OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Hunter, Lawrence ^a   Lu, Zhiyong ^b   Firby, James ^c   Baumgartner Jr , William A ^a   Johnson, Helen L ^a   Ogren, Philip V ^d   Cohen, K Bretonnel ^a  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c MICROSOFT   (United States)

^d UCB 450   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMEDICAL RESEARCH; EXTRACTING INFORMATION; FACTUAL INFORMATION; INFORMATION EXTRACTION SYSTEMS; PERFORMANCE STANDARDS; PROCESSING APPLICATIONS; PROTEIN INTERACTION; PROTEIN-PROTEIN INTERACTIONS;

GENE EXPRESSION; INFORMATION RETRIEVAL; INFORMATION RETRIEVAL SYSTEMS; KNOWLEDGE MANAGEMENT; KNOWLEDGE REPRESENTATION; PROTEINS; SEMANTICS; TEXT PROCESSING;

OPEN SYSTEMS;

ACCURACY; ANALYTICAL ERROR; ARTICLE; AUTOMATION; BIOINFORMATICS; CELL TYPE; COMPUTER SYSTEM; GENE EXPRESSION; INFORMATION RETRIEVAL; MEDICAL RESEARCH; MEDLINE; PROTEIN INTERACTION; PROTEIN TRANSPORT; SCORING SYSTEM; SEMANTICS; ALGORITHM; ATTITUDE TO HEALTH; BIOLOGICAL MODEL; CELL FUNCTION; COMPUTER PROGRAM; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PHYSIOLOGY; PROTEIN ANALYSIS; PUBLICATION;

ALGORITHMS; CELL PHYSIOLOGY; GENE EXPRESSION; HEALTH KNOWLEDGE, ATTITUDES, PRACTICE; INFORMATION STORAGE AND RETRIEVAL; MODELS, BIOLOGICAL; NATURAL LANGUAGE PROCESSING; PERIODICALS AS TOPIC; PROTEIN INTERACTION MAPPING; PROTEIN TRANSPORT; SOFTWARE;

EID: 41349107398     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-78     Document Type: Article

References (62)

1. Sparck Jones K Natural language processing: A historical review Current Issues in Computational Linguistics: In Honour of Don Walker (Ed Zampolli, Calzolari and Palmer), Amsterdam: Kluwer 1994.
2. Rebholz-Schuhmann D Kirsch H Couto F Facts from text - is text mining ready to deliver? PLoS Biol 2005, 3(2):e65. 548955 15719064 10.1371/ journal.pbio.0030065
3. Hoffmann R Valencia A A gene network for navigating the literature Nat Genet 2004/07/01 2004, 36(7):664. 10.1038/ng0704-664 15226743
4. Shah PK Jensen LJ Boué S Bork P Extraction of transcript diversity from scientific literature PLoS Comput Biol 2005, 1(1):e10. 1183516 16103899 10.1371/journal.pcbi.0010010
5. Horn F Lau AL Cohen FE Automated extraction of mutation data from the literature: Application of MuteXt to G protein-coupled receptors and nuclear hormone receptors Bioinformatics 2004, 20(4):557-568. 10.1093/ bioinformatics/btg449 14990452
6. Hu ZZ Narayanaswamy M Ravikumar KE Vijay-Shanker K Wu CH Literature mining and database annotation of protein phosphorylation using a rule-based system Bioinformatics 2005/04/09 2005, 21(11):2759-2765. 10.1093/bioinformatics/bti390 15814565
7. Saric J Jensen LJ Ouzounova R Rojas I Bork P Extraction of regulatory gene/protein networks from Medline Bioinformatics 2005/07/28 2006, 22(6):645-650. 10.1093/bioinformatics/bti597 16046493
8. Open Biomedical Ontologies Foundry http://obofoundry.org
9. Guarino N Formal ontology in information systems Trento, Italy, IOS Press 1998:3-15.
10. Hersh W Bhupatiraju R Ross L Johnson P Cohen A Kraemer D TREC 2004 Genomics track overview National Institute of Standards and Technology 2004.
11. Fellbaum C WordNet: An Electronic Lexical Database (Language, Speech, and Communication) MIT Press 1998.
12. Aronson A Effective Mapping of Biomedical Text to the UMLS Metathesaurus: The MetaMap Program AMIA Annu Symp Proc 2001:17-21.
13. Rindflesch TC Fiszman M The interaction of domain knowledge and linguistic structure in natural language processing: Interpreting hypernymic propositions in biomedical text J Biomed Inform 2003, 36(6):462-477. 10.1016/j.jbi.2003.11.003 14759819
14. Rindflesch TC Libbus B Hristovski D Aronson AR Kilicoglu H Semantic relations asserting the etiology of genetic diseases AMIA Annu Symp Proc 2004/01/20 2003:554-558. 1480275 14728234
15. Masseroli M Kilicoglu H Lang FM Rindflesch TC Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease BMC Bioinformatics 2006/06/10 2006, 7:291. 1564420 16762065 10.1186/1471-2105-7-291
16. Ahlers CB Fiszman M Demner-Fushman D Lang FM Rindflesch TC Extracting semantic predications from Medline citations for pharmacogenomics Pac Symp Biocomput 2007/11/10 2007:209-220. 17990493
17. Libbus B Kilicoglu H Rindflesch TC Mork JG Aronson AR Hirschman L Pustejovsky J Using Natural Language Processing, LocusLink and the Gene Ontology to Compare OMIM to MEDLINE HLT-NAACL 2004 Workshop: BioLINK 2004, Linking Biological Literature, Ontologies and Databases 2004:69-76.
18. 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 2000/04/29 1999:60-67. 10786287
19. Blaschke C Oliveros JC Valencia A Mining functional information associated with expression arrays Funct Integr Genomics 2002/01/17 2001, 1(4):256-268. 10.1007/s101420000036 11793245
20. Blaschke C Valencia A Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study Comparative and Functional Genomics 2001, 2(4):196-206. 10.1002/cfg.91
21. Huang M Zhu X Hao Y Payan DG Qu K Li M Discovering patterns to extract protein-protein interactions from biomedical full texts Proc JNLPBA,COLING 2004:22-28.
22. Temkin JM Gilder MR Extraction of protein interaction information from unstructured text using a context-free grammar Bioinformatics Oxford Univ Press 2003, 19(16):2046-2053. 10.1093/bioinformatics/btg279 14594709
23. Corney DP Buxton BF Langdon WB Jones DT BioRAT: Extracting biological information from full-length papers Bioinformatics 2004/07/03 2004, 20(17):3206-3213. 10.1093/bioinformatics/bth386 15231534
24. Park JC Kim HS Kim JJ Bidirectional incremental parsing for automatic pathway identification with combinatory categorial grammar Pac Symp Biocomput 2001:396-407. 11262958
25. Yakushiji A Tateisi Y Miyao Y Tsujii J Event extraction from biomedical papers using a full parser Pac Symp Biocomput 2001:408-419. 11262959
26. Gaizauskas R Demetriou G Artymiuk PJ Willett P Protein structures and information extraction from biological texts: The PASTA system Bioinformatics 2002/12/25 2003, 19(1):135-143. 10.1093/bioinformatics/ 19.1.135 12499303
27. Leroy G Chen H Martinez JD A shallow parser based on closed-class words to capture relations in biomedical text J Biomed Inform 2003, 36(3):145-158. 10.1016/S1532-0464(03)00039-X 14615225
28. Koike A Niwa Y Takagi T Automatic extraction of gene/protein biological functions from biomedical text Bioinformatics 2004/10/29 2005, 21(7):1227-1236. 10.1093/bioinformatics/bti084 15509601
29. 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. 1764447 17134476 10.1186/ 1471-2105-7-S3-S3
30. McInnes BT Pedersen T Pakhomov SV Determining the Syntactic Structure of Medical Terms in Clinical Notes Proc Assoc Comp Ling 2007.
31. Pyysalo S Ginter F Haverinen K Heimonen J Salakoski T Laippala V On the unification of syntactic annotations under the Stanford dependency scheme: A case study on BioInfer and GENIA Association for Computational Linguistics 2007.
32. Craven M Kumlien J Constructing biological knowledge bases by extracting information from text sources Proc Int Conf Intell Syst Mol Biol 1999:77-86. 10786289
33. Bunescu R Ge R Kate RJ Marcotte EM Mooney RJ Ramani AK Wong YW Comparative experiments on learning information extractors for proteins and their interactions Artif Intell Med 2005/04/07 2005, 33(2):139-155. 10.1016/j.artmed.2004.07.016 15811782
34. Krallinger M Leitner F Valencia A Assessment of the second BioCreative PPI task: Automatic extraction of protein-protein interactions. 2007:41-55.
35. Hunter L Cohen KB Biomedical Language Processing: What's Beyond PubMed? Molecular Cell Cell 2006, 21:589-594. 1702322 16507357 10.1016/ j.molcel.2006.02.012
36. Chen H Sharp BM Content-rich biological network constructed by mining PubMed abstracts BMC Bioinformatics 2004, 5:147. 528731 15473905 10.1186/ 1471-2105-5-147
37. NCBI Entrez Gene GeneRIF Help http://www.ncbi.nlm.nih.gov/projects/ GeneRIF/
38. Wattarujeekrit T Shah PK Collier N PASBio: Predicate-argument structures for event extraction in molecular biology BMC Bioinformatics 2004, 5:155-175. 535924 15494078 10.1186/1471-2105-5-155
39. Cohen KB Hunter L A critical review of PASBio's argument structures for biomedical verbs BMC Bioinformatics 2006, 7 Suppl. 3:S5. 1764449 17134478 10.1186/1471-2105-7-S3-S5
40. Rzhetsky A Iossifov I Koike T Krauthammer M Kra P Morris M Yu H Duboue PA Weng W Wilbur WJ Hatzivassiloglou V Friedman C GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data J Biomed Inform 2004/03/16 2004, 37(1):43-53. 10.1016/ j.jbi.2003.10.001 15016385
41. Narayanaswamy M Ravikumar KE Vijay-Shanker K Beyond the clause: extraction of phosphorylation information from medline abstracts Bioinformatics 2005, 21 Suppl 1. 15961474
42. BioCreAtIvE Challenge Evaluation http://biocreative.sourceforge.net
43. Hermjakob H Montecchi-Palazzi L Lewington C Mudali S Kerrien S Orchard S Vingron M Roechert B Roepstorff P Valencia A Margalit H Armstrong J Bairoch A Cesareni G Sherman D Apweiler R IntAct: An open source molecular interaction database Nucleic Acids Res 2003/12/19 2004, 32(Database issue):D452-5. 308786 14681455 10.1093/nar/gkh052
44. Ding J Berleant D Nettleton D Wurtele E Mining MEDLINE: Abstracts, Sentences, or Phrases? Pac Symp Biocomput 2002, 7:326-337.
45. Martin C Direct Memory Access Parsing Yale University 1992.
46. Fitzgerald W Building Embedded Conceptual Parsers Northwestern University 1994.
47. Noy NF Crubezy M Fergerson RW Knublauch H Tu SW Vendetti J Musen MA Protege-2000: An open-source ontology-development and knowledge-acquisition environment AMIA Annu Symp Proc 2004/01/20 2003:953. 1480139 14728458
48. Protégé http://protege.stanford.edu
49. Ferrucci D Lally A Building an example application with the unstructured information management architecture IBM Systems Journal IBM 2004, 43(3):455-475.
50. UIMA Java Framework http://uima-framework.sourceforge.net/
51. Apache UIMA http://incubator.apache.org/uima/
52. Hirschman L Colosimo M Morgan A Yeh A Overview of BioCreAtIvE task 1B: normalized gene lists BMC Bioinformatics 2005/06/18 2005, 6 Suppl 1:S11. 1869004 15960823 10.1186/1471-2105-6-S1-S11
53. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Harris MA Hill DP Issel-Tarver L Kasarskis A Lewis S Matese JC Richardson JE Ringwald M Rubin GM Sherlock G Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000/05/10 2000, 25(1):25-29. 10.1038/75556 10802651
54. Morgan A Lu Z Wang X Cohen AM Fluck J Ruch P Divoli A Fundel K Leaman R Hakenburg J Sun C Liu H Torres R Krauthhammer M Lau MW Hsu CN Schuemie M Hirschman L Overview of BioCreative II Gene Normalization Genome Biology 2008.
55. Settles B ABNER: An open source tool for automatically tagging genes, proteins and other entity names in text Bioinformatics 2005, 21(14):3191-3192. 10.1093/bioinformatics/bti475 15860559
56. Baumgartner WA Jr. Cohen KB Fox LM Acquaah-Mensah G Hunter L Manual curation is not sufficient for annotation of genomic databases Bioinformatics 2007, 23:14 e.
57. Leach SM Gabow AP Hunter L Goldberg D Assessing and combining reliability of protein interaction sources Pac Symp Biocomp 2007, 12:433-444.
58. Gabow AP Leach SM Baumgartner WA Jr. Hunter L Goldberg D Improving Protein Function Prediction Methods with Integrated Literature Data 2003.
59. Carpenter B Phrasal queries with LingPipe and Lucene: Ad hoc genomics text retrieval 13th Annual Text Retrieval Conference 2004.
60. Klein D Manning CD Fast Exact Inference with a Factored Model for Natural Language Parsing Advances in Neural Information Processing Systems MIT Press 2003:15.
61. Kehler A Appelt D Taylor L Simma A The (non) utility of predicate-argument frequencies for pronoun interpretation Proc of HLT-NAACL 2004, 4:289-296.
62. Ogren P Knowtator: A Protege plugin for annotated copus construction HLT-NAACL 2006:273.