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#600 #609

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Jan 15, 2024
Merged

#600 #609

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cbe7900
Fix for #600.
henrietteharmse Jan 15, 2024
7860ed4
Fix for #600.
henrietteharmse Jan 15, 2024
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67 changes: 67 additions & 0 deletions dataload/configs/ms.json
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{
"ontologies": [
{
"activity_status": "active",
"build": {
"method": "obo2owl",
"source_url": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo"
},
"contact": {
"email": "gerhard.mayer@rub.de",
"github": "germa",
"label": "Gerhard Mayer",
"orcid": "0000-0002-1767-2343"
},
"dependencies": [
{
"id": "pato"
},
{
"id": "uo"
}
],
"description": "A structured controlled vocabulary for the annotation of experiments concerned with proteomics mass spectrometry.",
"domain": "investigations",
"homepage": "http://www.psidev.info/groups/controlled-vocabularies",
"id": "ms",
"integration_server": "https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master",
"label": "MS",
"layout": "ontology_detail",
"license": {
"label": "CC BY 3.0",
"logo": "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by.png",
"url": "https://creativecommons.org/licenses/by/3.0/"
},
"mailing_list": "psidev-ms-vocab@lists.sourceforge.net",
"ontology_purl": "http://purl.obolibrary.org/obo/ms.owl",
"page": "http://www.psidev.info/groups/controlled-vocabularies",
"preferredPrefix": "MS",
"hierarchical_property":[
"http://purl.obolibrary.org/obo/ms#part_of",
"http://purl.obolibrary.org/obo/BFO_0000050"
],
"products": [
{
"id": "ms.obo",
"ontology_purl": "http://purl.obolibrary.org/obo/ms.obo"
},
{
"id": "ms.owl",
"ontology_purl": "http://purl.obolibrary.org/obo/ms.owl"
}
],
"publications": [
{
"id": "https://www.ncbi.nlm.nih.gov/pubmed/23482073",
"title": "The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary."
}
],
"repository": "https://github.com/HUPO-PSI/psi-ms-CV",
"tags": [
"MS experiments"
],
"title": "Mass spectrometry ontology",
"tracker": "https://github.com/HUPO-PSI/psi-ms-CV/issues"
}
]
}
9 changes: 8 additions & 1 deletion ebi_ontologies.json
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Expand Up @@ -2,7 +2,7 @@
"ontologies": [

{
"id": "semapv",
"id": "semapv",
"title": "Semantic Mapping Vocabulary",
"description": "The Semantic Mapping Vocabulary (SEMAPV) captures concepts and relations related to semantic matching, including types of matching (e.g. lexical, manually curated), preprocessing methods and specialised mapping relations.",
"ontology_purl": "https://raw.githubusercontent.com/mapping-commons/semantic-mapping-vocabulary/main/semapv.owl",
Expand Down Expand Up @@ -1176,6 +1176,13 @@
{
"id": "go",
"ontology_purl":"http://purl.obolibrary.org/obo/go/extensions/go-plus.owl"
},
{
"id": "ms",
"hierarchical_property":[
"http://purl.obolibrary.org/obo/ms#part_of",
"http://purl.obolibrary.org/obo/BFO_0000050"
]
}
]
}
10 changes: 9 additions & 1 deletion frontend/src/pages/ontologies/entities/EntityTree.tsx
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Expand Up @@ -270,13 +270,21 @@ export default function EntityTree({
key={randomString()}
>
{childNode.childRelationToParent ===
"http://purl.obolibrary.org/obo/BFO_0000050" && (
"http://purl.obolibrary.org/obo/BFO_0000050" && (
<img
className="mr-1"
src={urlJoin(process.env.PUBLIC_URL!, "/part.svg")}
style={{ height: "1em", display: "inline" }}
/>
)}
{childNode.childRelationToParent ===
"http://purl.obolibrary.org/obo/ms#part_of" && (
<img
className="mr-1"
src={urlJoin(process.env.PUBLIC_URL!, "/part.svg")}
style={{ height: "1em", display: "inline" }}
/>
)}
{childNode.childRelationToParent ===
"http://www.w3.org/1999/02/22-rdf-syntax-ns#type" && (
<img
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15 changes: 15 additions & 0 deletions testcases/hierarchical-properties/partof.json
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{
"ontologies": [
{
"id": "partof",
"preferredPrefix": "partof",
"title": "partof",
"hierarchical_property": [
"http://purl.obolibrary.org/obo/BFO_0000050",
"http://purl.obolibrary.org/obo/ms#part_of"
],
"oboSlims": false,
"ontology_purl": "./testcases/hierarchical-properties/partof.rdf"
}
]
}
100 changes: 100 additions & 0 deletions testcases/hierarchical-properties/partof.rdf
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.semanticweb.org/henriette007/ontologies/2024/0/untitled-ontology-980/"
xml:base="http://www.semanticweb.org/henriette007/ontologies/2024/0/untitled-ontology-980/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
<owl:Ontology rdf:about="http://www.ebi.ac.uk/testcases/hierarchical-properties/partof.owl">
<owl:versionIRI rdf:resource="http://www.ebi.ac.uk/testcases/hierarchical-properties/v0.0.1/partof.owl"/>
</owl:Ontology>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://purl.obolibrary.org/obo/BFO_0000050 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<rdfs:label>part_of</rdfs:label>
</owl:ObjectProperty>



<!-- http://purl.obolibrary.org/obo/ms#part_of -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/ms#part_of">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
</owl:ObjectProperty>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->




<!-- http://purl.obolibrary.org/obo/MS_1000353 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MS_1000353">
<rdfs:label>adduct ion</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MS_1003056 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MS_1003056">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/ms#part_of"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MS_1000353"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>adduct ion property</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/UBERON_0000916 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000916">
<rdfs:label>abdomen</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/UBERON_0003684 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0003684">
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000916"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:label>abdominal cavity</rdfs:label>
</owl:Class>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.24.2023-01-14T21:28:32Z) https://github.com/owlcs/owlapi -->

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