dc.contributor.author | Rodríguez González, Alejandro | |
dc.contributor.author | Callahan, Alison | |
dc.contributor.author | Cruz-Toledo, José | |
dc.contributor.author | García, Adrián | |
dc.contributor.author | Egaña Aranguren, Mikel | |
dc.contributor.author | Dumontier, Michel | |
dc.contributor.author | Wilkinson, Mark D. | |
dc.date.accessioned | 2015-10-09T11:14:30Z | |
dc.date.available | 2015-10-09T11:14:30Z | |
dc.date.issued | 2014-11-19 | |
dc.identifier.citation | Journal of Biomedical Semantics 5 : (2014) // Article ID 46 | es |
dc.identifier.issn | 2041-1480 | |
dc.identifier.uri | http://hdl.handle.net/10810/15822 | |
dc.description.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. | es |
dc.description.sponsorship | MDW is supported by the Isaac Peral and Marie Curie COFUND Programmes of the Universidad Politecnica de Madrid, Centre for Plant Biotechnology and Genomics UPM-INIA. ARG is supported by the Isaac Peral programme, UPM. Portions of this work have been funded by the Fundacion BBVA. We wish to express deep gratitude and appreciation to the National Bioscience Database Center (NBDC) and Database Center for Life Science (DBCLS) in Tokyo, Japan, and Dr. Toshiaki Katayama who has been organizing annual BioHackathon in Japan since 2008; The idea for OpenLifeData2SADI emerged as a result of the face-to-face contact facilitated by these extraordinary events | es |
dc.language.iso | eng | es |
dc.publisher | Biomed Central | es |
dc.rights | info:eu-repo/semantics/openAccess | es |
dc.subject | OpenLifeData | es |
dc.subject | bio2RDF | es |
dc.subject | SADI | es |
dc.subject | semantic web services | es |
dc.subject | SPARQL | es |
dc.subject | SHARE | es |
dc.subject | sentient knowledge explorer | es |
dc.subject | galaxy | es |
dc.subject | bioinformatics | es |
dc.subject | integration | es |
dc.title | Automatically exposing OpenLifeData via SADI semantic Web Services | es |
dc.type | info:eu-repo/semantics/article | es |
dc.rights.holder | © 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. | es |
dc.relation.publisherversion | http://www.jbiomedsem.com/content/5/1/46/abstract | es |
dc.identifier.doi | 10.1186/2041-1480-5-46 | |
dc.departamentoes | Genética, antropología física y fisiología animal | es_ES |
dc.departamentoeu | Genetika,antropologia fisikoa eta animalien fisiologia | es_ES |