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Goals

Encode BEL namespaces into an RDF model providing:

  • URIs for namespace values based on stable identifiers (Gene Id, ChEBI Id, SwissProt Accession numbers, etc.)
  • Preferred label for the namespace value
  • Edge connecting each namespace value to its namespace (e.g. HGNC:EGFR to HGNC)
  • As applicable:
    • identifier(s), including alt_ids
    • name
    • symbol
    • synonyms, including previous names and symbols
    • description
    • species (human mouse or rat)
  • Encoding types (e.g. EGFR can encode geneAbundance, rnaAbundance, proteinAbundance)
  • Equivalence relationships between values across different namespaces (EGID:1956 is equivalent to HGNC:EGFR)
  • Orthology relationships between namespace values
  • Track concept changes
  • Linked data relationships (e.g. owl:sameAs) between namespace values and external vocabularies (e.g. GO, CHEBI, etc.)
    • This can allow inferencing of edges since it implies that two RDF resource URIs identify the same thing.

Technology

RDF Model

RDF namespaces - current

@prefix affx: <http://www.openbel.org/bel/namespace/affy-probeset/> .
@prefix belv: <http://www.openbel.org/vocabulary/> .
@prefix chebi: <http://www.openbel.org/bel/namespace/chebi/> .
@prefix cl: <http://www.openbel.org/bel/namespace/cell-ontology/> .
@prefix clo: <http://www.openbel.org/bel/namespace/cell-line-ontology/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix do: <http://www.openbel.org/bel/namespace/disease-ontology/> .
@prefix efo: <http://www.openbel.org/bel/namespace/experimental-factor-ontology/> .
@prefix egid: <http://www.openbel.org/bel/namespace/entrez-gene/> .
@prefix gobp: <http://www.openbel.org/bel/namespace/go-biological-process/> .
@prefix gocc: <http://www.openbel.org/bel/namespace/go-cellular-component/> .
@prefix hgnc: <http://www.openbel.org/bel/namespace/hgnc-human-genes/> .
@prefix mesha: <http://www.openbel.org/bel/namespace/mesh-anatomy/> .
@prefix meshc: <http://www.openbel.org/bel/namespace/mesh-chemicals/> .
@prefix meshcs: <http://www.openbel.org/bel/namespace/mesh-cellular-structures/> .
@prefix meshd: <http://www.openbel.org/bel/namespace/mesh-diseases/> .
@prefix meshpp: <http://www.openbel.org/bel/namespace/mesh-processes/> .
@prefix mgi: <http://www.openbel.org/bel/namespace/mgi-mouse-genes/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix rgd: <http://www.openbel.org/bel/namespace/rgd-rat-genes/> .
@prefix schem: <http://www.openbel.org/bel/namespace/selventa-legacy-chemicals/> .
@prefix scomp: <http://www.openbel.org/bel/namespace/selventa-named-complexes/> .
@prefix sdis: <http://www.openbel.org/bel/namespace/selventa-legacy-diseases/> .
@prefix sfam: <http://www.openbel.org/bel/namespace/selventa-protein-families/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix sp: <http://www.openbel.org/bel/namespace/swissprot/> .
@prefix taxon: <http://www.openbel.org/bel/namespace/ncbi-taxonomy/> .
@prefix uberon: <http://www.openbel.org/bel/namespace/uberon/> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

RDF namespaces - future 

selected from the Miriam Registry

??? = Questions on how to deal with this
XXX = Should this be deleted?
 
@prefix affy: <http://identifiers.org/affy.probeset/> .
@prefix belv: <http://www.openbel.org/vocabulary/> .
@prefix chebi: <http://identifiers.org/chebi/> .
@prefix chembl.compound: <http://identifiers.org/chembl.compound/> .
@prefix chembl.target: <http://identifiers.org/chembl.target/> .
@prefix cl: <http://www.openbel.org/bel/namespace/cell-ontology/> .  ???
@prefix clo: <http://www.openbel.org/bel/namespace/cell-line-ontology/> .  ???
@prefix dcterms: <http://purl.org/dc/terms/> . 
@prefix do: <http://identifiers.org/doid/> .
@prefix efo: <http://identifiers.org/efo/> .
@prefix egid: <http://identifiers.org/ncbigene/> .
@prefix go: <http://identifiers.org/go/> .
@prefix gobp: <http://www.openbel.org/bel/namespace/go-biological-process/> .  XXX
@prefix gocc: <http://www.openbel.org/bel/namespace/go-cellular-component/> .  XXX
@prefix hgnc: <http://identifiers.org/hgnc/> .
@prefix hgnc.symbol: <http://identifiers.org/hgnc.symbol/> .
@prefix mesh: <http://identifiers.org/mesh.2013/> .
@prefix mesha: <http://www.openbel.org/bel/namespace/mesh-anatomy/> .  XXX
@prefix meshc: <http://www.openbel.org/bel/namespace/mesh-chemicals/> . XXX
@prefix meshcs: <http://www.openbel.org/bel/namespace/mesh-cellular-structures/> . XXX
@prefix meshd: <http://www.openbel.org/bel/namespace/mesh-diseases/> . XXX
@prefix meshpp: <http://www.openbel.org/bel/namespace/mesh-processes/> . XXX
@prefix mgd: <http://identifiers.org/mgd/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix rgd: <http://identifiers.org/rgd/> .
@prefix schem: <http://www.openbel.org/bel/namespace/selventa-legacy-chemicals/> .
@prefix scomp: <http://www.openbel.org/bel/namespace/selventa-named-complexes/> .
@prefix sdis: <http://www.openbel.org/bel/namespace/selventa-legacy-diseases/> .
@prefix sfam: <http://www.openbel.org/bel/namespace/selventa-protein-families/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix sp: <http://www.openbel.org/bel/namespace/swissprot/> . XXX replaced by uniprot
@prefix taxonomy: <http://identifiers.org/taxonomy/> .
@prefix uberon: <http://identifiers.org/uberon/> .
@prefix uniprot: <http://identifiers.org/uniprot/> .  
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix inchikey: <http://identifiers.org/inchikey> .

OpenBEL Resource Metadata

@prefix void: <http://rdfs.org/ns/void#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix wv: <http://vocab.org/waiver/terms/> .        
@prefix sd: <http://www.w3.org/ns/sparql-service-description#> .

@prefix : <#> .

BELFramework EquivalenceSubjectPredicateObjectExample
Section: Namespace    
 dataset_uriavoid:Dataset:BELaffx a void:Dataset .
Namestringdataset_uriskos:prefLabelSTRINGskos:prefLabel "Affymetrix Probe Set Identifiers"
Keyworddataset_uribelv:prefixSTRINGbelv:prefix "AFFX"
SpeciesStringdataset_uribelv:fromSpeciesSTRINGbelv:fromSpecies "10090"^^xsd:string
DescriptionStringdataset_uridcterms:descriptionSTRINGdcterms:description "description of dataset"
CreatedDateTimedataset_uridcterms:createdDATEdcterms:created "2015-10-10"^^xsd:date
Section: Author    
CopyrightStringdataset_uriwv:waiverURI or STRINGwv:waiver <http://creativecommons.org/publicdomain/zero/1.0/
 dataset_uridcterms:creatorauthor_uridcterms:creator :author (:author could equal the email address)
ContactInfoStringauthor_urifoaf:mboxSTRING<http://openbel.org> foaf:mbox "info@openbel.org"
NameStringauthor_urifoaf:nameSTRING<http://openbel.org> foaf:name "OpenBEL"
Section: Citation (Source)    
 dataset_uri
dcterms:source
SOURCE_URIdcterms:source <http://identifiers.org/affy.probeset/>
NameStringsource_uriskos:prefLabelSTRINGskos:prefLabel "Affymetrix, Santa Clara, California, USA"
DescriptionStringsource_uridcterms:descriptionSTRING 
PublishedDatesource_uridcterms:createdDATEdcterms:created "2015-04-16"
ReferenceURLsource_urifoaf:homepageURIfoaf:homepage <http://www.affymetrix.com/analysis>
Misc    
vocabulariesdataset_urivoid:vocabularyURIvoid:vocabulary <http://www.openbel.org/vocabulary/>

Legend: N = Namespace; E = Equivalence; A = Annotation

Namespace Values - current

SubjectPredicateObjectExample
namespace_value_uriaBELV CONCEPT URI<http://www.openbel.org/bel/namespace/affy-probeset/100000_at> a belv:RNAConcept
namespace_value_uridcterms:identifierSTRING<http://www.openbel.org/bel/namespace/affy-probeset/100000_at> dcterms:identifier "100000_at"^^xsd:string ;
namespace_value_uribelv:fromSpecies STRING<http://www.openbel.org/bel/namespace/affy-probeset/100000_at> belv:fromSpecies "10090"^^xsd:string ;
namespace_value_uriskos:exactMatchXREF URI<http://www.openbel.org/bel/namespace/affy-probeset/100000_at> skos:exactMatch <http://www.openbel.org/bel/namespace/entrez-gene/101118>
namespace_value_uriskos:inSchemeSCHEME URI<http://www.openbel.org/bel/namespace/affy-probeset/100000_at> skos:inScheme <http://www.openbel.org/bel/namespace/affy-probeset>
namespace_value_uriskos:prefLabelSTRING<http://www.openbel.org/bel/namespace/affy-probeset/100000_at> skos:prefLabel "100000_at"^^xsd:string
namespace_value_uriskos:closeMatchXREF URIskos:closeMatch <http://www.openbel.org/bel/namespace/entrez-gene/11677>,
namespace_value_uridcterms:titleSTRING

<http://www.openbel.org/bel/namespace/cell-line-ontology/0000008> dcterms:title "cell line repository"^^xsd:string ;

namespace_value_uriskos:altLabelSTRINGskos:altLabel "germline stem cell"^^xsd:string ;

Changelog

SubjectPredicateObjectExample
namespace_value_uribelv:statusSTRINGbelv:status "withdrawn"^^xsd:string ;
namespace_value_uridcterms:replacesURIdcterms:replaces <http://www.openbel.org/bel/namespace/cell-ontology/0000859> ;

Orthology

SubjectPredicateObjectExample
URIbelv:orthologousMatchURIbelv:orthologousMatch <http://www.openbel.org/bel/namespace/entrez-gene/304988>

RDF Examples

Example namespace - CHEBI

CHEBI Namespace
<http://www.selventa.com/bel/namespace/chebi> a skos:ConceptScheme ;
    a belv:NamespaceConceptScheme ;
    dc:creator "OpenBEL" ;
	owl:versionIRI "20131106" ;
	dc:title "ChEBI" ;
	dc:identifier "CHEBI" ;
	dc:type dc:dataset ;
	dc:rights "Copyright (c) 2013, OpenBEL Project. This work is licensed under a Creative Commons Attribution 3.0 Unported License." ;
	dc:subject "chemicals" ;
	dc:date "2013-11-06" ;
	dc:description "Chemical Entities of Biological Interest (ChEBI) identifiers. These identifiers may be used to specify abundances." ;
	dc:source <ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl> .

<ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl> rdfs:label "ChEBI Release version 108" ;
	a owl:Ontology ;
	dc:date "2013-10-04 23:40" ;
	dc:title "Chemical Entities of Biological Interest (ChEBI)" ;
	dc:description "Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on &#39;small&#39; chemical compounds." ;
	dc:creator "The ChEBI curation team" ;
	owl:versionIRI "108" .

Example namespace value 1 - HGNC:100 (ASIC1)

(does not include equivalence and orthology relationships)

HGNC ASIC1
<http://www.selventa.com/bel/namespace/hgnc/100> skos:inScheme <http://www.selventa.com/bel/namespace/hgnc> ;
	a belv:GeneConcept,
        belv:ProteinConcept,
        belv:RNAConcept ;
    dcterms:identifier "100" ;
    dcterms:title "acid-sensing (proton-gated) ion channel 1" ;
    belv:fromSpecies "9606" ;
	skos:prefLabel "ASIC1" ;
    skos:altLabel "ACCN2",
        "BNaC2",
        "amiloride-sensitive cation channel 2, neuronal",
        "hBNaC2" .
     
     

 

Example namespace value 2 - CHEBI:10110 (zidovudine)

 

CHEBI zidovudine
<http://www.selventa.com/bel/namespace/chebi/10110> skos:inScheme <http://www.selventa.com/bel/namespace/chebi> ;
	a belv:AbundanceConcept ;
    dcterms:identifier "10110",
        "619601" ;
	skos:prefLabel "zidovudine" ;
    skos:altLabel "3'-azido-3'-deoxythymidine",
        "AZT",
        "Azidothymidine",
        "C10H13N5O4",
        "Zidovudin",
        "Zidovudinum" .
    

Example namespace value 3 - GO cellular component 'enolase complex'

GOCC enolase complex
<http://www.selventa.com/bel/namespace/gocc/0000015> skos:inScheme <http://www.selventa.com/bel/namespace/go-cellular-component> ;
	a belv:ComplexConcept ;
    dcterms:identifier "0000015" ;
	skos:prefLabel "phosphopyruvate hydratase complex" ;
    skos:altLabel "enolase complex" .
    

 

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