SPARQL-enabled identifier conversion with Identifiers.org

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

doi:10.1093/bioinformatics/btv064

SPARQL-enabled identifier conversion with Identifiers.org

Sarala M. Wimalaratne^*, Jerven Bolleman, Nick Juty, Toshiaki Katayama, Michel Dumontier, Nicole Redaschi, Nicolas Le Novere, Henning Hermjakob, Camille Laibe

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

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.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.The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql.? The Author 2015. Published by Oxford University Press.

Original language	English
Pages (from-to)	1875-1877
Journal	Bioinformatics
Volume	31
Issue number	11
DOIs	https://doi.org/10.1093/bioinformatics/btv064
Publication status	Published - 1 Jun 2015
Externally published	Yes

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10.1093/bioinformatics/btv064Licence: CC BY

Cite this

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title = "SPARQL-enabled identifier conversion with Identifiers.org",

abstract = "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.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.The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql.? The Author 2015. Published by Oxford University Press.",

author = "Wimalaratne, {Sarala M.} and Jerven Bolleman and Nick Juty and Toshiaki Katayama and Michel Dumontier and Nicole Redaschi and {Le Novere}, Nicolas and Henning Hermjakob and Camille Laibe",

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AU - Wimalaratne, Sarala M.

AU - Bolleman, Jerven

AU - Juty, Nick

AU - Katayama, Toshiaki

AU - Dumontier, Michel

AU - Redaschi, Nicole

AU - Le Novere, Nicolas

AU - Hermjakob, Henning

AU - Laibe, Camille

PY - 2015/6/1

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AB - 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.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.The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql.? The Author 2015. Published by Oxford University Press.

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DO - 10.1093/bioinformatics/btv064

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