Automatically exposing OpenLifeData via SADI semantic Web Services


Autoria(s): Rodríguez González, Alejandro; Callahan, Alison; Cruz-Toledo, José; García, Adrián; Egaña Aranguren, Mikel; Dumontier, Michel; Wilkinson, Mark D.
Data(s)

09/10/2015

09/10/2015

19/11/2014

Resumo

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.

Identificador

Journal of Biomedical Semantics 5 2014 : (2014) // Article ID46

2041-1480

http://hdl.handle.net/10810/15822

10.1186/2041-1480-5-46

Idioma(s)

eng

Publicador

Biomed Central

Relação

http://www.jbiomedsem.com/content/5/1/46/abstract

Direitos

© 2014 González et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

info:eu-repo/semantics/openAccess

Palavras-Chave #OpenLifeData #bio2RDF #SADI #semantic web services #SPARQL #SHARE #sentient knowledge explorer #galaxy #bioinformatics #integration
Tipo

info:eu-repo/semantics/article