Ranking relations between diseases, drugs and genes for a curation task

Journal of Biomedical Semantics

Volumn 3, Issue 3, 2012, Pages

  Clematide, Simon ^a   Rinaldi, Fabio ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84887342400     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-3-S3-S5     Document Type: Article

References (30)

1. UniProt Consortium: The Universal Protein Resource (UniProt). Nucleic Acids Research. 2007, 35: D193-7.
2. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: A General Repository for Interaction Datasets. Nucleic Acids Research. 2006, 34: D535-9. 10.1093/nar/gkj109.
3. Baumgartner WA, Cohen KB, Fox LM, Acquaah-Mensah G, Hunter L: Manual curation is not sufficient for annotation of genomic databases. Bioinformatics. 2007, 23 (13): i41-48. 10.1093/bioinformatics/btm229. [ http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/i41 ]
4. Krallinger M, Leitner F, Rodriguez-Penagos C, Valencia A: Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biology. 2008, 9 (Suppl 2): S4-10.1186/gb-2008-9-s2-s4.
5. Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, Valencia A: An Overview of BioCreative II.5. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2010, 7 (3): 385-399.
6. Klein T, Chang J, Cho M, Easton K, Fergerson R, Hewett M, Lin Z, Liu Y, Liu S, Oliver D, Rubin D, Shafa F, Stuart J, Altman R: Integrating Genotype and Phenotype Information: An Overview of the PharmGKB Project. The Pharmacogenomics Journal. 2001, 1: 167-170. 10.1038/sj.tpj.6500035.
7. Sangkuhl K, Berlin DS, Altman RB, Klein TE: PharmGKB: Understanding the Effects of Individual Genetic Variants. Drug Metabolism Reviews. 2008, 40 (4): 539-551. 10.1080/03602530802413338. [ http://informahealthcare.com/doi/abs/10.1080/03602530802413338 ]
8. Davis A, King B, Mockus S, Murphy C, Saraceni-Richards C, Rosenstein M, Wiegers T, Mattingly C: The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res. 2011
9. Lindberg C: The Unified Medical Language System (UMLS) of the National Library of Medicine. J Am Med Rec Assoc. 1990, 61 (5): 40-42.
10. Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research. 2009, 37 (suppl 2): W170-W173. [ http://nar.oxfordjournals.org/content/37/suppl2/W170.abstract ]
11. Manning CD, Raghavan P, Schütze H: Introduction to Information Retrieval. 2008, Cambridge University Press
12. Carroll HD, Kann MG, Sheetlin SL, Spouge JL: Threshold Average Precision (TAP-k): a measure of retrieval designed for bioinformatics. Bioinformatics. 2010, 26 (14): 1708-1713. 10.1093/bioinformatics/btq270.
13. Rinaldi F, Kaljurand K, Saetre R: Terminological resources for Text Mining over Biomedical Scientific Literature. Journal of Artificial Intelligence in Medicine. 2011, 52 (2): 107-114. 10.1016/j.artmed.2011.04.011.
14. Kaljurand K, Kappeler T, Schneider G: Using existing biomedical resources to detect and ground terms in biomedical literature. Proceedings of the 12th Conference on Artificial Intelligence in Medicine (AIME09). 2009, 225-234.
15. Rinaldi F, Kappeler T, Kaljurand K, Schneider G, Klenner M, Clematide S, Hess M, von Allmen JM, Parisot P, Romacker M, Vachon T: OntoGene in BioCreative II. Genome Biology. 2008, 9 (Suppl 2): S13-10.1186/gb-2008-9-s2-s13. [ http://genomebiology.com/2008/9/S2/S13 ]
16. Rinaldi F, Schneider G, Kaljurand K, Clematide S, Vachon T, Romacker M: OntoGene in BioCreative II.5. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2010, 7 (3): 472-480.
17. Tsuruoka Y, McNaught J, Tsujii J, Ananiadou S: Learning string similarity measures for gene/protein name dictionary look-up using logistic regression. Bioinformatics. 2007, 23 (20): 2768-2774. 10.1093/bioinformatics/btm393. [ http://www.ncbi.nlm.nih.gov/pubmed/17698493 ]
18. Daumé H: Notes on CG and LM-BFGS Optimization of Logistic Regression. 2004, [Paper available at http://hal3.name/docs/daume04cg-bfgs.pdf , implementation available at http://hal3.name/megam/]
19. Dietterich TG: Approximate Statistical Tests for Comparing Supervised Classification Learning Algorithms. Neural Computation. 1998, 10 (7): 1895-1923. 10.1162/089976698300017197. [ http://www.mitpressjournals.org/doi/abs/10.1162/089976698300017197 ]
20. Nadeau C, Bengio Y: Inference for the Generalization Error. Machine Learning. 2003, 52 (3): 239-281. 10.1023/A:1024068626366.
21. Rinaldi F, Clematide S, Schneider G, Romacker M, Vachon T: ODIN: An Advanced Interface for the Curation of Biomedical Literature. Biocuration 2010, the Conference of the International Society for Biocuration and the 4th International Biocuration Conference. 2010
22. Arighi C, Roberts P, Agarwal S, Bhattacharya S, Cesareni G, Chatr-aryamontri A, Clematide S, Gaudet P, Giglio M, Harrow I, Huala E, Krallinger M, Leser U, Li D, Liu F, Lu Z, Maltais L, Okazaki N, Perfetto L, Rinaldi F, Saetre R, Salgado D, Srinivasan P, Thomas P, Toldo L, Hirschman L, Wu C: BioCreative III interactive task: an overview. BMC Bioinformatics. 2011, 12 (Suppl 8): S4-10.1186/1471-2105-12-S8-S4. [ http://www.biomedcentral.com/1471-2105/12/S8/S4 ]
23. Rinaldi F, Clematide S, Garten Y, Whirl-Carrillo M, Gong L, Hebert JM, Sangkuhl K, Thorn CF, Klein TE, Altman RB: Using ODIN for a PharmGKB re-validation experiment. Database: The Journal of Biological Databases and Curation. 2012
24. Rinaldi F, Clematide S, Hafner S: Ranking of CTD articles and interactions using the OntoGene pipeline. Proceedings of the 2012 BioCreative workshop, Washington DC, 04 April 2012 - 05 April 2012. 2012
25. Leaman R, Gonzalez G: BANNER: an executable survey of advances in biomedical named entity recognition. Pacific Symposium On Biocomputing Pacific Symposium On Biocomputing. 2008, 13: 652-663. [ http://www.ncbi.nlm.nih.gov/pubmed/18229723 ]
26. Aronson AR, Lang FM: An overview of MetaMap: historical perspective and recent advances. Journal of the American Medical Informatics Association. 2010, 17 (3): 229-236. [ http://www.ncbi.nlm.nih.gov/pubmed/20442139 ]
27. Tsai RTH, Hung HC, Dai HJ, Lin YW, Hsu WL: Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles. BMC Bioinformatics. 2008, 9 (Suppl 1): S3-10.1186/1471-2105-9-S1-S3. [ http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2259404n%26tool=pmcentrezn%26rendertype=abstract ]
28. Giuliano C, Lavelli A, Romano L: Exploiting shallow linguistic information for relation extraction from biomedical literature. Proceedings of the Eleventh Conference of the European Chapter of the Association for Computational Linguistics EACL2006. 2006, 18: 5-7. [ http://acl.ldc.upenn.edu/E/E06/E06-1051.pdf ]
29. Bundschus M, Dejori M, Stetter M, Tresp V, Kriegel HP: Extraction of semantic biomedical relations from text using conditional random fields. BMC Bioinformatics. 2008, 9: 207-10.1186/1471-2105-9-207. [ http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2386138n%26tool=pmcentrezn%26rendertype=abstract ]
30. Miyao Y, Sagae K, Sætre R, Matsuzaki T, Tsujii J: Evaluating contributions of natural language parsers to protein-protein interaction extraction. Bioinformatics. 2009, 25 (3): 394-400. 10.1093/bioinformatics/btn631. [ http://www.ncbi.nlm.nih.gov/pubmed/19073593 ]