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Table 1 Examples of D2RQ mappings

From: Towards linked open gene mutations data

Description Mapping Generated triple (example)
Create a triple that defines the value of the title of a given bibliographic reference. map:somatic_ref_Title a d2rq:PropertyBridge;
d2rq:belongsToClassMap map:somatic_ref;
d2rq:property bibtex:hasTitle;
d2rq:column "SomaticRef15.Title";.
<http://bioinformatics.istge.it/logvd/resource/somatic_refs/7>
<http://data.bibbase.org/ontology/#hasTitle>
"Mutations in the p53 gene occur in diverse human tumour types"
Create a triple that defines the value of the wild type aminoacid for a given gene variation. Conditional clauses avoid definitions for special cases (empty field, dash character and "NA" value). map:variation_hasWildTypeResidue a d2rq:PropertyBridge;
d2rq:belongsToClassMap map:variation;
d2rq:property mio:hasWildTypeResidue;
d2rq:column "mutations15.WT_AA";
d2rq:condition "mutations15.WT_AA ! = ('NA')";
d2rq:condition "mutations15.WT_AA ! = ('')";
d2rq:condition "mutations15.WT_AA ! = ('-')";.
<http://bioinformatics.istge.it/logvd/resource/variations/994>
<http://unbsj.biordf.net/ontologies/mutation-impact-ontology.owl#hasWildTypeResidue>"P"
Creates a triple that establishes a link to the TP53 human gene description in HGNC as implemented in Bio2RDF. map:gene_HGNC a d2rq:PropertyBridge;
d2rq:belongsToClassMap map:gene;
d2rq:property diseasome:hgncId;
d2rq:uriPattern "http://bio2rdf.org/hgnc:11998";.
<http://bioinformatics.istge.it/logvd/resource/genes/TP53>
<http://www4.wiwiss.fu-berlin.de/diseasome/resource/diseasome/hgncId>
<http://bio2rdf.org/hgnc:11998>
  1. Three examples of D2RQ mappings between the IARC TP53 Mutation database and its RDF representation. In the first one, the title of a paper is just extracted from the database and associated to an entity representing a given bibliographic reference by means of the bibtex:hasTitle property. In the second example, the one-letter code of the wild type aminoacid corresponding to the location of a given variation is associated to the entity representing the same variation through the mio:hasWildTypeResidue property. The third example creates a connection with an external entity, namely the HGNC identifier of the TP53 gene, by specifying its Linked Data URI.