PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Barbosa Silva, Adriano ^a   Fontaine, Jean Fred ^a   Donnard, Elisa R ^b,c   Stussi, Fernanda ^b   Ortega, J M ^b   Andrade Navarro, Miguel A ^a  

^a MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^b FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

^c LUDWIG INSTITUTE FOR CANCER RESEARCH   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

AMOUNT OF INTERACTION; BIOLOGICAL FUNCTIONS; BIOLOGICAL MECHANISMS; BIOMEDICAL LITERATURE; INTERACTION NETWORKS; PLATFORM INDEPENDENT; PROTEIN AGGREGATION; WEB-BASED TOOLS;

ABSTRACTING; ACTIVE NETWORKS; GENES; TOOLS;

PROTEINS;

PROTEIN;

ARTICLE; COLORECTAL TUMOR; COMPUTER PROGRAM; DATA MINING; DEGENERATIVE DISEASE; GENETICS; HUMAN; INTERNET; MEDLINE; METABOLISM;

COLORECTAL NEOPLASMS; DATA MINING; HUMANS; INTERNET; NEURODEGENERATIVE DISEASES; PROTEINS; PUBMED; SOFTWARE;

EID: 82455162310     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-435     Document Type: Article

References (40)

1. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2011, (39 Database):D38-51.
2. Lu Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database (Oxford) 2011, 2011:baq036.
3. Iliopoulos I, Enright AJ, Ouzounis CA. Textquest: document clustering of Medline abstracts for concept discovery in molecular biology. Pac Symp Biocomput 2001, 384-395.
4. Perez-Iratxeta C, Bork P, Andrade MA. XplorMed: a tool for exploring MEDLINE abstracts. Trends Biochem Sci 2001, 26(9):573-575. 10.1016/S0968-0004(01)01926-0, 11551795.
5. Kashyap A, Hristidis V, Petropoulos M, Tavoulari S. Effective Navigation of Query Results Based on Concept Hierarchies. IEEE Transactions on Knowledge and Data Engineering 2011, 23(4):540-553.
6. Fontaine JF, Priller F, Barbosa-Silva A, Andrade-Navarro MA. Genie: literature-based gene prioritization at multi genomic scale. Nucleic Acids Res 2011, (39 Web Server):W455-461.
7. Matos S, Arrais JP, Maia-Rodrigues J, Oliveira JL. Concept-based query expansion for retrieving gene related publications from MEDLINE. BMC Bioinformatics 2010, 11:212. 10.1186/1471-2105-11-212, 2873540, 20426836.
8. Hur J, Schuyler AD, States DJ, Feldman EL. SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics 2009, 25(6):838-840. 10.1093/bioinformatics/btp049, 2654801, 19188191.
9. Shatkay H, Edwards S, Wilbur WJ, Boguski M. Genes, themes and microarrays: using information retrieval for large-scale gene analysis. Proc Int Conf Intell Syst Mol Biol 2000, 8:317-328.
10. Renner A, Aszodi A. High-throughput functional annotation of novel gene products using document clustering. Pac Symp Biocomput 2000, 54-68.
11. Chagoyen M, Carmona-Saez P, Shatkay H, Carazo JM, Pascual-Montano A. Discovering semantic features in the literature: a foundation for building functional associations. BMC Bioinformatics 2006, 7:41. 10.1186/1471-2105-7-41, 1386711, 16438716.
12. Blaschke C, Andrade MA, Ouzounis C, Valencia A. Automatic extraction of biological information from scientific text: protein-protein interactions. Proc Int Conf Intell Syst Mol Biol 1999, 60-67.
13. Marcotte EM, Xenarios I, Eisenberg D. Mining literature for protein-protein interactions. Bioinformatics 2001, 17(4):359-363. 10.1093/bioinformatics/17.4.359, 11301305.
14. Hoffmann R, Valencia A. Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 2005, 21(Suppl 2):ii252-258. 10.1093/bioinformatics/bti1142, 16204114.
15. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, et al. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009, (37 Database):D412-416.
16. Plake C, Schiemann T, Pankalla M, Hakenberg J, Leser U. AliBaba: PubMed as a graph. Bioinformatics 2006, 22(19):2444-2445. 10.1093/bioinformatics/btl408, 16870931.
17. Barbosa-Silva A, Soldatos TG, Magalhaes IL, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM. LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships. BMC Bioinformatics 2010, 11:70. 10.1186/1471-2105-11-70, 3098111, 20122157.
18. Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2005, (33 Database):D54-58.
19. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, et al. The Universal Protein Resource (UniProt). Nucleic Acids Res 2005, (33 Database):D154-159.
20. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res 2008, (36 Database):D25-30.
21. Fontaine JF, Barbosa-Silva A, Schaefer M, Huska MR, Muro EM, Andrade-Navarro MA. MedlineRanker: flexible ranking of biomedical literature. Nucleic Acids Res 2009, (37 Web Server):W141-146.
22. Mika S, Rost B. NLProt: extracting protein names and sequences from papers. Nucleic Acids Res 2004, (32 Web Server):W634-637.
23. Xie H, Wasserman A, Levine Z, Novik A, Grebinskiy V, Shoshan A, Mintz L. Large-scale protein annotation through gene ontology. Genome Res 2002, 12(5):785-794. 10.1101/gr.86902, 186564, 11997345.
24. Perez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA. Gene annotation from scientific literature using mappings between keyword systems. Bioinformatics 2004, 20(13):2084-2091. 10.1093/bioinformatics/bth207, 15059832.
25. Hooper SD, Bork P. Medusa: a simple tool for interaction graph analysis. Bioinformatics 2005, 21(24):4432-4433. 10.1093/bioinformatics/bti696, 16188923.
26. Olson JM, Goddard KA, Dudek DM. The amyloid precursor protein locus and very-late-onset Alzheimer disease. Am J Hum Genet 2001, 69(4):895-899. 10.1086/323472, 1226076, 11500807.
27. Spillantini MG, Schmidt ML, Lee VM, Trojanowski JQ, Jakes R, Goedert M. Alpha-synuclein in Lewy bodies. Nature 1997, 388(6645):839-840. 10.1038/42166, 9278044.
28. Tsigelny IF, Crews L, Desplats P, Shaked GM, Sharikov Y, Mizuno H, Spencer B, Rockenstein E, Trejo M, Platoshyn O, et al. Mechanisms of hybrid oligomer formation in the pathogenesis of combined Alzheimer's and Parkinson's diseases. PLoS One 2008, 3(9):e3135. 10.1371/journal.pone.0003135, 2519786, 18769546.
29. Moussa CE. Parkin attenuates wild-type tau modification in the presence of beta-amyloid and alpha-synuclein. J Mol Neurosci 2009, 37(1):25-36. 10.1007/s12031-008-9099-x, 18561034.
30. Herbst A, Kolligs FT. Wnt signaling as a therapeutic target for cancer. Methods Mol Biol 2007, 361:63-91.
31. Gottardi CJ, Wong E, Gumbiner BM. E-cadherin suppresses cellular transformation by inhibiting beta-catenin signaling in an adhesion-independent manner. J Cell Biol 2001, 153(5):1049-1060. 10.1083/jcb.153.5.1049, 2174337, 11381089.
32. Guo L, Zhong D, Lau S, Liu X, Dong XY, Sun X, Yang VW, Vertino PM, Moreno CS, Varma V, et al. Sox7 Is an independent checkpoint for beta-catenin function in prostate and colon epithelial cells. Mol Cancer Res 2008, 6(9):1421-1430. 10.1158/1541-7786.MCR-07-2175, 2652859, 18819930.
33. Kolligs FT, Bommer G, Goke B. Wnt/beta-catenin/tcf signaling: a critical pathway in gastrointestinal tumorigenesis. Digestion 2002, 66(3):131-144. 10.1159/000066755, 12481159.
34. Dihlmann S, Kloor M, Fallsehr C, von Knebel Doeberitz M. Regulation of AKT1 expression by beta-catenin/Tcf/Lef signaling in colorectal cancer cells. Carcinogenesis 2005, 26(9):1503-1512. 10.1093/carcin/bgi120, 15888491.
35. Halder SK, Rachakonda G, Deane NG, Datta PK. Smad7 induces hepatic metastasis in colorectal cancer. Br J Cancer 2008, 99(6):957-965. 10.1038/sj.bjc.6604562, 2538763, 18781153.
36. Bunescu R, Ge R, Kate R, Marcotte E, Mooney R, Ramani A, Wong Y. Comparative Experiments on Learning Information Extractors for Proteins and their Interactions. Artif Intell Med, Summarization and Information Extraction from Medical Documents 2005, 33:139-155.
37. Leaman R, Gonzalez G. BANNER: an executable survey of advances in biomedical named entity recognition. Pac Symp Biocomput 2008, 652-663.
38. Aronson AR. MetaMap: Mapping Text to the UMLS Metathesaurus. 2006, , http://skr.nlm.nih.gov/papers/references/metamap06.pdf
39. Bjorne J, Ginter F, Pyysalo S, Tsujii J, Salakoski T. Complex event extraction at PubMed scale. Bioinformatics 2010, 26(12):i382-390. 10.1093/bioinformatics/btq180, 2881365, 20529932.
40. Miwa M, Saetre R, Kim JD, Tsujii J. Event extraction with complex event classification using rich features. J Bioinform Comput Biol 2010, 8(1):131-146. 10.1142/S0219720010004586, 20183879.