Table 1

Examples of D2RQ mappings

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>


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.

Zappa et al. BMC Bioinformatics 2012 13(Suppl 4):S7   doi:10.1186/1471-2105-13-S4-S7

Open Data