Thursday, April 02, 2009

Support provided for more non-Bio2RDF providers

The 0.3 Bio2RDF Servlet release implements support for more non-Bio2RDF SPARQL endpoints such as LinkedCT, DrugBank, Dailymed, Diseasome, Neurocommons, DBPedia, and Flyted/Flybase .

The relevant namespaces for these inside of Bio2RDF are:
  • DBpedia - dbpedia, dbpedia_property, dbpedia_class
  • LinkedCT - linkedct_ontology, linkedct_intervention, linkedct_trials, linkedct_collabagency, linkedct_condition, linkedct_link, linkedct_location, linkedct_overall_official, linkedct_oversight, linkedct_primary_outcomes, linkedct_reference, linkedct_results_reference, linkedct_secondary_outcomes, linkedct_arm_group
  • Dailymed - dailymed_ontology, dailymed_drugs, dailymed_inactiveingredient, dailymed_routeofadministration, dailymed_organization
  • DrugBank - drugbank_ontology, drugbank_druginteractions, drugbank_drugs, drugbank_enzymes, drugbank_drugtype, drugbank_drugcategory, drugbank_dosageforms, drugbank_targets
  • Diseasome - diseasome_ontology, diseasome_diseases, diseasome_genes, diseasome_chromosomallocation, diseasome_diseaseclass
  • Neurocommons - Uses the equivalent Bio2RDF namespaces, with live owl:sameAs links back to the relevant Neurocommons namespaces. Used for pubmed, geneid, taxonomy, mesh, prosite and go so far
  • Flyted/Flybase - Not converted yet, only direct access provided using search functionalities
Provide live owl:sameAs references which match the URI's used in SPARQL queries to keep linkages to the original databases without leaving the Bio2RDF database:identifier paradigm, so if people know the DBPedia, etc., URI's, the link to their current knowledge is given

Some http://database.bio2rdf.org/database:identifier URI's are produced by the owl:sameAs additions, but these aren't standard, and are only shown where there is still at least one SPARQL endpoint available which still uses them. People should utilise the http://bio2rdf.org/database:identifier versions when linking to Bio2RDF.

Any further contributions to this list, or additions of other datasets which already utilise Bio2RDF URI's would be very useful! See the list of namespaces already implemented here.

No comments: