OntoGene in BioCreative II

Genome Biology

Volumn 9, Issue SUPPL. 2, 2008, Pages

  Rinaldi, Fabio ^a   Kappeler, Thomas ^a   Kaljurand, Kaarel ^a   Schneider, Gerold ^a   Klenner, Manfred ^a   Clematide, Simon ^a   Hess, Michael ^a   von Allmen, Jean Marc ^b   Parisot, Pierre ^b   Romacker, Martin ^b   Vachon, Therese ^b  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; AUTOMATION; BIOINFORMATICS; CONTROLLED STUDY; DATA MINING; DATA SYNTHESIS; EXPERIMENTATION; GENOMICS; HUMAN; INFORMATION RETRIEVAL; INFORMATION STORAGE; MOLECULAR BIOLOGY; NONHUMAN; PROTEIN ANALYSIS; PROTEIN INTERACTION; PROTEIN PROCESSING; BIOLOGY; DOCUMENTATION; GENE; HEALTH CARE ORGANIZATION; INTERNET; METHODOLOGY; REPRODUCIBILITY;

ABSTRACTING AND INDEXING AS TOPIC; COMPUTATIONAL BIOLOGY; GENES; INTERNET; PROTEIN INTERACTION MAPPING; REPRODUCIBILITY OF RESULTS; SOCIETIES, SCIENTIFIC;

EID: 51049105083     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-s2-s13     Document Type: Article

References (53)

1. Krallinger M Valencia A Text-mining and information-retrieval services for molecular biology. Genome Biol 2005, 6:224. 1175978 15998455
2. Swanson DR Fish oil, Raynaud's syndrome, and undiscovered public knowledge. Perspect Biol Med 1986, 30:7-18. 3797213
3. Hirschman L Park JC Tsujii J Wong L Wu CH Accomplishments and challenges in literature data mining for biology. Bioinformatics 2002, 18:1553-1561. 12490438
4. Shatkay H Feldman R Mining the biomedical literature in the genomic era: an overview. J Comput Biol 2003, 10:821-855. 14980013
5. Cohen KB Hunter L Natural language processing and systems biology. Artificial Intelligence Methods and Tools for Systems Biology Springer Dubitzky W, Azuaje F 2004, 147-173.
6. Ananiadou S Kell DB Tsujii J Text mining and its potential applications in systems biology. Trends Biotechnol 2006, 24:571-579. 17045684
7. Temkin J Gilder M Extraction of protein interaction information from unstructured text using a context-free grammar. Bioinformatics 2003, 19:2046-2053. 14594709
8. Koike A Kobayashi Y Takagi T Kinase pathway database: An integrated protein-kinase and NLP-based protein-interaction resource. Genome Res 2003, 13:1231-1243. 403651 12799355
9. Miyao Y Ohta T Masuda K Tsuruoka Y Yoshida K Ninomiya T Tsujii J Semantic retrieval for the accurate identification of relational concepts in massive textbases. Proceedings of COLING-ACL; Sydney, Australia 2006. http://www-tsujii.is.s.u-tokyo.ac.jp/~yusuke/paper/ acl2006.pdf
10. Yakushiji A Tateisi Y Miyao Y Tsujii J Event extraction from biomedical papers using a full parser. Pac Symp Biocomp 2001, 408-419.
11. Ding J Berleant D Xu J Fulmer A Extracting biochemical interactions from MEDLINE using a link grammar parser. Proceedings of 15th IEEE International Conference on Tools with Artificial Intelligence 2003 http://www.bcb.iastate.edu/courses/JingDing.pdf
12. Pyysalo S Salakoski T Aubin S Nazarenko A Lexical adaptation of link grammar to the biomedical sublanguage: A comparative evaluation of three approaches. BMC Bioinformatics 2006, 7(suppl 3):S2. http://www.biomedcentral.com/1471-2105/7/S3/S2 1764446 17134475
13. Chun HW Tsuruoka Y Kim JD Shiba R Nagata N Hishiki T Tsujii J Extraction of gene-disease relations from Medline using domain dictionaries and machine learning. Pac Symp Biocomput 2006, 4:15. 17094223
14. Daraselia N Yuryev A Egorov S Novichkova S Nikitin A Mazo I Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics 2004, 20:604-611. 15033866
15. Smith L Tanabe LK nee Ando RJ Kuo CJ Chung IF Hsu CN Lin YS Klinger R Friedrich CM Ganchev K Torii M Liu H Haddow B Struble CA Povinelli RJ Vlachos A Baumgartner WA Hunter L Carpenter B Tsai RTH Dai HJ Liu F Chen Y Sun C Katrenko S Adriaans P Blaschke C Torres R Neves M Nakov P Divoli A Maña-López M Mata-Vázquez J Wilbur WJ Overview of BioCreative II gene mention recognition. Genome Biol 2008, 9(Suppl 2):S2.
16. Morgan AA Lu Z Wang X Cohen AM Fluck J Ruch P Divoli A Fundel K Leaman R Hakenberg J Sun C Liu H Torres R Krauthammer M Lau WW Liu H Hsu CN Schuemie Cohen KB Hirschman L Overview of BioCreative II gene normalization. Genome Biology 2008, 9(Suppl 2):S3.
17. Krallinger M Leitner F Rodriguez-Penagos C Valencia A Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol 2008, 9(Suppl 2):S4.
18. Schneider G Hybrid long-distance functional dependency parsing. PhD thesis University of Zurich, Institute of Computational Linguistics 2007
19. Clegg AB Shepherd AJ Benchmarking natural-language parsers for biological applications using dependency graphs. BMC Bioinformatics 2007, 8:24. http://www.biomedcentral.com/1471-2105/8/24/1797812 17254351
20. Pyysalo S Ginter F Heimonen J Bjorne J Boberg J Jarvinen J Salakoski T BioInfer: A corpus for information extraction in the biomedical domain. BMC Bioinformatics 2007, 8-50. http://www.biomedcentral.com/1471-2105/8/ 50/1808065 17291334
21. Fundel K Küffner R Zimmer R RelEx: Relation extraction using dependency parse trees. Bioinformatics 2007, 23:365-371. 17142812
22. Rinaldi F Schneider G Kaljurand K Hess M Romacker M An environment for relation mining over richly annotated corpora: The case of GENIA. BMC Bioinformatics 2006, 7(suppl 3):S3. http://www.biomedcentral.com/ 1471-2105/7/S3/S3 1764447 17134476
23. Kazama J Makino T Ohta Y Tsujii J Tuning support vector machines for biomedical named entity recognition. Proceedings of the Association for Computation Linguistics Workshop on Natural Language Processing in the Biomedical Domain; Philadelphia, PA 2002 http://www-tsujii.is.s.u-tokyo.ac.jp/~kazama/papers/kazama_aclbio02.pdf
24. Kim J Ohta T Tsuruoka Y Tateisi Y Collier N Introduction to the bio-entity recognition task at JNLPBA. Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA); Geneva, Switzerland 2004 http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/ERtask/shared_task_intro.pdf
25. Settles B ABNER: An open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics 2005, 21:3191-3192. 15860559
26. Song Y Kim E Lee GG Yi BK POSBIOTM-NER: A trainable biomedical named-entity recognition system. Bioinformatics 2005, 21:2794-2796. 15814561
27. Chinchor N Overview of MUC-7/MET-2. Proceedings of the Seventh Message Understanding Conference (MUC-7) 1997 http://www.fullsearcher.com/down/ InformationExtraction/7.pdf
28. Krauthammer M Nenadic G Term identification in the biomedical literature. J Biomed Informatics 2004, 37:512-526.
29. Hakenberg J Royer L Plake C Strobelt H Schroeder M Me and my friends: gene mention normalization with background knowledge. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007. http://www2.informatik.hu-berlin.de/~hakenber/publ/bc07_gn.pdf
30. Luong T Tran N Krauthammer M Context-aware mapping of gene names using trigrams. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007 http://www.cnio.es/eventos/descargas/Meeting/260454_1346,97_booklet.pdf
31. Fluck J Mevissen HT Dach H Oster M Hofmann-Apitius M ProMiner: recognition of human gene and protein names using regularly updated dictionaries. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007. http://www.scai.fraunhofer.de/fileadmin/prominer/ProMinerBioCreative2.pdf
32. Fundel K Zimmer R Human gene normalization by an integrated approach including abbreviation resolution and disambiguation. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007. http://www.cnio.es/ eventos/descargas/Meeting/260454_1346,97_booklet.pdf
33. Ono T Hishigaki H Tanigami A Takagi T Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 2001, 17:155-161. 11238071
34. Hakenberg J Schröder M Leser U Consensus pattern alignment to find protein-protein interactions in text. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007. http://alibaba.informatik.hu-berlin.de/publ/biocreative2_ips.pdf
35. Madkour A Darwish K Hassan H Hassan A Emam O BioNoculars: Extracting protein-protein interactions from biomedical text. Biological, Translational, and Clinical Language Processing Prague, Czech Republic: Association for Computational Linguistics 2007, 89-96. http://www.aclweb.org/anthology/W/W07/W07-1012
36. Ehrler F Gobeill J Tbahriti I Ruch P GeneTeam site report for biocreative ii: Customizing a simple toolkit for text mining in molecular biology. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology. 2007 http://www.cnio.es/eventos/descargas/Meeting/ 260454_1346,97_booklet.pdf
37. Blaschke C Andrade M Ouzounis C Valencia A Automatic extraction of biological information from scientific text: protein-protein interactions. Proceddings of the International Conference on Intelligent Systtems for Molecular Biology; Heidelberg, Germany 1999. http://citeseer.ist.psu.edu/cache/papers/cs/12608/ http:zSzzSzgredos.cnb.uam.eszSzmedline_interactionszSzCBlaschke99.pdf/ blaschke99automatic.pdf
38. Gonzalez G Tari L Gitter A Leaman R Nikkila S Wendt R Zeigler A Baral C Integrating knowledge extracted from biomedical literature: normalization and evidence statements for interactions. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007. http://www.cnio.es/ eventos/descargas/Meeting/260454_1346,97_booklet.pdf
39. Saetre R Yoshida K Yakushiji A Miyao Y Matsubayashi Y Ohta T AKANE system: protein-protein interaction pairs in the BioCreative2 challenge, PPI-IPS subtask. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007. http://www-tsujii.is.s.u-tokyo.ac.jp/~satre/papers/ BC2_PPI_IPS_T19_BC2.pdf
40. Erkan G Ozgur A Radev DR Extracting interacting protein pairs and evidence sentences by using dependency parsing and machine learning techniques. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007. http://tangra.si.umich.edu/clair/clair/bio_workshop.pdf
41. Figueroa A Neumann G Identifying Protein-Protein interactions in Biomedical publications. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007 http://www.dfki.de/∼neumann/publications/new-ps/ biocreative_final.pdf
42. Hunter L Baumgartner WA Jr Lu Z Caporaso JG Johnson HL Lindemann A Lu Z Medvedeva O Paquette J White EK Cohen KB An integrated approach to concept recognition in biomedical text. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007. http://www.cnio.es/eventos/ descargas/Meeting/260454_1346,97_booklet.pdf
43. Huang M Ding S Wang H Zhu X Mining physical protein-protein interactions by exploiting abundant features. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007. http://www.cnio.es/eventos/descargas/Meeting/ 260454_1346,97_booklet.pdf
44. Grover C Haddow B Klein E Matthews M Neilsen LA Tobin R Wang X Adapting a relation extraction pipeline for the BioCreeAtIvE II Task. Proceedings of the Second BioCreative Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology 2007. http://www.ltg.ed.ac.uk/np/publications/ltg/papers/Grover2007Adapting.pdf
45. Hirschman L Morgan AA Yeh AS Rutabaga by any other name: extracting biological names. J Biomed Informatics 2002, 35:247-259.
46. Chen L Liu H Friedman C Gene name ambiguity of eukaryotic nomenclatures. Bioinformatics 2005, 21:248-256. 15333458
47. UniProt Consortium The Universal Protein Resource (UniProt). Nucleic Acids Res 2007, 35:D193-D197. 1669721 17142230
48. Romacker M Grandjean N Parisot P Kreim O Cronenberger D Vachon T Peitsch M The UltraLink: an expert system for contextual hyperlinking in knowledge management. Computer Applications in Pharmaceutical Research and Development Wiley & Sons, New York Ekins S ISBN 0-471-73779-8
49. Kerrien S Alam-Faruque Y Aranda B Bancarz I Bridge A Derow C Dimmer E Feuermann M Friedrichsen A Huntley R Kohler C Khadake J Leroy C Liban A Lieftink C Montecchi-Palazzi L Orchard S Risse J Robbe K Roechert B Thorneycroft D Zhang Y Apweiler R Hermjakob H IntAct: open source resource for molecular interaction data. Nucleic Acids Res 2006, 35(Database):D561-D565. 1751531 17145710
50. Zanzoni A Montecchi-Palazzi L Quondam M Ausiello G Helmer-Citterich M Cesareni G MINT: a Molecular INTeraction database. FEBS Lett 2002, 513:135-140. 11911893
51. Kaljurand K Rinaldi F Schneider G Prolog-based Query Interface to Syntactic Dependencies Extracted from Biomedical Literature; tech rep Zurich, Sqitzerland: IFI, University of Zurich 2006. ftp://ftp.ifi.uzh.ch/pub/techreports/TR-2006/ifi-2006.04.pdf
52. Hermjakob H Montecchi-Palazzi L Bader G Wojcik J Salwinski L Ceol A Moore S Orchard S Sarkans U von Mering C Roechert B Poux S Jung E Mersch H Kersey P Lappe M Li Y Zeng R Rana D Nikolski M Husi H Brun C Shanker K Grant SG Sander C Bork P Zhu W Pandey A Brazma A Jacq B et al. The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data. Nat. Biotechnol 2004, 22:177-183. 14755292
53. Leitner F Krallinger M Rodriguez-Penagos C Hakenberg J Plake C Kuo CJ Hsu CN Tsai RTH Hung HC Lau WW Johnson CA Saetre R Yoshida K Chen YH Kim S Shin SY Zhang BT Baumgartner WA Hunter L Haddow B Matthews M Wang X Ruch P Ehrler F Özgür A Erkan G Radev DR Krauthammer M Luong T Hoffmann R et al. Introducing meta-services for biomedical information extraction. Genome Biol 2008, 9(Suppl 2):S6.