Text mining for the biocuration workflow
Autor(a) principal: | |
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Data de Publicação: | 2012 |
Outros Autores: | , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/23460 |
Resumo: | Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community. |
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Text mining for the biocuration workflowScience & TechnologyMolecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community.National Science Foundation (grant IIS-0844419 to L.H.); US National Institutes of Health National Library of Medicine (grant 1G08LM10720-01 to C.N.A. and C. H. W.); Work related to BioCreative III was supported by the US National Science Foundation (grant DBI-0850319 to C.N.A., L.H., C.H.W.); the US National Institute of General Medical Sciences (grant R01-GM083871 to G.A.P.C.B.); the National Science Foundation (DBI-0849977 to G.A.P.G.B); the European Union Seventh Framework MICROME project (Grant Agreement Number 222886-2 to M.K. and A.V.); the US National Science Foundation IGERT (Grant 0221625 to K.G.D) and a PhRMA Foundation predoctoral fellowship in informatics; US National Science Foundation (grant DBI-0850219 to E.H.); US National Human Genome Research Institute (grant HG001315 to R.N.); National Institutes of Health (NIH) (grant 2U01HG02712-04 to A.L.V.) and European Commission contract FELICS (grant 021902RII3); National Institute of Environmental Health Sciences (NIEHS) and the National Library of Medicine (NLM) (R01ES014065 to T.W.); NIEHS (R01ES014065-04S1 to T.W.); National Institutes of Health National Center for Research Resources(P20RR016463 to T.W.); Biotechnology and Biological Sciences Research Council of the UK (grant BB/F010486/1 to A.G.W); the National Institutes of Health National Center for Research Resources (1R01RR024031 to A.G.W); the European Commission FP7 Program (2007223411 to A.G.W). Funding for open access charge: The MITRE Corporation.Oxford University PressOxford PressUniversidade do MinhoHirschman, L.Burns, G. A. P. C.Krallinger, M.Arighi, C.Cohen, K. B.Valencia, A.Hu, C. H.Chatr-Aryamontri, A.Dowell, K. G.Huala, E.Lourenço, AnáliaNash, R.Veuthey, A. L.Wiegers, T.Winter, A. G.20122012-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/23460eng1758-04631758-046310.1093/database/bas02022513129info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:30:31Zoai:repositorium.sdum.uminho.pt:1822/23460Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:25:42.690444Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Text mining for the biocuration workflow |
title |
Text mining for the biocuration workflow |
spellingShingle |
Text mining for the biocuration workflow Hirschman, L. Science & Technology |
title_short |
Text mining for the biocuration workflow |
title_full |
Text mining for the biocuration workflow |
title_fullStr |
Text mining for the biocuration workflow |
title_full_unstemmed |
Text mining for the biocuration workflow |
title_sort |
Text mining for the biocuration workflow |
author |
Hirschman, L. |
author_facet |
Hirschman, L. Burns, G. A. P. C. Krallinger, M. Arighi, C. Cohen, K. B. Valencia, A. Hu, C. H. Chatr-Aryamontri, A. Dowell, K. G. Huala, E. Lourenço, Anália Nash, R. Veuthey, A. L. Wiegers, T. Winter, A. G. |
author_role |
author |
author2 |
Burns, G. A. P. C. Krallinger, M. Arighi, C. Cohen, K. B. Valencia, A. Hu, C. H. Chatr-Aryamontri, A. Dowell, K. G. Huala, E. Lourenço, Anália Nash, R. Veuthey, A. L. Wiegers, T. Winter, A. G. |
author2_role |
author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Hirschman, L. Burns, G. A. P. C. Krallinger, M. Arighi, C. Cohen, K. B. Valencia, A. Hu, C. H. Chatr-Aryamontri, A. Dowell, K. G. Huala, E. Lourenço, Anália Nash, R. Veuthey, A. L. Wiegers, T. Winter, A. G. |
dc.subject.por.fl_str_mv |
Science & Technology |
topic |
Science & Technology |
description |
Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community. |
publishDate |
2012 |
dc.date.none.fl_str_mv |
2012 2012-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
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article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1822/23460 |
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http://hdl.handle.net/1822/23460 |
dc.language.iso.fl_str_mv |
eng |
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eng |
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1758-0463 1758-0463 10.1093/database/bas020 22513129 |
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info:eu-repo/semantics/openAccess |
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openAccess |
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application/pdf |
dc.publisher.none.fl_str_mv |
Oxford University Press Oxford Press |
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Oxford University Press Oxford Press |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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