSequenceUnit
:hasSequenceUnit rdf:type owl:ObjectProperty ;
rdfs:domain [ rdf:type owl:Class ;
owl:unionOf ( :AbsenceExpression
:Expression
)
] ;
rdfs:range orth:SequenceUnit ;
rdfs:label "has sequence unit"@en .
### http://purl.org/genex#hasStrain
:hasStrain rdf:type owl:ObjectProperty ,
owl:FunctionalProperty ;
rdfs:domain :ExpressionCondition ;
rdfs:range efo:EFO_0005135 ;
rdfs:label "has strain"@en .
### http://purl.org/genex#isAbsentIn
:isAbsentIn rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002330 ;
rdfs:domain orth:SequenceUnit ;
rdfs:range [ rdf:type owl:Class ;
owl:unionOf ( :AnatomicalEntity
:ExpressionCondition
efo:EFO_0000399
efo:EFO_0005135
)
] ;
rdfs:comment "A sequence unit is absent (not expressed) in some expression condition (e.g. anatomical entity and/or developmental stage). Examples how to assign this property (at a high level of abstraction): GeneA \"is absent in\" Brain; GeneA \"is abent in\" adult stage."@en ,
"""Recommendation: prefer to instatiate 'absence of gene expression' and 'gene expression experiment condition' classes to represent Gene expression data. For example, rather than materializing this property at the data store level, it shoud be inferred by applying the logical rules:
rule1- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?cond);
rule2- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has a developmental stage'(?cond, ?stage), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?stage)
rule3- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has strain'(?cond, ?strain), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?strain)
rule4- 'expressed gene'(?e),'has an expression condition'(?e, ?cond), 'has anatomical entity'(?cond, ?anat), 'has sequence unit'(?e, ?seq) -> 'is expressed in'(?seq, ?anat)
These rules are currently defined in Genex ontology as a SWRL (Semantic Web Rule Language) rule. It can be tanslated into another semantic web language such as RIF."""@en ;
rdfs:label "is absent in"@en ;
skos:altLabel "is not expressed in"@en .
### http://purl.org/genex#isExpressedIn
:isExpressedIn rdf:type owl:ObjectProperty ;
rdfs:subPropertyOf obo:RO_0002206 ;
rdfs:domain orth:SequenceUnit ;
rdfs:range [ rdf:type owl:Class ;
owl:unionOf ( :AnatomicalEntity
:ExpressionCondition
efo:EFO_0000399
efo:EFO_0005135
)
] ;
rdfs:comment "A sequence unit (e.g. gene) is present (expressed) in some expression condition (e.g. anatomical entity and/or developmental stage). Examples how to assign this property (at a high level of abstraction): GeneA \"is expressed in\" Brain; GeneA \"is expressed in\" adult stage."@en ,
"""Recommendation: prefer to instatiate 'expressed gene' and 'gene expression experiment condition' classes to represent Gene expression data. For example, rather than materializing this property at the data store level, it shoud be inferred by applying the logical rules:
- 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?cond);
- 'absence of gene expression'?e),'has an expression condition'(?e, ?cond), 'has a developmental stage'(?cond, ?stage), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?stage)
- 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has strain'(?cond, ?strain), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?strain)
- 'absence of gene expression'(?e),'has an expression condition'(?e, ?cond), 'has anatomical entity'(?cond, ?anat), 'has sequence unit'(?e, ?seq) -> 'is absent in'(?seq, ?anat)
These rules are currently defined in Genex ontology as a SWRL (Semantic Web Rule Language) rule. It can be tanslated into another semantic web language such as RIF."""@en ;
rdfs:label "is expressed in"@en .
### http://purl.org/net/orth#organism
orth:organism rdf:type owl:ObjectProperty ;
rdfs:domain orth:SequenceUnit ;
rdfs:range orth:Organism .
### http://purl.uniprot.org/core/rank
up:rank rdf:type owl:ObjectProperty ,
owl:FunctionalProperty ;
rdfs:domain up:Taxon ;
rdfs:range up:Rank ;
rdfs:comment "The rank of a taxon."^^xsd:string .
### http://purl.uniprot.org/core/replaces
up:replaces rdf:type owl:ObjectProperty ;
rdfs:domain up:Taxon ;
rdfs:range up:Taxon ;
rdfs:comment "A resource that is replaced by this resource."^^xsd:string .
### http://semanticscience.org/resource/SIO_010078
sio:SIO_010078 rdf:type owl:ObjectProperty ;
rdfs:label "encodes"@en .
#################################################################
# Data properties
#################################################################
### http://purl.org/dc/elements/1.1/description
dc:description rdf:type owl:DatatypeProperty ;
rdfs:range rdfs:Literal ;
terms:description "Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource."@en ;
rdfs:comment "An account of the resource."@en ;
rdfs:isDefinedBy dc: ;
rdfs:label "Description"@en .
### http://purl.org/dc/terms/identifier
terms:identifier rdf:type owl:DatatypeProperty ;
rdfs:range rdfs:Literal ;
terms:description "Recommended practice is to identify the resource by means of a string conforming to an identification system. Examples include International Standard Book Number (ISBN), Digital Object Identifier (DOI), and Uniform Resource Name (URN). Persistent identifiers should be provided as HTTP URIs."@en ;
rdfs:comment "An unambiguous reference to the resource within a given context."@en ;
rdfs:isDefinedBy terms: ;
rdfs:label "Identifier"@en .
### http://purl.org/genex#hasExpressionLevel
:hasExpressionLevel rdf:type owl:DatatypeProperty ;
rdfs:domain [ rdf:type owl:Class ;
owl:unionOf ( :AbsenceExpression
:Expression
)
] ;
rdfs:range xsd:double ;
rdfs:label "has expression level score"@en ;
skos:altLabel "expression score"@en .
### http://purl.org/genex#hasFDRpvalue
:hasFDRpvalue rdf:type owl:DatatypeProperty ;
rdfs:domain [ rdf:type owl:Class ;
owl:unionOf ( :AbsenceExpression
:Expression
)
] ;
rdfs:range xsd:double ;
rdfs:label "has false discovery rate p-value"@en ;
skos:altLabel "has FDR p-value"@en .
### http://purl.org/genex#hasSex
:hasSex rdf:type owl:DatatypeProperty ,
owl:FunctionalProperty ;
rdfs:domain :ExpressionCondition ;
rdfs:range [ rdf:type rdfs:Datatype ;
owl:oneOf [ rdf:type rdf:List ;
rdf:first "NA"^^xsd:string ;
rdf:rest [ rdf:type rdf:List ;
rdf:first "any"^^xsd:string ;
rdf:rest [ rdf:type rdf:List ;
rdf:first "female"^^xsd:string ;
rdf:rest [ rdf:type rdf:List ;
rdf:first "hermaphrodite"^^xsd:string ;
rdf:rest [ rdf:type rdf:List ;
rdf:first "male"^^xsd:string ;
rdf:rest [ rdf:type rdf:List ;
rdf:first "mixed"^^xsd:string ;
rdf:rest [ rdf:type rdf:List ;
rdf:first "not annotated"^^xsd:string ;
rdf:rest rdf:nil
]
]
]
]
]
]
]
] ;
terms:modified "2021-06-04"^^xsd:date ;
skos:changeNote "Added the following value in the range list: any." .
### http://purl.uniprot.org/core/commonName
up:commonName rdf:type owl:DatatypeProperty ,
owl:FunctionalProperty ;
rdfs:range xsd:string ;
rdfs:isDefinedBy "http://purl.uniprot.org/core/" ;
rdfs:label "common name"^^xsd:string .
### http://purl.uniprot.org/core/mnemonic
up:mnemonic rdf:type owl:DatatypeProperty ;
rdfs:range xsd:string ;
rdfs:comment "A easy to remember identifier for a UniProtKB entry, but it is not a stable identifier and should not be used by programs to identify entries."@en ,
"A rememberable string that can be used to find entries, not a stable identifier!"^^xsd:string ;
rdfs:label "Mnemonic"^^xsd:string ;
rdfs:seeAlso "http://www.uniprot.org/manual/entry_name" .
### http://purl.uniprot.org/core/scientificName
up:scientificName rdf:type owl:DatatypeProperty ,
owl:FunctionalProperty ;
rdfs:range xsd:string ;
rdfs:isDefinedBy "http://purl.uniprot.org/core/" ;
rdfs:label "scientific name"^^xsd:string .
#################################################################
# Classes
#################################################################
### http://purl.obolibrary.org/obo/BFO_0000001
obo:BFO_0000001 rdf:type owl:Class ;
obo:IAO_0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en ,
"Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"@en ;
obo:IAO_0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en ;
rdfs:isDefinedBy obo:bfo.owl ;
rdfs:label "entity"@en .
### http://purl.obolibrary.org/obo/BFO_0000002
obo:BFO_0000002 rdf:type owl:Class ;
rdfs:subClassOf obo:BFO_0000001 ;
obo:IAO_0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en ,
"Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en ;
obo:IAO_0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en ;
rdfs:isDefinedBy obo:bfo.owl ;
rdfs:label "continuant"@en .
### http://purl.obolibrary.org/obo/BFO_0000004
obo:BFO_0000004 rdf:type owl:Class ;
rdfs:subClassOf obo:BFO_0000002 ;
obo:IAO_0000112 "a chair"@en ,
"a heart"@en ,
"a leg"@en ,
"a molecule"@en ,
"a spatial region"@en ,
"an atom"@en ,
"an orchestra."@en ,
"an organism"@en ,
"the bottom right portion of a human torso"@en ,
"the interior of your mouth"@en ;
obo:IAO_0000115 "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en ;
rdfs:isDefinedBy obo:bfo.owl ;
rdfs:label "independent continuant"@en .
### http://purl.obolibrary.org/obo/CARO_0000000
obo:CARO_0000000 rdf:type owl:Class ;
rdfs:subClassOf :AnatomicalEntity ;
obo:IAO_0000115 "A part of a multicellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a multicellular organism with granularity above the level of a protein complex."^^xsd:string ;
oboInOwl:id "CARO:0000000"^^xsd:string ;
rdfs:comment "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure." ;
rdfs:label "anatomical entity"^^xsd:string .
### http://purl.obolibrary.org/obo/CARO_0030000
obo:CARO_0030000 rdf:type owl:Class ;
rdfs:subClassOf obo:BFO_0000004 ;
obo:IAO_0000115 "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them." ;
rdfs:comment "Important for alignment with Darwin Core class \"Organism\"." ;
rdfs:label "biological entity" .
### http://purl.obolibrary.org/obo/CDAO_0000140
obo:CDAO_0000140 rdf:type owl:Class ;
rdfs:comment "Basic unit of graphs and trees"@en ;
rdfs:label "Node"^^xsd:string .
### http://purl.obolibrary.org/obo/NCIT_C14250
obo:NCIT_C14250 rdf:type owl:Class ;
owl:equivalentClass orth:Organism ;
rdfs:label "Organism" .
### http://purl.obolibrary.org/obo/OBI_0000181
obo:OBI_0000181 rdf:type owl:Class ;
obo:IAO_0000115 "A population is a group of material entities consisting of individuals which share a particular characteristic such as inhabiting a particular region or area or ability to interbreed."^^xsd:string ;
rdfs:label "population"^^xsd:string .
### http://purl.obolibrary.org/obo/SO_0000104
obo:SO_0000104 rdf:type owl:Class ;
owl:equivalentClass orth:Protein ;
rdfs:label "polypeptide"^^xsd:string .
### http://purl.obolibrary.org/obo/SO_0000704
obo:SO_0000704 rdf:type owl:Class ;
owl:equivalentClass orth:Gene ;
rdfs:label "gene"^^xsd:string .
### http://purl.org/genex#AbsenceExpression
:AbsenceExpression rdf:type owl:Class ;
rdfs:subClassOf [ owl:intersectionOf ( [ rdf:type owl:Restriction ;
owl:onProperty :hasExpressionCondition ;
owl:someValuesFrom :ExpressionCondition
]
[ rdf:type owl:Restriction ;
owl:onProperty :hasSequenceUnit ;
owl:someValuesFrom orth:SequenceUnit
]
) ;
rdf:type owl:Class
] ,
[ rdf:type owl:Class ;
owl:complementOf :Expression
] ;
rdfs:label "absence of gene expression"@en ;
skos:altLabel "Not expressed gene"@en ,
"Not expressed sequence unit"@en .
### http://purl.org/genex#AnatomicalEntity
:AnatomicalEntity rdf:type owl:Class ;
rdfs:subClassOf obo:CARO_0030000 ;
rdfs:comment "An anatomical entity can be an organism part (e.g. brain, blood, liver and so on) or a material anatomical entity such as a cell." ;
rdfs:label "Anatomical entity"@en .
### http://purl.org/genex#Expression
:Expression rdf:type owl:Class ;
rdfs:subClassOf [ owl:intersectionOf ( [ rdf:type owl:Restriction ;
owl:onProperty :hasExpressionCondition ;
owl:someValuesFrom :ExpressionCondition
]
[ rdf:type owl:Restriction ;
owl:onProperty :hasSequenceUnit ;
owl:someValuesFrom orth:SequenceUnit
]
) ;
rdf:type owl:Class
] ,
[ rdf:type owl:Restriction ;
owl:onProperty :hasExpressionCharacteristic ;
owl:allValuesFrom [ rdf:type owl:Class ;
owl:oneOf ( :AVERAGE_EXPRESSED
:HIGHLY_EXPRESSED
:HIGH_EXPRESSED
:LOWLY_EXPRESSED
:LOW_EXPRESSED
:UBIQUITOUSLY_EXPRESSED
)
]
] ,
[ rdf:type owl:Restriction ;
owl:onProperty :hasExpressionLevel ;
owl:allValuesFrom xsd:double
] ;
rdfs:comment "All sequence units (e.g. Gene) that are expressed in some condition (e.g. organ and/or adult stage)."@en ;
rdfs:label "gene expression"@en ;
skos:altLabel "expression"@en ,
"sequence unit expression"@en .
### http://purl.org/genex#ExpressionCondition
:ExpressionCondition rdf:type owl:Class ;
owl:equivalentClass [ rdf:type owl:Class ;
owl:unionOf ( [ rdf:type owl:Restriction ;
owl:onProperty :hasAnatomicalEntity ;
owl:someValuesFrom :AnatomicalEntity
]
[ rdf:type owl:Restriction ;
owl:onProperty :hasDevelopmentalStage ;
owl:someValuesFrom efo:EFO_0000399
]
[ rdf:type owl:Restriction ;
owl:onProperty :hasStrain ;
owl:someValuesFrom efo:EFO_0005135
]
[ rdf:type owl:Restriction ;
owl:onProperty :hasSex ;
owl:someValuesFrom xsd:string
]
)
] ;
rdfs:subClassOf [ rdf:type owl:Restriction ;
owl:onProperty obo:RO_0002162 ;
owl:allValuesFrom up:Taxon
] ;
rdfs:comment "A sequence unit (e.g. Gene) is expressed in some expression condition (e.g. anatomical entity and/or developmental stage)."@en ;
rdfs:label "gene expression experiment condition"@en ;
skos:altLabel "expression condition"@en ,
"sequence unit expression condition"@en .
### http://purl.org/net/orth#Gene
orth:Gene rdf:type owl:Class ;
rdfs:subClassOf orth:SequenceUnit ,
[ rdf:type owl:Restriction ;
owl:onProperty orth:organism ;
owl:someValuesFrom orth:Organism
] ,
[ rdf:type owl:Restriction ;
owl:onProperty obo:RO_0001018 ;
owl:allValuesFrom sio:SIO_000750
] ;
rdfs:label "Gene"@en .
### http://purl.org/net/orth#GeneTreeNode
orth:GeneTreeNode rdf:type owl:Class ;
rdfs:subClassOf obo:CDAO_0000140 ;
rdfs:comment "A node of a tree whose leaf nodes are sequence units and whose internal nodes are clusters of homologs"@en ;
rdfs:label "Gene tree node"@en .