메뉴 건너뛰기




Volumn 42, Issue 5, 2009, Pages 824-830

Text-mining approach to evaluate terms for ontology development

Author keywords

Hypergeometric test; Ontology development; PubMed; Text mining

Indexed keywords

HYPERGEOMETRIC TEST; LITERATURE DATABASE; OBJECTIVE METHODS; ONTOLOGY DEVELOPMENT; PUBMED; TEXT MINING;

EID: 70349459664     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2009.03.009     Document Type: Article
Times cited : (14)

References (37)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The gene ontology consortium
    • Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25 1 (2000) 25-29
    • (2000) Nat Genet , vol.25 , Issue.1 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5    Cherry, J.M.6
  • 2
    • 13244249634 scopus 로고    scopus 로고
    • Handling multiple testing while interpreting microarrays with the Gene Ontology Database
    • Osier M.V., Zhao H., and Cheung K.H. Handling multiple testing while interpreting microarrays with the Gene Ontology Database. BMC Bioinformatics 5 1 (2004) 124
    • (2004) BMC Bioinformatics , vol.5 , Issue.1 , pp. 124
    • Osier, M.V.1    Zhao, H.2    Cheung, K.H.3
  • 3
    • 1542399989 scopus 로고    scopus 로고
    • FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
    • Al-Shahrour F., Diaz-Uriarte R., and Dopazo J. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20 4 (2004) 578-580
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 578-580
    • Al-Shahrour, F.1    Diaz-Uriarte, R.2    Dopazo, J.3
  • 4
    • 1242314757 scopus 로고    scopus 로고
    • Targeted cellular process profiling approach for uterine leiomyoma using cDNA microarray, proteomics and gene ontology analysis
    • Ahn W.S., Kim K.W., Bae S.M., Yoon J.H., Lee J.M., Namkoong S.E., et al. Targeted cellular process profiling approach for uterine leiomyoma using cDNA microarray, proteomics and gene ontology analysis. Int J Exp Pathol 84 6 (2003) 267-279
    • (2003) Int J Exp Pathol , vol.84 , Issue.6 , pp. 267-279
    • Ahn, W.S.1    Kim, K.W.2    Bae, S.M.3    Yoon, J.H.4    Lee, J.M.5    Namkoong, S.E.6
  • 5
    • 0042128690 scopus 로고    scopus 로고
    • Functional discrimination of gene expression patterns in terms of the gene ontology
    • Badea L. Functional discrimination of gene expression patterns in terms of the gene ontology. Pac Symp Biocomput (2003) 565-576
    • (2003) Pac Symp Biocomput , pp. 565-576
    • Badea, L.1
  • 6
    • 0037263812 scopus 로고    scopus 로고
    • MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
    • Doniger S.W., Salomonis N., Dahlquist K.D., Vranizan K., Lawlor S.C., and Conklin B.R. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol 4 1 (2003) R7
    • (2003) Genome Biol , vol.4 , Issue.1
    • Doniger, S.W.1    Salomonis, N.2    Dahlquist, K.D.3    Vranizan, K.4    Lawlor, S.C.5    Conklin, B.R.6
  • 7
    • 0038729567 scopus 로고    scopus 로고
    • Learning rule-based models of biological process from gene expression time profiles using gene ontology
    • Hvidsten T.R., Laegreid A., and Komorowski J. Learning rule-based models of biological process from gene expression time profiles using gene ontology. Bioinformatics 19 9 (2003) 1116-1123
    • (2003) Bioinformatics , vol.19 , Issue.9 , pp. 1116-1123
    • Hvidsten, T.R.1    Laegreid, A.2    Komorowski, J.3
  • 8
    • 0038492417 scopus 로고    scopus 로고
    • A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
    • Troyanskaya O.G., Dolinski K., Owen A.B., Altman R.B., and Botstein D. A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci USA 100 14 (2003) 8348-8353
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.14 , pp. 8348-8353
    • Troyanskaya, O.G.1    Dolinski, K.2    Owen, A.B.3    Altman, R.B.4    Botstein, D.5
  • 9
    • 0042121250 scopus 로고    scopus 로고
    • ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis
    • Zhong S., Li C., and Wong W.H. ChipInfo: software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res 31 13 (2003) 3483-3486
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3483-3486
    • Zhong, S.1    Li, C.2    Wong, W.H.3
  • 10
    • 13244249628 scopus 로고    scopus 로고
    • Visualization and analysis of microarray and gene ontology data with treemaps
    • Baehrecke E.H., Dang N., Babaria K., and Shneiderman B. Visualization and analysis of microarray and gene ontology data with treemaps. BMC Bioinformatics 5 1 (2004) 84
    • (2004) BMC Bioinformatics , vol.5 , Issue.1 , pp. 84
    • Baehrecke, E.H.1    Dang, N.2    Babaria, K.3    Shneiderman, B.4
  • 11
    • 12344269924 scopus 로고    scopus 로고
    • GO: TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • Boyle E.I., Weng S., Gollub J., Jin H., Botstein D., Cherry J.M., et al. GO: TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20 18 (2004) 3710-3715
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3710-3715
    • Boyle, E.I.1    Weng, S.2    Gollub, J.3    Jin, H.4    Botstein, D.5    Cherry, J.M.6
  • 12
    • 3242887152 scopus 로고    scopus 로고
    • Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments
    • Khatri P., Bhavsar P., Bawa G., and Draghici S. Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. Nucleic Acids Res 32 Web Server issue (2004) W449-W456
    • (2004) Nucleic Acids Res , vol.32 , Issue.Web Server issue
    • Khatri, P.1    Bhavsar, P.2    Bawa, G.3    Draghici, S.4
  • 13
    • 3142673366 scopus 로고    scopus 로고
    • Using the gene ontology for mi-croarray data mining: a comparison of methods and application to age effects in human prefrontal cortex
    • Pavlidis P., Qin J., Arango V., Mann J.J., and Sibille E. Using the gene ontology for mi-croarray data mining: a comparison of methods and application to age effects in human prefrontal cortex. Neurochem Res 29 6 (2004) 1213-1222
    • (2004) Neurochem Res , vol.29 , Issue.6 , pp. 1213-1222
    • Pavlidis, P.1    Qin, J.2    Arango, V.3    Mann, J.J.4    Sibille, E.5
  • 14
    • 0004745667 scopus 로고    scopus 로고
    • Study and implementation of combined techniques for automatic extraction of terminology
    • Resnik P., and Klavans J. (Eds), MIT Press, Cambridge, MA
    • Daille B. Study and implementation of combined techniques for automatic extraction of terminology. In: Resnik P., and Klavans J. (Eds). The balancing act: combining symbolic and statistical approaches to language (1996), MIT Press, Cambridge, MA 49-66
    • (1996) The balancing act: combining symbolic and statistical approaches to language , pp. 49-66
    • Daille, B.1
  • 15
    • 78650633610 scopus 로고    scopus 로고
    • Automatic recognition of multi-word terms: the C-value/NC-value method
    • Frantzi K., Ananiadou S., and Mima H. Automatic recognition of multi-word terms: the C-value/NC-value method. Int J Digit Librar 3 2 (2000) 115-130
    • (2000) Int J Digit Librar , vol.3 , Issue.2 , pp. 115-130
    • Frantzi, K.1    Ananiadou, S.2    Mima, H.3
  • 16
    • 0034567337 scopus 로고    scopus 로고
    • A general method for sifting linguistic knowledge from structured terminologies
    • Grabar N., and Zweigenbaum P. A general method for sifting linguistic knowledge from structured terminologies. Proc AMIA Symp (2000) 310-314
    • (2000) Proc AMIA Symp , pp. 310-314
    • Grabar, N.1    Zweigenbaum, P.2
  • 17
    • 0042096721 scopus 로고    scopus 로고
    • Corpus linguistics and terminology extraction
    • Wright S, Budin G, editors, Amsterdam & Philadelphia: John Benjamins Publishing Co
    • Ahmad K, Rogers MA. Corpus linguistics and terminology extraction. In: Wright S, Budin G, editors. Hand-book of terminology management, vol. 2. Amsterdam & Philadelphia: John Benjamins Publishing Co.;2001. p. 725-60.
    • (2001) Hand-book of terminology management , vol.2 , pp. 725-760
    • Ahmad, K.1    Rogers, M.A.2
  • 18
    • 16544388629 scopus 로고    scopus 로고
    • A data-driven approach for extracting "the most specific term" for ontology development
    • Savova G.K., Harris M., Johnson T., Pakhomov S.V., and Chute C.G. A data-driven approach for extracting "the most specific term" for ontology development. AMIA Annu Symp Proc (2003) 579-583
    • (2003) AMIA Annu Symp Proc , pp. 579-583
    • Savova, G.K.1    Harris, M.2    Johnson, T.3    Pakhomov, S.V.4    Chute, C.G.5
  • 19
    • 25144475427 scopus 로고    scopus 로고
    • Cimiano P, Volker J. Text2Onto - A framework for ontology learning and data-driven change discovery. In: 10th International Conference on Applications of Natural Language to Information Systems (NLDB 2005): 2005; Alicante. Spain: Springer; 2005. p. 227-38.
    • Cimiano P, Volker J. Text2Onto - A framework for ontology learning and data-driven change discovery. In: 10th International Conference on Applications of Natural Language to Information Systems (NLDB 2005): 2005; Alicante. Spain: Springer; 2005. p. 227-38.
  • 20
    • 9544255696 scopus 로고    scopus 로고
    • Retrieving definitional content for ontology development
    • Smith L., and Wilbur W.J. Retrieving definitional content for ontology development. Comput Biol Chem 28 5-6 (2004) 387-391
    • (2004) Comput Biol Chem , vol.28 , Issue.5-6 , pp. 387-391
    • Smith, L.1    Wilbur, W.J.2
  • 21
    • 33746752066 scopus 로고    scopus 로고
    • The use of concept maps during knowledge elicitation in ontology development processes - the nutrigenomics use case
    • Castro A.G., Rocca-Serra P., Stevens R., Taylor C., Nashar K., Ragan M.A., et al. The use of concept maps during knowledge elicitation in ontology development processes - the nutrigenomics use case. BMC Bioinformatics 7 (2006) 267
    • (2006) BMC Bioinformatics , vol.7 , pp. 267
    • Castro, A.G.1    Rocca-Serra, P.2    Stevens, R.3    Taylor, C.4    Nashar, K.5    Ragan, M.A.6
  • 22
    • 44649186340 scopus 로고    scopus 로고
    • Terminologies for text-mining; an experiment in the lipoprotein metabolism domain
    • Alexopoulou D., Wachter T., Pickersgill L., Eyre C., and Schroeder M. Terminologies for text-mining; an experiment in the lipoprotein metabolism domain. BMC Bioinformatics 9 Suppl. 4 (2008) S2
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 4
    • Alexopoulou, D.1    Wachter, T.2    Pickersgill, L.3    Eyre, C.4    Schroeder, M.5
  • 23
    • 22944440839 scopus 로고    scopus 로고
    • Learning domain ontologies from document warehouses and dedicated web sites
    • Navigli R., and Velardi P. Learning domain ontologies from document warehouses and dedicated web sites. Comput Linguist 30 2 (2004) 151-179
    • (2004) Comput Linguist , vol.30 , Issue.2 , pp. 151-179
    • Navigli, R.1    Velardi, P.2
  • 24
    • 0034571816 scopus 로고    scopus 로고
    • Ontology acquisition from on-line knowledge sources
    • Li Q., Shilane P., Noy N.F., and Musen M.A. Ontology acquisition from on-line knowledge sources. Proc AMIA Symp (2000) 497-501
    • (2000) Proc AMIA Symp , pp. 497-501
    • Li, Q.1    Shilane, P.2    Noy, N.F.3    Musen, M.A.4
  • 25
    • 0037396730 scopus 로고    scopus 로고
    • The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro
    • Camon E., Magrane M., Barrell D., Binns D., Fleischmann W., Kersey P., et al. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res 13 4 (2003) 662-672
    • (2003) Genome Res , vol.13 , Issue.4 , pp. 662-672
    • Camon, E.1    Magrane, M.2    Barrell, D.3    Binns, D.4    Fleischmann, W.5    Kersey, P.6
  • 26
    • 33847264343 scopus 로고    scopus 로고
    • Enrichment or depletion of a GO category within a class of genes: which test?
    • Rivals I., Personnaz L., Taing L., and Potier M.C. Enrichment or depletion of a GO category within a class of genes: which test?. Bioinformatics 23 4 (2007) 401-407
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 401-407
    • Rivals, I.1    Personnaz, L.2    Taing, L.3    Potier, M.C.4
  • 27
    • 70349468319 scopus 로고    scopus 로고
    • OCI. Available from
    • OCI. Available from: http://www.bioontology.org/wiki/index.php/OCI:Main_Page.
  • 28
    • 0017547820 scopus 로고
    • A fast string searching algorithm
    • Boyer R., and Moore J. A fast string searching algorithm. Commun ACM 20 (1977) 762-772
    • (1977) Commun ACM , vol.20 , pp. 762-772
    • Boyer, R.1    Moore, J.2
  • 30
    • 0003535936 scopus 로고    scopus 로고
    • 2nd ed. Hoboken, New Jersey: John Wiley & Sons, Inc
    • Agresti A. Categorical data analysis, 2nd ed. Hoboken, New Jersey: John Wiley & Sons, Inc.; 2002.
    • (2002) Categorical data analysis
    • Agresti, A.1
  • 32
    • 70349454531 scopus 로고    scopus 로고
    • GSL-GNU Scientific Library. Available from
    • GSL-GNU Scientific Library. Available from: http://www.gnu.org/software/gsl/.
  • 33
    • 24744459879 scopus 로고    scopus 로고
    • Ceramide regulation of the tumor suppressor phosphatase PTEN in rafts isolated from neurotumor cell lines
    • Goswami R., Singh D., Phillips G., Kilkus J., and Dawson G. Ceramide regulation of the tumor suppressor phosphatase PTEN in rafts isolated from neurotumor cell lines. J Neurosci Res 81 4 (2005) 541-550
    • (2005) J Neurosci Res , vol.81 , Issue.4 , pp. 541-550
    • Goswami, R.1    Singh, D.2    Phillips, G.3    Kilkus, J.4    Dawson, G.5
  • 34
    • 70349470141 scopus 로고    scopus 로고
    • Available from
    • Available from: http://www.cdisc.org/index.html.
  • 35
    • 49949083854 scopus 로고    scopus 로고
    • The gene ontology as a source of lexical semantic knowledge for a biological natural language processing application
    • August, 1st, Toronto, CA;
    • Verspoor CM, Joslyn C, Papcun GJ. The gene ontology as a source of lexical semantic knowledge for a biological natural language processing application. In: SIGIR'03 workshop on text analysis and search for bioinformatics, August, 1st 2003. Toronto, CA; 2003. p. 51-6.
    • (2003) SIGIR'03 workshop on text analysis and search for bioinformatics , pp. 51-56
    • Verspoor, C.M.1    Joslyn, C.2    Papcun, G.J.3
  • 36
    • 84937298585 scopus 로고
    • Principled disambiguation: discriminating adjective senses with modified nouns
    • Justeson J.S., and Katz S.M. Principled disambiguation: discriminating adjective senses with modified nouns. Comput Linguist 21 1 (1995) 1-27
    • (1995) Comput Linguist , vol.21 , Issue.1 , pp. 1-27
    • Justeson, J.S.1    Katz, S.M.2
  • 37
    • 41649118959 scopus 로고    scopus 로고
    • An open-source framework for large-scale, flexible evaluation of biomedical text mining systems
    • Baumgartner Jr. W.A., Cohen K.B., and Hunter L. An open-source framework for large-scale, flexible evaluation of biomedical text mining systems. J Biomed Discov Collab 3 (2008) 1
    • (2008) J Biomed Discov Collab , vol.3 , pp. 1
    • Baumgartner Jr., W.A.1    Cohen, K.B.2    Hunter, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.