Commit ee08b11c authored by Andrea's avatar Andrea

v1.1 update

parent 68e106de
......@@ -6,7 +6,7 @@
<!-- SCHEMA.ORG METADATA -->
<script type="application/ld+json">{"@context":"https://schema.org","@type":"TechArticle","url":"http://medal.ctb.upm.es/projects/DISNET/ontologies/sem-disnet","image":"http://vowl.visualdataweb.org/webvowl/#iri=http://medal.ctb.upm.es/projects/DISNET/ontologies/sem-disnet","name":"SEM-DISNET", "headline":"SEM-DISNET ontology provides a integrated ontology used to describe the define entities, which appear in the DISNET database. It is an ontology aimed at facilitating the analysis of biomedical data, allowing the discovery of new patterns and associations between genes, drugs and their targets to be applied in cases of drug repositioning.This project has been carried out within the DISNET project of MEDAL Laboratory (Medical Data Analytics) at the CTB-UPM, together with DRUGS4COVID, developed by the OEG-UPM (Ontology Engineering Group).DISNET website: https://disnet.ctb.upm.es/OEG website: https://oeg.fi.upm.es/", "datePublished":"2022-03-30", "license":"http://purl.org/NET/rdflicense/cc-by-nc-sa4.0", "author":[{"@type":"Person","name":"MEDAL: https://medal.ctb.upm.es/"},{"@type":"Person","name":"OEG: https://oeg.fi.upm.es/"}],
<script type="application/ld+json">{"@context":"https://schema.org","@type":"TechArticle","url":"http://medal.ctb.upm.es/projects/DISNET/ontologies/sem-disnet","image":"http://vowl.visualdataweb.org/webvowl/#iri=http://medal.ctb.upm.es/projects/DISNET/ontologies/sem-disnet","name":"SEM-DISNET", "headline":"SEM-DISNET ontology provides a integrated ontology used to describe the define entities, which appear in the DISNET database. It is an ontology aimed at facilitating the analysis of biomedical data, allowing the discovery of new patterns and associations between genes, drugs and their targets to be applied in cases of drug repositioning.This project has been carried out within the DISNET project of MEDAL Laboratory (Medical Data Analytics) at the CTB-UPM, together with DRUGS4COVID, developed by the OEG-UPM (Ontology Engineering Group).DISNET website: https://disnet.ctb.upm.es/OEG website: https://oeg.fi.upm.es/", "datePublished":"2022-03-30", "version":"1.1", "license":"http://purl.org/NET/rdflicense/cc-by-nc-sa4.0", "author":[{"@type":"Person","name":"MEDAL: https://medal.ctb.upm.es/"},{"@type":"Person","name":"OEG: https://oeg.fi.upm.es/"}],
"contributor":[{"@type":"Person","name":"Andrea Álvarez Pérez (MEDAL)"},{"@type":"Person","name":"Ana Iglesias Molina (OEG)"},{"@type":"Person","name":"Lucía Prieto Santamaría (MEDAL)"},{"@type":"Person","name":"Alejandro Rodríguez González (MEDAL)"}]}</script>
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......@@ -57,6 +57,10 @@
<h1><b>SEM-DISNET</b></h1>
<h2>Release 2022-06-10</h2>
<dl>
<dt>Version:</dt>
<dd>1.1</dd>
<dl>
<dt>Contributors:</dt>
......
......@@ -1750,6 +1750,7 @@ OEG website: https://oeg.fi.upm.es/</terms:description>
<!-- https://w3id.org/eboca/sem-disnet#synonymous -->
<owl:DatatypeProperty rdf:about="https://w3id.org/eboca/sem-disnet#synonymous">
<rdfs:domain rdf:resource="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C7057"/>
<rdfs:domain rdf:resource="http://rdf.ebi.ac.uk/terms/chembl#Substance"/>
<rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
<rdfs:label>Synonymous</rdfs:label>
......@@ -2790,6 +2791,231 @@ The measure is defined here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#pl
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#AlteredExpression -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#AlteredExpression">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#Biomarker"/>
<dc:description xml:lang="en">This relationship indicates that an altered expression of the gene is associated with the disease phenotype.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;altered_expression&quot; (LHGDN)
&quot;altered_expression&quot; (BeFree)</rdfs:comment>
<rdfs:label xml:lang="en">Altered Expression Association</rdfs:label>
<sem-disnet:disnetLabel>Altered Expression</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#Biomarker -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#Biomarker">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/SIO_000983"/>
<dc:description xml:lang="en">This relationship indicates that the gene either plays a role in the aetiology of the disease (e.g. participates in the molecular mechanism that leads to disease) or is a biomarker for a disease (this is a very broad classification that we use when we do not have more information on the type of association between the gene and the disease).</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;marker/mechanism&quot; (CTD)
&quot;marker/mechanism|therapeutic&quot; (CTD)
&quot;marker/mechanism&quot; (CTD_mouse)
&quot;marker/mechanism|therapeutic&quot; (CTD_mouse)
&quot;marker/mechanism&quot; (CTD_rat)
&quot;marker/mechanism|therapeutic&quot; (CTD_rat)
&quot;marker&quot; (MGD)
&quot;marker&quot; (RGD)
&quot;any_relation&quot; (LHGDN)
&quot;biomarker&quot; (BeFree)</rdfs:comment>
<rdfs:label xml:lang="en">Biomarker Association</rdfs:label>
<sem-disnet:disnetLabel>Biomarker Association</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#CausalMutation -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#CausalMutation">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#GeneticVariation"/>
<dc:description xml:lang="en">This relationship indicates that there are allelic variants or mutations known to cause the disease.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;Pathogenic&quot; (ClinVar)
&quot;phenotype&quot; (OMIM)</rdfs:comment>
<rdfs:label xml:lang="en">Causal Mutation Association</rdfs:label>
<sem-disnet:disnetLabel>Causal Mutation</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#ChromosomalRearrangement -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#ChromosomalRearrangement">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#&apos;GenomicAlterations&apos;"/>
<dc:description xml:lang="en">This relationship indicates that a gene is included in a chromosomal rearrangement associated with a particular manifestation of the disease.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;Role in the phenotype of&quot; (Orphanet)</rdfs:comment>
<rdfs:label xml:lang="en">Chromosomal Rearrangement Association</rdfs:label>
<sem-disnet:disnetLabel>Chromosomal Rearrangement</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#FusionGene -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#FusionGene">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#&apos;GenomicAlterations&apos;"/>
<dc:description xml:lang="en">This relationship indicates that the fusion between two different genes (between promoter and/or other coding DNA regions) is associated with the disease.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;Part of a fusion gene in&quot; (Orphanet)</rdfs:comment>
<rdfs:label xml:lang="en">Fusion Gene Association</rdfs:label>
<sem-disnet:disnetLabel>Fusion Gene</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#GeneticVariation -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#GeneticVariation">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#&apos;GenomicAlterations&apos;"/>
<dc:description xml:lang="en">This relationship indicates that a sequence variation (a mutation, a SNP) is associated with the disease phenotype, but there is still no evidence to say that the variation causes the disease.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;genetic_variation&quot; (UniProt)
&quot;Candidate gene tested in&quot; (Orphanet)
&quot;Affects&quot; (ClinVar)
&quot;Likely pathogenic&quot; (ClinVar)
&quot;susceptibility&quot; (OMIM)
&quot;genetic_variation&quot; (GWASCAT)
&quot;genetic_variation&quot; (GAD)
&quot;genetic_variation&quot; (LHGDN)
&quot;genetic_variation&quot; (BeFree)</rdfs:comment>
<rdfs:label xml:lang="en">Genetic Variation Association</rdfs:label>
<sem-disnet:disnetLabel>Genetic Variation</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#GermlineCausalMutation -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#GermlineCausalMutation">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#CausalMutation"/>
<dc:description xml:lang="en">This relationship indicates that there are germline allelic variants or mutations known to cause the disease, and they may be passed on to offspring.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;Disease-causing germline mutation(s) in&quot; (Orphanet)
&quot;Disease-causing germline mutation(s) (loss of function) in&quot; (Orphanet)
&quot;Disease-causing germline mutation(s) (gain of function) in&quot; (Orphanet)</rdfs:comment>
<rdfs:label xml:lang="en">Germline Causal Mutation Association</rdfs:label>
<sem-disnet:disnetLabel>Germline Causal Mutation</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#GermlineModifyingMutation -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#GermlineModifyingMutation">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#ModifyingMutation"/>
<dc:description xml:lang="en">This relationship indicates that a germline gene mutation modifies the clinical presentation of the disease, and it may be passed on to offspring.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;Modifying germline mutation in&quot; (Orphanet)</rdfs:comment>
<rdfs:label xml:lang="en">Germline Modifying Mutation</rdfs:label>
<sem-disnet:disnetLabel>Germline Modifying Mutation</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#ModifyingMutation -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#ModifyingMutation">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#GeneticVariation"/>
<dc:description xml:lang="en">This relationship indicates that a gene mutation is known to modify the clinical presentation of the disease.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;disease_progression&quot; (RGD)
&quot;onset&quot; (RGD)
&quot;severity&quot; (RGD)</rdfs:comment>
<rdfs:label xml:lang="en">Modifying Mutation Association</rdfs:label>
<sem-disnet:disnetLabel>Modifying Mutation</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#PostTranslationalModification -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#PostTranslationalModification">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#Biomarker"/>
<dc:description xml:lang="en">This relationship indicates that alterations in the function of the protein by means of post-translational modifications (methylation or phosphorylation of the protein) are associated with the disease phenotype.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;methylation|phosphorylation&quot; (LHGDN)
&quot;methylation|phosphorylation&quot; (BeFree)</rdfs:comment>
<rdfs:label xml:lang="en">Post-translational Modification Association</rdfs:label>
<sem-disnet:disnetLabel>Post-translational Modification</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#SomaticCausalMutation -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#SomaticCausalMutation">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#CausalMutation"/>
<dc:description xml:lang="en">This relationship indicates that there are somatic allelic variants or mutations known to cause the disease, but they may not be passed on to offspring.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;Disease-causing somatic mutation(s) in&quot; (Orphanet)</rdfs:comment>
<rdfs:label xml:lang="en">Somatic Causal Mutation</rdfs:label>
<sem-disnet:disnetLabel>Somatic Causal Mutation</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#SomaticModifyingMutation -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#SomaticModifyingMutation">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#ModifyingMutation"/>
<dc:description xml:lang="en">This relationship indicates that a somatic gene mutation modifies the clinical presentation of the disease, but it may not be passed on to offspring.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;Modifying somatic mutation in&quot; (Orphanet)</rdfs:comment>
<rdfs:label xml:lang="en">Somatic Modifying Mutation</rdfs:label>
<sem-disnet:disnetLabel>Somatic Modifying Mutation</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#SusceptibilityMutation -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#SusceptibilityMutation">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#GeneticVariation"/>
<dc:description xml:lang="en">This relationship indicates that a gene mutation in a germ cell that predisposes to the development of a disorder, and that is necessary but not sufficient for the manifestation of the disease.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;Major susceptibility factor in&quot; (Orphanet)
&quot;risk factor&quot; (ClinVar)
&quot;confers sensitivity&quot; (ClinVar)
&quot;susceptibility&quot; (RGD)</rdfs:comment>
<rdfs:label xml:lang="en">Susceptibility Mutation Association</rdfs:label>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#Therapeutic -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#Therapeutic">
<rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/SIO_000983"/>
<dc:description xml:lang="en">This relationship indicates that the gene/protein has a therapeutic role in the amelioration of the disease.</dc:description>
<rdfs:comment xml:lang="en">Relationships mapped to this class:
&quot;therapeutic&quot; (CTD)
&quot;marker/mechanism|therapeutic&quot; (CTD)
&quot;therapeutic&quot; (CTD_mouse)
&quot;marker/mechanism|therapeutic&quot; (CTD_mouse)
&quot;therapeutic&quot; (CTD_rat)
&quot;marker/mechanism|therapeutic&quot; (CTD_rat)
&quot;treatment&quot; (RGD)</rdfs:comment>
<rdfs:label xml:lang="en">Therapeutic Association</rdfs:label>
<sem-disnet:disnetLabel>Therapeutic Association</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#&apos;GenomicAlterations&apos; -->
<owl:Class rdf:about="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#&apos;GenomicAlterations&apos;">
<rdfs:subClassOf rdf:resource="http://www.disgenet.org/ds/DisGeNET/files/GeneDiseaseAssociation.owl#Biomarker"/>
<dc:description xml:lang="en">This relationship indicates that a genomic alteration is linked to the gene associated with the disease phenotype.</dc:description>
<rdfs:label xml:lang="en">Genomic Alterations Association</rdfs:label>
<sem-disnet:disnetLabel>Genomic Alteration</sem-disnet:disnetLabel>
</owl:Class>
<!-- http://www.drugtargetontology.org/dto/DTO_00102000 -->
<owl:Class rdf:about="http://www.drugtargetontology.org/dto/DTO_00102000">
......
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