Biblio-MetReS: A bibliometric network reconstruction application and server

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Usié, Anabel ^a,b   Karathia, Hiren ^b   Teixidó, Ivan ^a   Valls, Joan ^b   Faus, Xavier ^a   Alves, Rui ^b   Solsona, Francesc ^a  

^a UNIVERSITY OF LLEIDA   (Spain)

^b UNIVERSITY OF LLEIDA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED ANALYSIS; BIOLOGICAL ENTITIES; BIOMEDICAL RESEARCH; FULL-TEXT DOCUMENTS; MOLECULAR NETWORKS; NETWORK RECONSTRUCTION; SCIENTIFIC DOCUMENTS; USER-FRIENDLY TOOL;

ABSTRACTING; DATA MINING; GENES;

TOOLS;

ANIMAL; ARTICLE; BIBLIOMETRICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA MINING; GENE REGULATORY NETWORK; INTERNET; PUBLICATION;

ANIMALS; BIBLIOMETRICS; DATA MINING; GENE REGULATORY NETWORKS; INTERNET; PUBLICATIONS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 80053502299     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-387     Document Type: Article

References (40)

1. Alves R, Sorribas A. In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae. BMC Syst Biol 2007, 1:10. 10.1186/1752-0509-1-10, 1839888, 17408500.
2. Markowetz F, Spang R. Inferring cellular networks--a review. BMC Bioinformatics 2007, 8(Suppl 6):S5. 10.1186/1471-2105-8-S6-S5, 2230506, 18269699.
3. 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.
4. Hoffmann R, Valencia A. A gene network for navigating the literature. Nat Genet 2004, 36(7):664. 10.1038/ng0704-664, 15226743.
5. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Kruger B, Snel B, Bork P. STRING 7--recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 2007, (35 Database):D358-362.
6. 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.
7. Kemper B, Matsuzaki T, Matsuoka Y, Tsuruoka Y, Kitano H, Ananiadou S, Tsujii J. PathText: a text mining integrator for biological pathway visualizations. Bioinformatics 2010, 26(12):i374-381. 10.1093/bioinformatics/btq221, 2881405, 20529930.
8. Walport M, Kiley R. Open access, UK PubMed Central and the Wellcome Trust. J R Soc Med 2006, 99(9):438-439. 10.1258/jrsm.99.9.438, 1557892, 16946384.
9. Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R. Reflect: augmented browsing for the life scientist. Nat Biotechnol 2009, 27(6):508-510. 10.1038/nbt0609-508, 19513049.
10. Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A. Text processing through Web services: calling Whatizit. Bioinformatics 2008, 24(2):296-298. 10.1093/bioinformatics/btm557, 18006544.
11. Hakenberg J, Plake C, Schiemann T, Pankalla M, Leser U. ALIBABA: PubMed as a graph. Bioinformatics 2006, 22(19):2444-2445. 10.1093/bioinformatics/btl408, 16870931.
12. Krallinger M, Leitner F, Valencia A. Analysis of biological processes and diseases using text mining approaches. Methods Mol Biol 2010, 593:341-382. 10.1007/978-1-60327-194-3_16, 19957157.
13. Krallinger M, Valencia A, Hirschman L. Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol 2008, 9(Suppl 2):S8. 10.1186/gb-2008-9-s2-s8, 2559992, 18834499.
14. Hahn U, Valencia A. Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005). Bioinformatics 2006, 22(6):643-644. 10.1093/bioinformatics/btl084, 16527834.
15. Yuryev A, Mulyukov Z, Kotelnikova E, Maslov S, Egorov S, Nikitin A, Daraselia N, Mazo I. Automatic pathway building in biological association networks. BMC Bioinformatics 2006, 7:171. 10.1186/1471-2105-7-171, 1435941, 16563163.
16. Overby CL, Tarczy-Hornoch P, Demner-Fushman D. The potential for automated question answering in the context of genomic medicine: an assessment of existing resources and properties of answers. BMC Bioinformatics 2009, 10(Suppl 9):S8. 10.1186/1471-2105-10-S9-S8, 2788359, 19958518.
17. Krallinger M, Morgan A, Smith L, Leitner F, Tanabe L, Wilbur J, Hirschman L, Valencia A. Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge. Genome Biol 2008, 9(Suppl 2):S1. 10.1186/gb-2008-9-s2-s1, 2559980, 18834487.
18. Hu ZZ, Mani I, Hermoso V, Liu H, Wu CH. iProLINK: an integrated protein resource for literature mining. Comput Biol Chem 2004, 28(5-6):409-416. 10.1016/j.compbiolchem.2004.09.010, 15556482.
19. de Bruijn B, Martin J. Getting to the ©ore of knowledge: mining biomedical literature. Int J Med Inform 2002, 67(1-3):7-18. 10.1016/S1386-5056(02)00050-3, 12460628.
20. Shah PK, Perez-Iratxeta C, Bork P, Andrade MA. Information extraction from full text scientific articles: where are the keywords?. BMC Bioinformatics 2003, 4:20. 10.1186/1471-2105-4-20, 166134, 12775220.
21. Nuzzo A, Mulas F, Gabetta M, Arbustini E, Zupan B, Larizza C, Bellazzi R. Text Mining approaches for automated literature knowledge extraction and representation. Stud Health Technol Inform 2010, 160(Pt 2):954-958.
22. Song YL, Chen SS. Text mining biomedical literature for constructing gene regulatory networks. Interdiscip Sci 2009, 1(3):179-186.
23. Ananiadou S, Pyysalo S, Tsujii J, Kell DB. Event extraction for systems biology by text mining the literature. Trends Biotechnol 2010, 28(7):381-390. 10.1016/j.tibtech.2010.04.005, 20570001.
24. Laakso M, Hautaniemi S. Integrative platform to translate gene sets to networks. Bioinformatics 2010, 26(14):1802-1803. 10.1093/bioinformatics/btq277, 20507894.
25. Bandy J, Milward D, McQuay S. Mining protein-protein interactions from published literature using Linguamatics I2E. Methods Mol Biol 2009, 563:3-13. 10.1007/978-1-60761-175-2_1, 19597777.
26. 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.
27. Saetre R, Yoshida K, Miwa M, Matsuzaki T, Kano Y, Tsujii J. Extracting Protein Interactions from Text with the Unified AkaneRE Event Extraction System. Ieee-Acm Transactions on Computational Biology and Bioinformatics 2010, 7(3):442-453.
28. Kolchinsky A, Abi-Haidar A, Kaur J, Hamed AA, Rocha LM. Classification of Protein-Protein Interaction Full-Text Documents Using Text and Citation Network Features. Ieee-Acm Transactions on Computational Biology and Bioinformatics 2010, 7(3):400-411.
29. Dai HJ, Lai PT, Tsai RTH. Multistage Gene Normalization and SVM-Based Ranking for Protein Interactor Extraction in Full-Text Articles. Ieee-Acm Transactions on Computational Biology and Bioinformatics 2010, 7(3):412-420.
30. Chen YF, Liu F, Manderick B. BioLMiner System: Interaction Normalization Task and Interaction Pair Task in the BioCreative II.5 Challenge. Ieee-Acm Transactions on Computational Biology and Bioinformatics 2010, 7(3):428-441.
31. Ohta T, Matsuzaki T, Okazaki N, Miwa M, Saetre R, Pyysalo S, Tsujii J. Medie and Info-pubmed: 2010 update. BMC Bioinformatics 2010, 11(Suppl 5):7. 10.1186/1471-2105-11-S5-P7, 2806359, 20051126.
32. Lin J. Is searching full text more effective than searching abstracts?. BMC Bioinformatics 2009, 10:46. 10.1186/1471-2105-10-46, 2695361, 19192280.
33. McIntosh T, Curran JR. Challenges for automatically extracting molecular interactions from full-text articles. BMC Bioinformatics 2009, 10:311. 10.1186/1471-2105-10-311, 2761905, 19778419.
34. Lourenco A, Carreira R, Carneiro S, Maia P, Glez-Pena D, Fdez-Riverola F, Ferreira EC, Rocha I, Rocha M. @Note: a workbench for biomedical text mining. J Biomed Inform 2009, 42(4):710-720. 10.1016/j.jbi.2009.04.002, 19393341.
35. Lourenco A, Carreira R, Glez-Pena D, Mendez JR, Carneiro S, Rocha LM, Diaz F, Ferreira EC, Rocha I, Fdez-Riverola F, et al. BioDR: Semantic indexing networks for biomedical document retrieval. Expert Systems with Applications 2010, 37(4):3444-3453.
36. Aoki KF, Kanehisa M. Using the KEGG database resource. Curr Protoc Bioinformatics 2005, Chapter 1. Unit 1 12.
37. Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH. The NCBI BioSystems database. Nucleic Acids Res 2010, (38 Database):D492-496.
38. 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.
39. Stapley B, Benoit G. Bibliometrics: Information Retrieval and Visualization from Co-occurrence of Gene Names in Medline Abstracts. Proceedings of the Pacific Symposium on Bio-computing 2000,
40. Steele E, Tucker A, t Hoen PA, Schuemie MJ. Literature-based priors for gene regulatory networks. Bioinformatics 2009, 25(14):1768-1774. 10.1093/bioinformatics/btp277, 19389730.