SPARQL-enabled identifier conversion with Identifiers.org

Sarala M Wimalaratne; Jerven Bolleman; Nick Juty; Toshiaki Katayama; Michel Dumontier; Nicole Redaschi; Nicolas Le Novère; Henning Hermjakob; Camille Laibe

doi:10.1093/bioinformatics/btv064

SPARQL-enabled identifier conversion with Identifiers.org

Bioinformatics. 2015 Jun 1;31(11):1875-7. doi: 10.1093/bioinformatics/btv064. Epub 2015 Jan 31.

Authors

Sarala M Wimalaratne¹, Jerven Bolleman¹, Nick Juty¹, Toshiaki Katayama¹, Michel Dumontier¹, Nicole Redaschi¹, Nicolas Le Novère², Henning Hermjakob¹, Camille Laibe¹

Affiliations

¹ European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
² European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot group, Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneve, Switzerland, Database Center for Life Science (DCLS), Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan, Stanford Center for Biomedical Informatics Research, Stanford University, CA 94305-5479, USA and Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.

Abstract

Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data.

Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data.

Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Biological Science Disciplines
Databases, Factual*
Internet
Semantics
Systems Integration

Abstract

Publication types

MeSH terms

Grants and funding