Evaluation of text-mining systems for biology: Overview of the Second BioCreative community challenge

Genome Biology

Volumn 9, Issue SUPPL. 2, 2008, Pages

  Krallinger, Martin ^a   Morgan, Alexander ^b   Smith, Larry ^c   Leitner, Florian ^a   Tanabe, Lorraine ^c   Wilbur, John ^c   Hirschman, Lynette ^d   Valencia, Alfonso ^a  

^a Centro Nacional de Investigaciones Oncológicas   (Spain)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d MITRE CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPARATIVE STUDY; CONTROLLED STUDY; DATA EXTRACTION; DATA MINING; DATA SYNTHESIS; GENOME ANALYSIS; HUMAN; INFORMATION RETRIEVAL; INFORMATION TECHNOLOGY; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; PERFORMANCE MEASUREMENT SYSTEM; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; REVIEW; ARTICLE; BIOLOGY; GENE; HEALTH CARE ORGANIZATION; INSTRUMENTATION; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PROTEIN ANALYSIS;

COMPUTATIONAL BIOLOGY; GENES; NATURAL LANGUAGE PROCESSING; PROTEIN INTERACTION MAPPING; SOCIETIES, SCIENTIFIC;

EID: 51049084462     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-s2-s1     Document Type: Review

References (23)

1. Krallinger M Hirschman L Valencia A Current use of text mining and literature search systems for genome sciences. Genome Biol 2008, 9(Suppl 2):S8
2. Menne K Hermjakob H Apweiler R A comparison of signal sequence prediction methods using a test set of signal peptides. Bioinformatics 2000, 16:741-742 10.1093/bioinformatics/16.8.741
3. Sprenger J Fink J Teasdale R Evaluation and comparison of mammalian subcellular localization prediction methods. BMC Bioinformatics 2006, 7:S3 10.1186/1471-2105-7-S5-S3
4. Dalal S Balasubramanian S Regan L Protein alchemy: Changing beta-sheet into alpha-helix. Nat Struct Biol 1997, 4:548-552 10.1038/nsb0797-548
5. Lopez G Rojas A Tress M Valencia A Assessment of predictions submitted for the CASP7 function prediction category. Proteins 2007, 69(suppl 8):165-174 10.1002/prot.21651
6. Guigo R Flicek P Abril J Reymond A Lagarde J Denoeud F Antonarakis S Ashburner M Bajic V Birney E Castelo R Eyras E Ucla C Gingeras T Harrow J Hubbard T Lewis S Reese M EGASP: The human ENCODE Genome Annotation Assessment Project. Genome Biol 2006, 7:1-31 10.1186/gb-2006-7-s1-s2
7. Hirschman L The evolution of evaluation: Lessons from the message understanding conference. Computer Speech Lang 1998, 12:281-305 10.1006/ csla.1998.0102
8. Bar-Haim R Dagan I Dolan B Ferro L Giampiccolo D Magnini B Szpektor I The Second PASCAL Recognising Textual Entailment Challenge. Proceedings of the Second PASCAL Challenges Workshop on Recognising Textual Entailment 2006 http://www.cs.biu.ac.il/~szpekti/papers/ RTE2-organizers.pdf
9. Yeh A Hirschman L Morgan A Evaluation of text data mining for database curation: Lessons learned from the KDD Challenge Cup. Bioinformatics 2003, 19:331-339 10.1093/bioinformatics/btg1046
10. Hersh W Cohen A Roberts P Rekapalli H TREC 2006 Genomics Track Overview. TREC Notebook 2006 http://trec.nist.gov/pubs/trec15/papers/ GEO06.OVERVIEW.pdf
11. Nedellec C Learning language in logic-genic interaction extraction challenge. Proceedings of the LLL05 workshop 2005. http://www.cs.york.ac.uk/aig/lll/lll05/lll05-nedellec.pdf
12. Kim J Ohta T Tsuruoka Y Tateisi Y Collier N Introduction to the Bio-Entity Task at JNLPBA. Proceedings of the BioCreative Challenge Evaluation Workshop 2004.
13. Hirschman L Yeh A Blaschke C Valencia A Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics 2005, 6:S1 10.1186/1471-2105-6-S1-S1
14. Yeh A Morgan A Colosimo M Hirschman L BioCreAtIvE Task 1A: Gene mention finding evaluation. BMC Bioinformatics 2005, 6:S2 10.1186/ 1471-2105-6-S1-S2
15. Hirschman L Colosimo M Morgan A Yeh A Overview of BioCreAtIvE task 1B: normalized gene lists. BMC Bioinformatics 2005, 6:S11 10.1186/ 1471-2105-6-S1-S11
16. Blaschke C Andres Leon E Krallinger M Valencia A Evaluation of BioCreative assessment of task 2. BMC Bioinformatics 2005, 6:S16 10.1186/ 1471-2105-6-S1-S16
17. Morgan A Lu Z Wang X Cohen AM Fluck J Ruch P Divoli A Fundel K Leaman R Hakenberg J Sun C Liu Hh Torres R Krauthammer M Lau WW Liu H Hsu CN Schuemie M Cohen KB Hirschman L Overview of BioCreative II gene normalization. Genome Biol 2008, 9(Suppl 2):S3
18. Smith L Tanabe L Ando R Kuo C Chung I Hsu C Lin Y Klinger R Friedrich C Ganchev K Torii M Liu H Haddow B Struble C Povinelli R Vlachos A Baumgartner W Hunter L Carpenter B Tsai R Dai H Liu F Chen Y Sun C Katrenko S Adriaans P Blaschke C Torres R Neves M Nakov P et al. Overview of BioCreative II gene mention recognition. Genome Biol 2008, 9(Suppl 2):S2
19. Chatr-aryamontri A Kerrien S Khadake J Orchard S Ceol A Licata L Castagnoli L Costa S Derow C Huntley R Aranda B Leroy C Thorneycroft D Apweiler R Cesareni G Hermjakob H MINT and IntAct contribute to the Second BioCreative Challenge: Serving the text-mining community with high quality molecular interaction data. Genome Biol 2008, 9(Suppl 2):S5
20. Noble W What is a support vector machine? Nat Biotechnol 2006, 24:1565-1567 10.1038/nbt1206-1565
21. Lafferty J McCallum A Pereira F Conditional random fields: Probabilistic models for segmenting and labeling sequence data. Proceedings of the ICML 01 2001 http://www.cis.upenn.edu/~pereira/papers/crf.pdf
22. Tsuruoka Y Tsujii J Bidirectional inference with the easiest-first strategy for tagging sequence data. Proceedings of HLT/EMNLP 2005 http://www-tsujii.is.s.u-tokyo.ac.jp/~tsuruoka/papers/emnlp05bidir.pdf
23. McCallum AK MALLET: A Machine Learning for Language Toolkit. http://mallet.cs.umass.edu