publication . Article . Other literature type . 2016

SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data.

Patrick Ruch; Julien Gobeill; McEntyre J; Francesco Talo'; Aravind Venkatesan; Michele Ide-Smith;
Open Access
  • Published: 12 Dec 2016 Journal: Wellcome Open Research, volume 1, page 25 (eissn: 2398-502X, Copyright policy)
  • Publisher: F1000 Research Ltd
Abstract
<ns4:p>The tremendous growth in biological data has resulted in an increase in the number of research papers being published. This presents a great challenge for scientists in searching and assimilating facts described in those papers. Particularly, biological databases depend on curators to add highly precise and useful information that are usually extracted by reading research articles. Therefore, there is an urgent need to find ways to improve linking literature to the underlying data, thereby minimising the effort in browsing content and identifying key biological concepts.  </ns4:p><ns4:p> As part of the development of Europe PMC, we have developed a new pl...
Subjects
free text keywords: Bioinformatics, Medicine, R, Science, Q, Software Tool Article, Articles, Open Access, Biocuration, Text-Mining, Data Integration, Semantic Web, Web Annotations, RDF, SPARQL, SciLite
Funded by
EC| ELIXIR-EXCELERATE
Project
ELIXIR-EXCELERATE
ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.
  • Funder: European Commission (EC)
  • Project Code: 676559
  • Funding stream: H2020 | RIA
,
EC| ERC-EuropePMC-2015
Project
ERC-EuropePMC-2015
Support to the Europe PMC initiative – Co-funding grant for the 2016-2021 period
  • Funder: European Commission (EC)
  • Project Code: 699257
  • Funding stream: H2020 | CSA
,
WT| The continued support of the Europe PMC infrastructure.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 108758
  • Funding stream: Cross-Remit
,
WT| Uk PubMed Central Phase 3 Developments 2012 - 2016
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 098231
  • Funding stream: Medical Humanities
30 references, page 1 of 2

Ananiadou S Thompson P Nawaz R: Event-based text mining for biology and functional genomics.Brief Funct Genomics.2015;14(3):213–30. PubMed Abstract| 10.1093/bfgp/elu015| Free Full Text 24907365 [OpenAIRE] [PubMed] [DOI]

Attwood TK Kell DB McDermott P: Utopia documents: linking scholarly literature with research data.Bioinformatics.2010;26(18):i568–i574. PubMed Abstract| 10.1093/bioinformatics/btq383| Free Full Text 20823323 [OpenAIRE] [PubMed] [DOI]

Bateman A: Curators of the world unite: the International Society of Biocuration.Bioinformatics.2010;26(8):991 PubMed Abstract| 10.1093/bioinformatics/btq101 20305270 [OpenAIRE] [PubMed] [DOI]

Beagrie N Houghton J: The Value and Impact of the European Bioinformatics Institute.2016 Reference Source

Chang YM Kuo CJ Huang HS: Analysis and Enhancement of Conditional Random Fields Gene Mention Taggers in BioCreative II Challenge Evaluation. In LBM (Short Papers)2007; 7:1 Reference Source

Comeau DC Islamaj Doğan R Ciccarese P: BioC: a minimalis t approach to interoperability for biomedical text processing.Database (Oxford).2013;2013:bat064 PubMed Abstract| 10.1093/database/bat064| Free Full Text 24048470 [OpenAIRE] [PubMed] [DOI]

Dauga D: Biocuration: a new challenge for the tunicate community.Genesis.2015;53(1):132–142. PubMed Abstract| 10.1002/dvg.22842 25399717 [OpenAIRE] [PubMed] [DOI]

Druzinsky RE Balhoff JP Crompton AW: Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.PLoS One.2016;11(2):e0149102 PubMed Abstract| 10.1371/journal.pone.0149102| Free Full Text 26870952 [OpenAIRE] [PubMed] [DOI]

Europe PMC Consortium: Europe PMC: a full-text literature database for the life sciences and platform for innovation.Nucleic Acids Res.[Accessed June 7, 2016],2015;43(Database issue):D1042–8. PubMed Abstract| 10.1093/nar/gku1061| Free Full Text 25378340 [OpenAIRE] [PubMed] [DOI]

Fernández JM Hoffmann R Valencia A: iHOP web services.Nucleic Acids Res.2007;35(Web Server issue):W21–6. PubMed Abstract| 10.1093/nar/gkm298| Free Full Text 17485473 [OpenAIRE] [PubMed] [DOI]

Gobeill J Gaudinat A Pasche E: Deep Question Answering for protein annotation.Database (Oxford).2015;2015: pii: bav081. PubMed Abstract| 10.1093/database/bav081| Free Full Text [OpenAIRE] [DOI]

Gobeill J Tbahriti I Ehrler F: Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction.BMC Bioinformatics.2008;9(Suppl 3):S9 PubMed Abstract| 10.1186/1471-2105-9-S3-S9| Free Full Text [OpenAIRE] [DOI]

Gobeill J Patsche E Theodoro D: Question answering for biology and medicine. In 2009 9th International Conference on Information Technology and Applications in Biomedicine 2009;1–5. 10.1109/ITAB.2009.5394361 [DOI]

Hirschman L Burns GA Krallinger M: Text mining for the biocuration workflow.Database (Oxford).2012;2012:bas020 PubMed Abstract| 10.1093/database/bas020| Free Full Text 22513129 [OpenAIRE] [PubMed] [DOI]

KafkasŞPi X Marinos N: Section level search functionality in Europe PMC.J Biomed Semantics.2015;6(1):7 PubMed Abstract| 10.1186/s13326-015-0003-7| Free Full Text 25774284 [OpenAIRE] [PubMed] [DOI]

30 references, page 1 of 2
Abstract
<ns4:p>The tremendous growth in biological data has resulted in an increase in the number of research papers being published. This presents a great challenge for scientists in searching and assimilating facts described in those papers. Particularly, biological databases depend on curators to add highly precise and useful information that are usually extracted by reading research articles. Therefore, there is an urgent need to find ways to improve linking literature to the underlying data, thereby minimising the effort in browsing content and identifying key biological concepts.  </ns4:p><ns4:p> As part of the development of Europe PMC, we have developed a new pl...
Subjects
free text keywords: Bioinformatics, Medicine, R, Science, Q, Software Tool Article, Articles, Open Access, Biocuration, Text-Mining, Data Integration, Semantic Web, Web Annotations, RDF, SPARQL, SciLite
Funded by
EC| ELIXIR-EXCELERATE
Project
ELIXIR-EXCELERATE
ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.
  • Funder: European Commission (EC)
  • Project Code: 676559
  • Funding stream: H2020 | RIA
,
EC| ERC-EuropePMC-2015
Project
ERC-EuropePMC-2015
Support to the Europe PMC initiative – Co-funding grant for the 2016-2021 period
  • Funder: European Commission (EC)
  • Project Code: 699257
  • Funding stream: H2020 | CSA
,
WT| The continued support of the Europe PMC infrastructure.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 108758
  • Funding stream: Cross-Remit
,
WT| Uk PubMed Central Phase 3 Developments 2012 - 2016
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 098231
  • Funding stream: Medical Humanities
30 references, page 1 of 2

Ananiadou S Thompson P Nawaz R: Event-based text mining for biology and functional genomics.Brief Funct Genomics.2015;14(3):213–30. PubMed Abstract| 10.1093/bfgp/elu015| Free Full Text 24907365 [OpenAIRE] [PubMed] [DOI]

Attwood TK Kell DB McDermott P: Utopia documents: linking scholarly literature with research data.Bioinformatics.2010;26(18):i568–i574. PubMed Abstract| 10.1093/bioinformatics/btq383| Free Full Text 20823323 [OpenAIRE] [PubMed] [DOI]

Bateman A: Curators of the world unite: the International Society of Biocuration.Bioinformatics.2010;26(8):991 PubMed Abstract| 10.1093/bioinformatics/btq101 20305270 [OpenAIRE] [PubMed] [DOI]

Beagrie N Houghton J: The Value and Impact of the European Bioinformatics Institute.2016 Reference Source

Chang YM Kuo CJ Huang HS: Analysis and Enhancement of Conditional Random Fields Gene Mention Taggers in BioCreative II Challenge Evaluation. In LBM (Short Papers)2007; 7:1 Reference Source

Comeau DC Islamaj Doğan R Ciccarese P: BioC: a minimalis t approach to interoperability for biomedical text processing.Database (Oxford).2013;2013:bat064 PubMed Abstract| 10.1093/database/bat064| Free Full Text 24048470 [OpenAIRE] [PubMed] [DOI]

Dauga D: Biocuration: a new challenge for the tunicate community.Genesis.2015;53(1):132–142. PubMed Abstract| 10.1002/dvg.22842 25399717 [OpenAIRE] [PubMed] [DOI]

Druzinsky RE Balhoff JP Crompton AW: Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.PLoS One.2016;11(2):e0149102 PubMed Abstract| 10.1371/journal.pone.0149102| Free Full Text 26870952 [OpenAIRE] [PubMed] [DOI]

Europe PMC Consortium: Europe PMC: a full-text literature database for the life sciences and platform for innovation.Nucleic Acids Res.[Accessed June 7, 2016],2015;43(Database issue):D1042–8. PubMed Abstract| 10.1093/nar/gku1061| Free Full Text 25378340 [OpenAIRE] [PubMed] [DOI]

Fernández JM Hoffmann R Valencia A: iHOP web services.Nucleic Acids Res.2007;35(Web Server issue):W21–6. PubMed Abstract| 10.1093/nar/gkm298| Free Full Text 17485473 [OpenAIRE] [PubMed] [DOI]

Gobeill J Gaudinat A Pasche E: Deep Question Answering for protein annotation.Database (Oxford).2015;2015: pii: bav081. PubMed Abstract| 10.1093/database/bav081| Free Full Text [OpenAIRE] [DOI]

Gobeill J Tbahriti I Ehrler F: Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction.BMC Bioinformatics.2008;9(Suppl 3):S9 PubMed Abstract| 10.1186/1471-2105-9-S3-S9| Free Full Text [OpenAIRE] [DOI]

Gobeill J Patsche E Theodoro D: Question answering for biology and medicine. In 2009 9th International Conference on Information Technology and Applications in Biomedicine 2009;1–5. 10.1109/ITAB.2009.5394361 [DOI]

Hirschman L Burns GA Krallinger M: Text mining for the biocuration workflow.Database (Oxford).2012;2012:bas020 PubMed Abstract| 10.1093/database/bas020| Free Full Text 22513129 [OpenAIRE] [PubMed] [DOI]

KafkasŞPi X Marinos N: Section level search functionality in Europe PMC.J Biomed Semantics.2015;6(1):7 PubMed Abstract| 10.1186/s13326-015-0003-7| Free Full Text 25774284 [OpenAIRE] [PubMed] [DOI]

30 references, page 1 of 2
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