neXtA5: accelerating annotation of articles via automated approaches in neXtProt

Database

Volumn 2016, Issue , 2016, Pages

  Mottin, Luc ^a,b   Gobeill, Julien ^a,b   Pasche, Emilie ^a,b   Michel, Pierre André ^b   Cusin, Isabelle ^b   Gaudet, Pascale ^b   Ruch, Patrick ^a,b  

^a University of Applied Sciences

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DATA MINING; INFORMATION PROCESSING; MEDLINE; PROCEDURES; SEARCH ENGINE;

AUTOMATIC DATA PROCESSING; DATA CURATION; DATA MINING; MEDLINE; SEARCH ENGINE;

EID: 85037713952     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/baw098     Document Type: Article

References (44)

1. Lu,Z. (2011) PubMed and beyond: a survey of web tools for searching biomedical literature. Database, 2011, baq036.
2. Hirschman,L., Burns,G.A.P.C., Krallinger,M. et al. (2012) Text mining for the biocuration workflow. Database, 2012, bas020.
3. Lu,Z. and Hirschman,L. (2012) Biocuration workflows and text mining: overview of the BioCreative Workshop Track II. Database, 2012, bas043.
4. Krallinger,M., Morgan,A., Smith,L. et al. (2008) Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol., Suppl 2, S1.
5. Dai,H.-J., Chang,Y.-C., Tzong-Han Tsai,R. et al. (2010) New challenges for biological text-mining in the next decade. J. Comput. Sci. Technol., 25, 169–179.
6. Müller,H.M., Kenny,E.E. and Sternberg,P.W. (2004) Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol., 2, e309.
7. Doms,A. and Schroeder,M. (2005) GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res., 33, W783–W786.
8. Rebholz-Schuhmann,D., Arregui,M., Gaudan,S. et al. (2007) Text processing through Web services: calling Whatizit. Bioinformatics, 24, 296–298.
9. Tsuruoka,Y., Tsujii,J. and Ananiadou,S. (2008) FACTA: a text search engine for finding associated biomedical concepts. Bioinformatics, 24, 2559–2560.
10. Du,Z., Zhou,X., Ling,Y. et al. (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res., 38, W64–W70.
11. Gobeill,J., Pasche,E., Vishnyakova,D. et al. (2013) Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database, 2013, bat041.
12. Wei,C.H., Kao,H.Y. and Lu,Z. (2013) PubTator: a Web-based text mining tool for assisting Biocuration. Nucleic Acids Res., 41, W518–W522.
13. Rinaldi,F., Clematide,S., Marques,H. et al. (2014) OntoGene web services for biomedical text mining. BMC Bioinformatics, 15(Suppl 14), S6.
14. Kwon,D., Kim,S., Shin,S.Y. et al. (2014) Assisting manual literature curation for protein–protein interactions using BioQRator. Database, 2014, bau067.
15. Lane,L., Argoud-Puy,G., Britan,A. et al. (2012) neXtProt: a knowledge platform for human proteins. Nucleic Acid Res., 40, D76–D83.
16. Gaudet,P., Michel,P.A., Zahn-Zabal,M. et al. (2015) The neXtProt knowledgebase on human proteins: current status. Nucleic Acids Res., 43, D764–D770.
17. SIB Swiss Institute of Bioinformatics Members. (2015) The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic Acid Res., 44, 27–37.
18. Sioutos,N., de Coronado,S., Haber,M.W. et al. (2007) NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. J. Biomed. Inform., 40, 30–43.
19. Ceusters,W., Smith,B. and Goldberg,L. (2005) A terminological and ontological analysis of the NCI Thesaurus. Methods Inf. Med., 44, 498–507.
20. de Coronado,S., Wright,L.W., Fragoso,G. et al. (2009) The NCI Thesaurus quality assurance life cycle. J. Biomed. Inform., 42, 530–539.
21. Jimeno-Yepes,A., Berlanga-Llavori,R. and Rebholz-Schuhmann,D. (2009) Ontology refinement for improved information retrieval. Inf. Process. Manag., 46, 426–435.
22. The Gene Ontology Consortium, Ashburner,M., Ball,C.A. et al. (2000) Gene Ontology: tool for the unification of biology. Nat. Genet., 25, 25–29.
23. The Gene Ontology Consortium. (2008) The Gene Ontology project in 2008. Nucleic Acids Res., 36, D440–D444.
24. Harris,T.W., Antoshechkin,I., Bieri,T. et al. (2010) WormBase: a comprehensive resource for nematode research. Nucleic Acids Res., 38, D463–D467.
25. Ruch,P. (2016) Text mining to support gene ontology curation and vice versa. In: Dessimoz. et al. (eds). The Gene Ontology Handbook, ISBN: 9781493937417. First published July 29, 2016.
26. Chawla,N.V., Japkowicz,N. and Kolcz,A. (2004) Editorial: special issue on learning from imbalanced data sets. SIGKDD Explor., 6, 1–6.
27. Liu,T.Y. (2009) Learning to rank for information retrieval. Found. Trends Inform. Retr. 3, 225–331.
28. Wu,C.H., Arighi,C.N., Cohen,K.B. et al. (2012) BioCreative-2012 virtual issue. Database, 2012, bas049.
29. Mattingly,C.J., Colby,G.T., Forrest,J.N. et al. (2003) The comparative toxicogenomics database (CTD). Environ. Health Perspect., 111, 793–795.
30. Vishnyakova,D., Gobeill,J., Pasche,E. et al. (2013) ToxiCat: hybrid named entity recognition services to support curation of the comparative toxicogenomic database. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, 2013, 1, 108–113.
31. Gobeill,J., Gaudinat,A., Pasche,E. et al. (2015) Deep question answering for protein annotation. Database, bav081.
32. Pasche,E., Gobeill,J., Kreim,O. et al. (2014) Development and tuning of an original search engine for patent libraries in medicinal chemistry. BMC Bioinformatics, 15(Suppl 1), S15.
33. Ounis,I., Lioma,C., Macdonald,C. et al. (2007) Research directions in terrier: a search engine for advanced retrieval on the web. Novatica/UPGRADE Special Issue on Next Generation Web Search, 8, 49–56.
34. Robertson,S.E., Walker,S. and Beaulieu,M. (2000) Experimentation as a way of life: Okapi at TREC. Inf. Process. Manag., 36, 95–108.
35. Amati,G. and Van Rijsbergen,C.J. (2002) Probabilistic models of information retrieval based on measuring the divergence from randomness. ACM Trans. Inf. Syst., 20, 357–389.
36. Shaw,J.A. and Fox,E.A. (1994) Combination of multiple searches. TREC Proc., TREC-2, 1994, NIST Special Publication, 500-215 243–252.
37. Aronson,A.R., Demner-Fushman,D., Humphrey,S.M. et al. (2005) Fusion of knowledge-intensive and statistical approaches for retrieving and annotating textual genomics documents. TREC Proc., 2005, NIST Special Publication 500–266.
38. Singhal,A. (2001) Modern information retrieval: a brief overview. IEEE Data Eng. Bull., 24, 35–43.
39. Manning,C.D. and Schütze,H. (1999) Foundations of Statistical Natural Language Processing. The MIT Press, Cambridge, p.680.
40. Abdou,S., Ruch,P. and Savoy,J. (2005) Evaluation of stemming, query expansion and manual indexing approches for the genomics track. TREC Proc., 2005, NIST Special Publication, 500–266.
41. Gobeill,J., Gaudinat,A., Ruch,P. et al. (2011) Bitem group report for TREC medical records track 2011. TREC Proc., 2011, NIST Special Publication, 500–296.
42. Gobeill,J., Gaudinat,A., Pasche,E. et al. (2014) Full-texts representation with medical subjects headings, and co-citations network reranking strategies for TREC 2014 clinical decision support track. TREC Proc., 2014, NIST Special Publication, 500–308.
43. Canese,K. (2013) PubMed relevance sort. NLM Tech. Bull., 394, e2.
44. Müller,B., Klinger,R., Gurulingappa,H. et al. (2010) Abstracts versus full texts and patents: a quantitative analysis of biomedical entities. Adv. Multidiscip. Retriev. 6107, 152–165.