Semantic annotation of biological concepts interplaying microbial cellular responses

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Carreira, Rafael ^a   Carneiro, Sónia ^a   Pereira, Rui ^a   Rocha, Miguel ^a   Rocha, Isabel ^a   Ferreira, Eugénio C ^a   Lourenço, Anália ^a  

^a UNIVERSITY OF MINHO   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATED EXTRACTION; BIOLOGICAL NETWORKS; BIOMEDICAL TEXT MININGS; GENETIC INFORMATION; LABORATORY TECHNIQUES; NUTRIENT-STARVATION; PHYSIOLOGICAL STATE; SEMANTIC ANNOTATIONS;

BIOMEDICAL ENGINEERING; COMPLEX NETWORKS; DATA MINING; ESCHERICHIA COLI; NATURAL LANGUAGE PROCESSING SYSTEMS; PROTEINS; RNA; SEMANTICS;

GENES;

ESCHERICHIA COLI;

BACTERIAL PROTEIN;

ARTICLE; COMPUTER PROGRAM; CYTOLOGY; DATA MINING; ESCHERICHIA COLI; GENETICS; HUMAN; LINGUISTICS; METABOLISM; NATURAL LANGUAGE PROCESSING; SEMANTICS;

BACTERIAL PROTEINS; DATA MINING; ESCHERICHIA COLI; HUMANS; NATURAL LANGUAGE PROCESSING; SEMANTICS; SOFTWARE; VOCABULARY, CONTROLLED;

EID: 82155187091     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-460     Document Type: Article

References (48)

1. Harmston N, Filsell W, Stumpf MP. What the papers say: Text mining for genomics and systems biology. Hum Genomics 2010, 5:17-29.
2. 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.
3. Kowald A, Schmeier S. Text mining for systems modeling. Methods Mol Biol 2011, 696:305-318. 10.1007/978-1-60761-987-1_19, 21063956.
4. 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:i374-i381. 10.1093/bioinformatics/btq221, 2881405, 20529930.
5. Rodriguez-Penagos C, Salgado H, Martinez-Flores I, Collado-Vides J. Automatic reconstruction of a bacterial regulatory network using Natural Language Processing. BMC Bioinformatics 2007, 8.
6. Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van LP, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De BP, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res 2008, 36:D107-D113. 10.1093/nar/gkn457, 2239002, 18006570.
7. Heinen S, Thielen B, Schomburg D. KID--an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes. BMC Bioinformatics 2010, 11:375. 10.1186/1471-2105-11-375, 2912889, 20626859.
8. Scheer M, Grote A, Chang A, Schomburg I, Munaretto C, Rother M, Sohngen C, Stelzer M, Thiele J, Schomburg D. BRENDA, the enzyme information system in 2011. Nucleic Acids Res 2011, 39:D670-D676. 10.1093/nar/gkq1089, 3013686, 21062828.
9. Bult CJ, Kadin JA, Richardson JE, Blake JA, Eppig JT. The Mouse Genome Database: enhancements and updates. Nucleic Acids Res 2010, 38:D586-D592. 10.1093/nar/gkp880, 2808942, 19864252.
10. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von MC. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009, 37:D412-D416. 10.1093/nar/gkn760, 2686466, 18940858.
11. Zaremba S, Ramos-Santacruz M, Hampton T, Shetty P, Fedorko J, Whitmore J, Greene JM, Perna NT, Glasner JD, Plunkett G, Shaker M, Pot D. Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens. BMC Bioinformatics 2009, 10:177. 10.1186/1471-2105-10-177, 2704210, 19515247.
12. Spasic I, Simeonidis E, Messiha HL, Paton NW, Kell DB. KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways. Bioinformatics 2009, 25:1404-1411. 10.1093/bioinformatics/btp175, 19336445.
13. Lourenço A, Carreira R, Carneiro S, Maia P, Glez-Peña D, Fdez-Riverola F, Ferreira EC, Rocha I, Rocha M. @Note: A workbench for Biomedical Text Mining. Journal of Biomedical Informatics 2009,
14. Kano Y, Dobson P, Nakanishi M, Tsujii J, Ananiadou S. Text mining meets workflow: linking U-Compare with Taverna. Bioinformatics 2010, 26:2486-2487. 10.1093/bioinformatics/btq464, 2944208, 20709690.
15. Krallinger M, Valencia A. BioCreative III, PPI Task. 2010, , http://www.biocreative.org/tasks/biocreative-iii/ppi/
16. Leitner F, Mardis SA, Krallinger M, Cesareni G, Hirschman LA, Valencia A. An Overview of BioCreative II.5. IEEE/ACM Trans Comput Biol Bioinform 2010, 7:385-399.
17. Hersh W, Bhupatiraju RT. TREC Genomics Track Overview. 2003, 14-23.
18. Hersh W, Bhupatiraju RT, Ross L, Johnson P, Cohen AM, Kraemer DF. TREC 2004 Genomics Track Overview. 2004, 13-31.
19. Kim JD, Ohta T, Pyysalo S, Kano Y, Tsujii J. Overview of BioNLP'09 shared task on event extraction. 2009, 1-9.
20. Kim JD, Ohta T, Tateisi Y, Tsujii J. GENIA corpus--semantically annotated corpus for bio-textmining. Bioinformatics 2003, 19(Suppl 1):i180-i182. 10.1093/bioinformatics/btg1023, 12855455.
21. 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.
22. Pyysalo S, Airola A, Heimonen J, Bjorne J, Ginter F, Salakoski T. Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics 2008, 9.
23. Tanabe L, Xie N, Thom LH, Matten W, Wilbur WJ. GENETAG: a tagged corpus for gene/protein named entity recognition. BMC Bioinformatics 2005, 6.
24. Thompson P, Iqbal SA, McNaught J, Ananiadou S. Construction of an annotated corpus to support biomedical information extraction. BMC Bioinformatics 2009, 10.
25. Leitner F, Krallinger M, Cesareni G, Valencia A. The FEBS Letters SDA corpus: a collection of protein interaction articles with high quality annotations for the BioCreative II.5 online challenge and the text mining community. FEBS Lett 2010, 584:4129-4130. 10.1016/j.febslet.2010.08.026, 20728446.
26. Cohen KB, Johnson HL, Verspoor K, Roeder C, Hunter LE. The structural and content aspects of abstracts versus bodies of full text journal articles are different. BMC Bioinformatics 2010, 11:492. 10.1186/1471-2105-11-492, 3098079, 20920264.
27. Settles B. ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text. Bioinformatics 2005, 21:3191-3192. 10.1093/bioinformatics/bti475, 15860559.
28. Corbett P, Batchelor C, Teufel S. Annotation of chemical named entities. BioNLP 2007: Biological, translational, and clinical language processing 2007, 57-64.
29. Mika S, Rost B. NLProt: extracting protein names and sequences from papers. Nucleic Acids Res 2004, 32:W634-W637. 10.1093/nar/gkh427, 441565, 15215466.
30. Tsuruoka Y, Tateishi Y, Kim JD, Ohta T, McNaught J, Ananiadou S, Tsujii J. Developing a robust part-of-speech tagger for biomedical text. Advances in Informatics, Proceedings 2005, 3746:382-392.
31. Leaman R, Gonzalez G. BANNER: an executable survey of advances in biomedical named entity recognition. Pac Symp Biocomput 2008, 652-663.
32. 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.
33. Wang H, Huang M, Zhu X. Extract interaction detection methods from the biological literature. BMC Bioinformatics 2009, 10(Suppl 1):S55. 10.1186/1471-2105-10-S1-S55, 2648772, 19208158.
34. Gerner M, Nenadic G, Bergman CM. LINNAEUS: a species name identification system for biomedical literature. BMC Bioinformatics 2010, 11:85. 10.1186/1471-2105-11-85, 2836304, 20149233.
35. Kim JD, Ohta T, Tsujii J. Corpus annotation for mining biomedical events from literature. BMC Bioinformatics 2008, 9.
36. Rajagopala SV, Goll J, Gowda ND, Sunil KC, Titz B, Mukherjee A, Mary SS, Raviswaran N, Poojari CS, Ramachandra S, Shtivelband S, Blazie SM, Hofmann J, Uetz P. MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions. Bioinformatics 2008, 24:2622-2627. 10.1093/bioinformatics/btn481, 2720748, 18786976.
37. Oda K, Kim JD, Ohta T, Okanohara D, Matsuzaki T, Tateisi Y, Tsujii J. New challenges for text mining: mapping between text and manually curated pathways. BMC Bioinformatics 2008, 9.
38. Rocha I, Forster J, Nielsen J. Design and application of genome-scale reconstructed metabolic models. Microbial Gene Essentiality: Protocols and Bioinformatics 2008, 416:409-431. Osterman AL, Gerdes S, In series: Methods in Molecular Biology.
39. Pinto JP, Dias O, Lourenço A, Carneiro S, Ferreira EC, Rocha I, Rocha M. Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. Advances in Soft Computing 2009, 92-101.
40. Mendes R, Lourenço A, Carneiro S, Ferreira EC, Rocha I, Rocha M. A Framework for the Integrated Analysis of Metabolic and Regulatory Networks. The 8th IEEE International Conference on BioInformatics and BioEngineering (IEEE BIBE 2008) 2008,
41. Carneiro S, Rocha I, Ferreira EC. Application of a genome-scale metabolic model to the inference of nutritional requirements and metabolic bottlenecks during recombinant protein production in Escherichia coli. Microb Cell Fact 2006, 5(Suppl 1).
42. Carneiro S, Amaral AL, Veloso AC, Dias T, Peres AM, Ferreira EC, Rocha I. Assessment of physiological conditions in E. coli fermentations by epifluorescent microscopy and image analysis. Biotechnol Prog 2009, 25:882-891. 10.1002/btpr.134, 19496165.
43. Carneiro S, Villas-Bôas S, Rocha I, Ferreira EC. Applying a metabolic footprinting approach to characterize the impact of the recombinant protein production in Escherichia coli. Advances in Soft Computing edition 2010, 193-200.
44. Lourenço A, Carreira R, Glez-Peña D, Méndez JR, Carneiro S, Rocha LM, Díaz F, Ferreira EC, Rocha I, Fdez-Riverola F, Rocha M. BioDR: Semantic indexing networks for biomedical document retrieval. Expert Systems with Applications 2010, 37:3444-3453.
45. Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD. EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 2010,
46. Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H. MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biol 2008, 9(Suppl 2):S5. 10.1186/gb-2008-9-s2-s5, 2559989, 18834496.
47. Lourenço A, Carreira R, Carneiro S, Maia P, Glez-Peña D, Fdez-Riverola F, Ferreira EC, Rocha I, Rocha M. @Note: A workbench for Biomedical Text Mining. Journal of Biomedical Informatics 2009,
48. Brants T. Inter-annotator agreement for a German newspaper corpus. In the Second International Conference on Language Resources and Evaluation (LREC-2000) 2000, 1435-1439.