Utilize este identificador para referenciar este registo:
https://hdl.handle.net/1822/32460
Registo completo
Campo DC | Valor | Idioma |
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dc.contributor.author | Glez-Peña, Daniel | por |
dc.contributor.author | Lourenço, Anália | por |
dc.contributor.author | López-Fernández, Hugo | por |
dc.contributor.author | Reboiro-Jato, Miguel | por |
dc.contributor.author | Fdez-Riverola, Florentino | por |
dc.date.accessioned | 2015-01-07T13:42:37Z | - |
dc.date.available | 2015-01-07T13:42:37Z | - |
dc.date.issued | 2014 | - |
dc.identifier.issn | 1477-4054 | por |
dc.identifier.uri | https://hdl.handle.net/1822/32460 | - |
dc.description.abstract | Web services are the de facto standard in biomedical data integration. However, there are data integration scenarios that cannot be fully covered by Web services. A number of Web databases and tools do not support Web services, and existing Web services do not cover for all possible user data demands. As a consequence, Web data scraping, one of the oldest techniques for extracting Web contents, is still in position to offer a valid and valuable service to a wide range of bioinformatics applications, ranging from simple extraction robots to online meta-servers. This article reviews existing scraping frameworks and tools, identifying their strengths and limitations in terms of extraction capabilities. The main focus is set on showing how straightforward it is today to set up a data scraping pipeline, with minimal programming effort, and answer a number of practical needs. For exemplification purposes, we introduce a biomedical data extraction scenario where the desired data sources, well-known in clinical microbiology and similar domains, do not offer programmatic interfaces yet. Moreover, we describe the operation of WhichGenes and PathJam, two bioinformatics meta-servers that use scraping as means to cope with gene set enrichment analysis. | por |
dc.description.sponsorship | This work was partially funded by (i) the [TIN2009-14057-C03-02] project from the Spanish Ministry of Science and Innovation, the Plan E from the Spanish Government and the European Union from the European Regional Development Fund (ERDF), (ii) the Portugal-Spain cooperation action sponsored by the Foundation of Portuguese Universities [E 48/11] and the Spanish Ministry of Science and Innovation [AIB2010PT-00353] and (iii) the Agrupamento INBIOMED [2012/273] from the DXPCTSUG (Direccion Xeral de Promocion Cientifica e Tecnoloxica do Sistema Universitario de Galicia) from the Galician Government and the European Union from the ERDF unha maneira de facer Europa. H. L. F. was supported by a pre-doctoral fellowship from the University of Vigo. | por |
dc.language.iso | eng | por |
dc.publisher | Oxford University Press | por |
dc.rights | openAccess | por |
dc.subject | Web scraping | por |
dc.subject | Data integration | por |
dc.subject | Interoperability | por |
dc.subject | Database interfaces | por |
dc.title | Web scraping technologies in an API world | por |
dc.type | article | - |
dc.peerreviewed | yes | por |
dc.comments | CEB14738 | por |
sdum.publicationstatus | published | por |
oaire.citationStartPage | 788 | por |
oaire.citationEndPage | 797 | por |
oaire.citationIssue | 5 | por |
oaire.citationConferencePlace | United Kingdom | - |
oaire.citationTitle | Briefings in bioinformatics | por |
oaire.citationVolume | 15 | por |
dc.date.updated | 2015-01-05T20:51:40Z | - |
dc.identifier.eissn | 1467-5463 | - |
dc.identifier.doi | 10.1093/bib/bbt026 | por |
dc.identifier.pmid | 23632294 | por |
dc.subject.wos | Science & Technology | por |
sdum.journal | Briefings in bioinformatics | por |
Aparece nas coleções: | CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series |
Ficheiros deste registo:
Ficheiro | Descrição | Tamanho | Formato | |
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document_14738_1.pdf | 548,87 kB | Adobe PDF | Ver/Abrir |