Collective instance-level gene normalization on the IGN corpus

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Dai, Hong Jie ^a   Wu, Johnny Chi Yang ^b   Tsai, Richard Tzong Han ^c  

^a TAIPEI MEDICAL UNIVERSITY   (Taiwan)

^b INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^c NATIONAL CENTRAL UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGY; COMPUTER PROGRAM; DATA MINING; GENETIC DATABASE; HUMAN; MOLECULAR GENETICS; NATURAL LANGUAGE PROCESSING; PROCEDURES;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, GENETIC; HUMANS; MOLECULAR SEQUENCE ANNOTATION; NATURAL LANGUAGE PROCESSING; SOFTWARE;

EID: 84894235491     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0079517     Document Type: Article

References (35)

1. Dogan RI, Murray GC, Névéol A, Lu Z (2009) Understanding PubMed user search behavior through log analysis. Database: the journal of biological databases and curation 2009.
2. Mihalcea R, Moldovan D (2001) Document indexing using named entities. Studies in Informatics and Control 10: 21-28.
3. Gerner M, Sarafraz F, Bergman CM, Nenadic G (2012) BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events. Bioinformatics 28: 2154-2161.
4. Landeghem SV, Ginter F, Peer YVd, Salakoski T (2011) EVEX: a pubmed-scale resource for homology-based generalization of text mining predictions. Proceedings of BioNLP 2011 Workshop. Portland, Oregon: Association for Computational Linguistics. pp. 28-37.
5. Huang M, Liu J, Zhu X (2011) GeneTUKit: a software for document-level gene normalization. Bioinformatics 27: 1032-1033.
6. Wei C-H, Kao H-Y (2011) Cross-species gene normalization by species inference. BMC Bioinformatics 12: S5.
7. Khalid MA, Jijkoun V, Rijke Md (2008) The impact of named entity normalization on information retrieval for question answering. Proceedings of the IR research, 30th European conference on Advances in information retrieval (ECIR'08). pp. 705-710.
8. McNamee P, Mayfield J, Lawrie D, Oard D, Doermann D (2011) Cross-Language Entity Linking. In: AFNLP, editor. Proceedings of the 5th International Joint Conference on Natural Language Processing (IJCNLP2011). Chiang Mai, Thailand. pp. 255-263.
9. Ceol A, Chatr-Aryamontri A, Licata L, Cesareni G (2008) Linking entries in protein interaction database to structured text: The FEBS Letters experiment. FEBS Letters 582: 1171-1177.
10. Huang M, Névéol A, Lu Z (2011) Recommending MeSH terms for annotating biomedical articles. Journal of the American Medical Informatics Association 18: 660-667.
11. Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, et al. (2008) Big data: The future of biocuration. Nature 455: 47-50.
12. Baran J, Gerner M, Haeussler M, Nenadic G, Bergman CM (2011) pubmed2ensembl: a resource for mining the biological literature on genes. PLoS ONE 6: e24716.
13. Dai H-J, Tsai W-C, Tsai RT-H, Hsu W-L (2011) Enhancing Search Results with Semantic Annotation Using Augmented Browsing. Proceedings of the Twenty-Second International Joint Conference on Artificial Intelligence (IJCAI11). Barcelona, Catalonia (Spain). pp. 248-2423.
14. Hirschman L, Colosimo M, Morgan A, Yeh A (2005) Overview of BioCreAtIvE task 1B: normalized gene lists. BMC Bioinformatics 6: S11.
15. Lu Z, Kao H-Y, Wei C-H, Huang M, Liu J, et al. (2011) The gene normalization task in BioCreative III. BMC Bioinformatics 12: S2.
16. Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, et al. (2008) Overview of BioCreative II gene normalization. Genome Biology 9: S3.
17. Van Landeghem S, Björne J, Wei C-H, Hakala K, Pyysalo S, et al. (2013) Large-scale event extraction from literature with multi-level gene normalization. PLoS ONE 8: e55814.
18. Oda K, Kim J-D, Ohta T, Okanohara D, Matsuzaki T, et al. (2008) New challenges for text mining: mapping between text and manually curated pathways. BMC Bioinformatics 9: S5.
19. Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzalez G (2008) Interspecies normalization of gene mentions with GNAT. Bioinformatics 24: 126-132.
20. Dai H-J, Chang Y-C, Tsai RT-H, Hsu W-L (2011) Integration of gene normalization stages and co-reference resolution using a Markov logic network. Bioinformatics 27: 2586-2594.
21. Smith L, Tanabe LK, Ando RJn, Kuo C-J, Chung I-F, et al. (2008) Overview of BioCreative II gene mention recognition. Genome Biology 9: S2.
22. Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, et al. (2010) An Overview of BioCreative II.5. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 7: 385-399.
23. Kafkas Ş, Lewin I, Milward D, van Mulligen E, Kors J, et al. (2012) CALBC: Releasing the Final Corpora. Proceedings of the eighth international conference on Language Resources and Evaluation (LREC). Istanbul, Turkey.
24. Cucerzan S (2007) Large-scale named entity disambiguation based on Wikipedia data. Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning. Prague, Czech Republic. pp. 708-716.
25. Kulkarni S, Singh A, Ramakrishnan G, Chakrabarti S (2009) Collective annotation of wikipedia entities in web text; Paris, France. ACM. pp. 457-466.
26. Bada M, Eckert M, Evans D, Garcia K, Shipley K, et al. (2012) Concept annotation in the CRAFT corpus. BMC Bioinformatics 13: 161.
27. Neves M, Carazo J-M, Pascual-Montano A (2010) Moara: a Java library for extracting and normalizing gene and protein mentions. BMC Bioinformatics 11: 157.
28. Richardson M, Domingos P (2006) Markov logic networks. Machine Learning 62: 107-136. (Pubitemid 43202307)
29. Comeau DC, Doǧan RI, Ciccarese P, Cohen KB, Krallinger M, et al. (2013) BIoC: A Minimalist Approach to Interoperability for Biomedical Text Processing. Database: the journal of biological databases and curation.
30. Tsai RT-H, Sung C-L, Dai H-J, Hung H-C, Sung T-Y, et al. (2006) NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition. BMC Bioinformatics 7: S11.
31. Sen P, Namata G, Bilgic M, Getoor L, Galligher B, et al. (2008) Collective classification in network data. AI Magazine 29: 93.
32. Soon WM, Ng HT, Lim DCY (2001) A machine learning approach to coreference resolution of noun phrases. Computational Linguistics 27: 521-544. (Pubitemid 33597451)
33. Dai H-J, Chang Y-C, Tsai RT-H, Hsu W-L (2010) New challenges for biological text-mining in the next decade. Journal of Computer Science and Technology 25: 169-179.
34. Dai H-J, Hung H-C, Tsai RT-H, Hsu W-L (2007) IASL Systems in the Gene Mention Tagging Task and Protein Interaction Article Sub-task. Proceedings of Second BioCreAtIvE Challenge Evaluation Workshop. Madrid, Spain. 69-76.
35. Tsai RT-H, Dai H-J, Lai P-T, Huang C-H (2009) PubMed-EX: A web browser extension to enhance PubMed search with text mining features. Bioinformatics 25: 3031-3032.