Using UMLS to construct a generalized hierarchical concept-based dictionary of brain functions for information extraction from the fMRI literature

Journal of Biomedical Informatics

Volumn 42, Issue 5, 2009, Pages 912-922

  Hsiao, Mei Yu ^a   Chen, Chien Chung ^a   Chen, Jyh Horng ^a  

^a NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

Brain function association model; Human brain study; Neuroinformatics; Term classification; Term recognition

Indexed keywords

AUTOMATIC INFORMATION EXTRACTION; BRAIN FUNCTIONS; CONCEPT-BASED; HUMAN BRAIN; HUMAN BRAIN STUDY; HUMAN EXPERT; INFORMATION EXTRACTION; INFORMATION EXTRACTION SYSTEMS; NEUROINFORMATICS; PRECISION AND RECALL; TERM CLASSIFICATION; TERM RECOGNITION; UNIFIED MEDICAL LANGUAGE SYSTEMS;

BRAIN;

INFORMATION ANALYSIS;

ARTICLE; BRAIN FUNCTION; CLASSIFICATION ALGORITHM; CLINICAL FEATURE; CONCEPT ANALYSIS; CONTROLLED STUDY; DATA ANALYSIS; DATA EXTRACTION; FUNCTIONAL MAGNETIC RESONANCE IMAGING; IMAGE ANALYSIS; INFORMATION RETRIEVAL; INFORMATION SYSTEM; PRIORITY JOURNAL;

ALGORITHMS; BRAIN; BRAIN MAPPING; DICTIONARIES, MEDICAL; HUMANS; INFORMATION STORAGE AND RETRIEVAL; MAGNETIC RESONANCE IMAGING; MEDICAL INFORMATICS; MODELS, NEUROLOGICAL; NATURAL LANGUAGE PROCESSING; TERMINOLOGY AS TOPIC; UNIFIED MEDICAL LANGUAGE SYSTEM;

EID: 70349438867     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2009.04.003     Document Type: Article

References (34)

1. Ogawa S., Tank D.W., Menon R., Ellermann J.M., Kim S.G., Merkle H., et al. Intrinsic signal changes accompanying sensory stimulation: functional brain mapping with magnetic resonance imaging. Proc Natl Acad Sci USA 89 13 (1992) 5951-5965
2. BrainMap. Available from: http://brainmap.org/.
3. Laird A.R., Lancaster J.L., and Fox P.T. BrainMap: the social evolution of a human brain mapping database. Neuroinformatics 3 1 (2005) 65-78
4. Lancaster J.L., Woldorff M.G., Parsons L.M., Liotti M., Freitas C.S., Rainey L., et al. Automated Talairach Atlas labels for functional brain mapping. Hum Brain Mapp 10 3 (2000) 120-131
5. Zhou L., Tao Y., Cimino J.J., Chen E.S., Liu H., Lussier Y.A., et al. Terminology model discovery using natural language processing and visualization techniques. J Biomed Inform 39 6 (2006) 626-636
6. Califf M.E., and Mooney R.J. Relational learning of pattern-match rules for information extraction. Working notes of AAAI spring symposium on applying machine learning to discourse processing (1998) 6-11
7. Hu Z.Z., Narayanaswamy M., Ravikumar K.E., Vijay-Shanker K., and Wu C.H. Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinformatics 21 11 (2005) 2759-2765
8. Jimeno A., Jimenez-Ruiz E., Lee V., Gaudan S., Berlanga R., and Rebholz-Schuhmann D. Assessment of disease named entity recognition on a corpus of annotated sentences. BMC Bioinformatics 9 Suppl. 3 (2008) S3
9. Hou W.J., and Chen H.H. Enhancing performance of protein and gene name recognizers with filtering and integration strategies. J Biomed Inform 37 6 (2004) 448-460
10. Schuemie M.J., Mons B., Weeber M., and Kors J.A. Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification. J Biomed Inform 40 3 (2007) 316-324
11. Tsuruoka Y., and Tsujii J. Improving the performance of dictionary-based approaches in protein name recognition. J Biomed Inform 37 6 (2004) 461-470
12. Saric J., Jensen L.J., Ouzounova R., Rojas I., and Bork P. Extraction of regulatory gene/protein networks from Medline. Bioinformatics 22 6 (2006) 645
13. Domedel-Puig N., and Wernisch L. Applying GIFT, a gene interactions finder in text, to fly literature. Bioinformatics 21 17 (2005) 3582-3583
14. Liu Y., Navathe S.B., Civera J., Dasigi V., Ram A., Ciliax B.J., et al. Text mining biomedical literature for discovering gene-to-gene relationships: a comparative study of algorithms. IEEE/ACM Trans Comput Biol Bioinform 2 1 (2005) 62-76
15. Rinaldi F., Schneider G., Kaljurand K., Hess M., Andronis C., Konstandi O., et al. Mining of relations between proteins over biomedical scientific literature using a deep-linguistic approach. Artif Intell Med 39 2 (2007) 127-136
16. Crasto C.J., Marenco L.N., Migliore M., Mao B., Nadkarni P.M., Miller P., et al. Text mining neuroscience journal articles to populate neuroscience databases. Neuroinformatics 1 3 (2003) 215-237
17. Burns G.A., Khan A.M., Ghandeharizadeh S., O'Neill M.A., and Chen Y.S. Tools and approaches for the construction of knowledge models from the neuroscientific literature. Neuroinformatics 1 1 (2003) 81-109
18. Kotter R. Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac database. Neuroinformatics 2 2 (2004) 127-144
19. Srinivas P.R., Gusfield D., Mason O., Gertz M., Hogarth M., Stone J., et al. Neuroanatomical term generation and comparison between two terminologies. Neuroinformatics 1 2 (2003) 177-192
20. Talos I.F., Rubin D.L., Halle M., Musen M., and Kikinis R. A prototype symbolic model of canonical functional neuroanatomy of the motor system. J Biomed Inform 41 2 (2008) 251-263
21. NeuroScholar. Available from: http://www.neuroscholar.org/.
22. Burns G., and Hovy E. The NeuroScholar system as a natural language processing platform for the neuroscience literature (2006), The Society for Neuroscience Annual Meeting, Washington, DC
23. Burns G, Feng D, Ingulfsen T, Hovy E. Infrastructure for annotation-driven information extraction from the primary scientific literature: principles and practice. Services on 2007 IEEE Congress; 2007. p. 122-9.
24. Nielsen F.A., Hansen L.K., and Balslev D. Mining for associations between text and brain activation in a functional neuroimaging database. Neuroinformatics 2 4 (2004) 369-380
25. Foundational Model of Anatomy. Available from: http://fma.biostr.washington.edu.
26. NeuroNames. Available from: http://braininfo.rprc.washington.edu/indexabout.html.
27. Bowden D.M., and Martin R.F. NeuroNames brain hierarchy. Neuroimage 2 1 (1995) 63-83
28. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res 32 Database issue (2004) D267-D270
29. Zhang L., Perl Y., Halper M., Geller J., and Hripcsak G. A lexical metaschema for the UMLS semantic network. Artif Intell Med 33 1 (2005) 41-59
30. Brill E. A simple rule-based part of speech tagger. In: Proceedings of the third conference on applied natural language processing. Trento, Italy; 1992.
31. Heja G., and Surjan G. Using n-gram method in the decomposition of compound medical diagnoses. Int J Med Inform 70 2-3 (2003) 229-236
32. Efron B., and Tibshirani R. Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. Stat Sci 1 1 (1986) 54-77
33. Solso R.L., MacLin O.H., and MacLin M.K. Cognitive psychology. 8th ed. (2007), Allyn and Bacon, Boston
34. Kolb B., and Whishaw I.Q. Fundamentals of human neuropsychology. 5th ed. (2003), Worth Publishers, New York