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González AR, Callahan A, Cruz-Toledo J, et al. Automatically exposing OpenLifeData via SADI semantic Web Services. J Biomed Semantics. 2014;5:46doi: 10.1186/2041-1480-5-46.
González, A. R., Callahan, A., Cruz-Toledo, J., Garcia, A., Egaña Aranguren, M., Dumontier, M., & Wilkinson, M. D. (2014). Automatically exposing OpenLifeData via SADI semantic Web Services. Journal of biomedical semantics, 546. https://doi.org/10.1186/2041-1480-5-46
González, Alejandro Rodríguez, et al. "Automatically exposing OpenLifeData via SADI semantic Web Services." Journal of biomedical semantics vol. 5 (2014): 46. doi: https://doi.org/10.1186/2041-1480-5-46
González AR, Callahan A, Cruz-Toledo J, Garcia A, Egaña Aranguren M, Dumontier M, Wilkinson MD. Automatically exposing OpenLifeData via SADI semantic Web Services. J Biomed Semantics. 2014 Nov 19;5:46. doi: 10.1186/2041-1480-5-46. eCollection 2014. PMID: 25937881; PMCID: PMC4417525.
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J Biomed Semantics. 2014 Nov 19;5:46. doi: 10.1186/2041-1480-5-46. eCollection 2014.

Automatically exposing OpenLifeData via SADI semantic Web Services.

Journal of biomedical semantics

Alejandro Rodríguez González, Alison Callahan, José Cruz-Toledo, Adrian Garcia, Mikel Egaña Aranguren, Michel Dumontier, Mark D Wilkinson

Affiliations

  1. Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain.
  2. Center for Biomedical Informatics Research, Stanford University, Stanford, CA USA.
  3. Department of Biology, Carleton University, Ottawa, ON Canada.
  4. Genomic Resources Group, University of the Basque Country (UPV-EHU), Bilbao, Spain.

PMID: 25937881 PMCID: PMC4417525 DOI: 10.1186/2041-1480-5-46

Abstract

BACKGROUND: Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location.

RESULTS: We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries.

CONCLUSIONS: We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.

Keywords: Bio2RDF; Galaxy; OpenLifeData; SADI; SHARE; SPARQL; Semantic web services; Sentient knowledge explorer

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