메뉴 건너뛰기




Volumn 5, Issue 3, 2004, Pages 213-222

Ontologies in biology: Design, applications and future challenges

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; BIOINFORMATICS; CYTOLOGY; DATA BASE; GENE EXPRESSION; GENE MAPPING; GENETIC ANALYSIS; GENETIC CODE; PHENOTYPE; PRIORITY JOURNAL; PUBLICATION; QUANTITATIVE TRAIT LOCUS; REVIEW; SEMANTICS;

EID: 1542290452     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrg1295     Document Type: Review
Times cited : (285)

References (34)
  • 4
    • 0038745614 scopus 로고    scopus 로고
    • Integrating biological databases
    • Stein, L. D. Integrating biological databases. Nature Rev. Genet. 4, 337-345 (2003).
    • (2003) Nature Rev. Genet. , vol.4 , pp. 337-345
    • Stein, L.D.1
  • 6
    • 18444394318 scopus 로고    scopus 로고
    • Rat Genome Database (RGD): Mapping disease onto the genome
    • Twigger, S. et al Rat Genome Database (RGD): mapping disease onto the genome. Nucleic Acids Res. 30, 125-128 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 125-128
    • Twigger, S.1
  • 7
    • 19044393068 scopus 로고    scopus 로고
    • TAIR: A resource for integrated Arabidopsis data
    • Garcia-Hernandez, M. et al. TAIR: a resource for integrated Arabidopsis data. Funct. Integr. Genomics 2, 230-253 (2002).
    • (2002) Funct. Integr. Genomics , vol.2 , pp. 230-253
    • Garcia-Hernandez, M.1
  • 9
    • 0035293755 scopus 로고    scopus 로고
    • Phenotypic data in FlyBase
    • Drysdale, R. Phenotypic data in FlyBase. Brief Bioinform. 2, 68-80 (2001). An early example of the use of multiple ontologies to describe phenotype.
    • (2001) Brief Bioinform. , vol.2 , pp. 68-80
    • Drysdale, R.1
  • 10
    • 12244283747 scopus 로고    scopus 로고
    • Gramene, a tool for grass genomics
    • Ware, D. H. et al. Gramene, a tool for grass genomics. Plant Physiol. 130, 1606-1613 (2002).
    • (2002) Plant Physiol. , vol.130 , pp. 1606-1613
    • Ware, D.H.1
  • 12
    • 9144226240 scopus 로고    scopus 로고
    • Pathbase: A database of mutant mouse pathology
    • Schofield, P. N. et al. Pathbase: a database of mutant mouse pathology. Nucleic Acids Res. 32, D512-D515 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Schofield, P.N.1
  • 13
    • 0346494819 scopus 로고    scopus 로고
    • MetaCyc: A multiorganism database of metabolic pathways and enzymes
    • Krieger, C. J. et al. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32, D438-D442 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Krieger, C.J.1
  • 14
    • 0036088113 scopus 로고    scopus 로고
    • PharmGKB: The Pharmacogenetics Knowledge Base
    • Hewett, M. et al. PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res. 30, 163-165 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 163-165
    • Hewett, M.1
  • 15
    • 0036907158 scopus 로고    scopus 로고
    • Extension and integration of the gene ontology (GO): Combining GO vocabularies with external vocabulanes
    • Hill, D. P., Blake, J. A., Richardson, J. E. & Ringwald, M. Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabulanes. Genome Res. 12, 1982-1991 (2002). Proposes a way to generate more specific ontologies by combining concepts from two orthogonal ontologies.
    • (2002) Genome Res. , vol.12 , pp. 1982-1991
    • Hill, D.P.1    Blake, J.A.2    Richardson, J.E.3    Ringwald, M.4
  • 16
    • 0037316317 scopus 로고    scopus 로고
    • Positional candidate gene selection from livestock EST databases using Gene Ontology
    • Harhay, G. P. & Keele, J. W. Positional candidate gene selection from livestock EST databases using Gene Ontology. Bioinformatics 19, 249-255 (2003).
    • (2003) Bioinformatics , vol.19 , pp. 249-255
    • Harhay, G.P.1    Keele, J.W.2
  • 17
    • 0037109195 scopus 로고    scopus 로고
    • GeneCensus: Genome comparisons in terms of metabolic pathway activity and protein family sharing
    • Lin, J. et al. GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. Nucleic Acids Res. 30, 4574-4582 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4574-4582
    • Lin, J.1
  • 18
    • 0042121055 scopus 로고    scopus 로고
    • Onto-Tools, the toolkit of the modem biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
    • Draghici, S. et al. Onto-Tools, the toolkit of the modem biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res. 31, 3775-3781 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3775-3781
    • Draghici, S.1
  • 19
    • 9144256665 scopus 로고    scopus 로고
    • Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms
    • Christie, K. R. et al. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 32, D311-D314 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Christie, K.R.1
  • 20
    • 1542272766 scopus 로고    scopus 로고
    • Predicting phenotype from patterns of annotation
    • King, O. D. et al. Predicting phenotype from patterns of annotation. Bioinformatics 19 (Suppl. 1), 1183-1189 (2003). Uses decision trees to predict phenotypes of yeast mutants on the basis of genes' annotations to GO and other phenotypic descriptions.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1 , pp. 1183-1189
    • King, O.D.1
  • 21
    • 0041627703 scopus 로고    scopus 로고
    • Linking molecular imaging terminology to the gene ontology (GO)
    • Tulipano, P. K., Millar, W. S. & Cimino, J. J. Linking molecular imaging terminology to the gene ontology (GO). Pac. Symp. Biocomput. 613-623 (2003).
    • (2003) Pac. Symp. Biocomput. , pp. 613-623
    • Tulipano, P.K.1    Millar, W.S.2    Cimino, J.J.3
  • 22
    • 0036357370 scopus 로고    scopus 로고
    • Evaluation of the UMLS as a terminology and knowledge resource for biomedical informatics
    • Bodenreider, O., Mitchell, J. A. & McCray, A. T. Evaluation of the UMLS as a terminology and knowledge resource for biomedical informatics. Proc. AMIA Symp. 61-65 (2002).
    • (2002) Proc. AMIA Sym. , pp. 61-65
    • Bodenreider, O.1    Mitchell, J.A.2    McCray, A.T.3
  • 23
    • 0035530511 scopus 로고    scopus 로고
    • Meeting medical terminology needs - The Ontology-Enhanced Medical Concept Mapper
    • Leroy, G. & Chen, H. Meeting medical terminology needs - the Ontology-Enhanced Medical Concept Mapper. IEEE Trans. Inf Technol. Biomed. 5, 261-270 (2001). Describes a query tool that involves the mapping of different concepts using human-created ontologies and natural language processing.
    • (2001) IEEE Trans. Inf Technol. Biomed. , vol.5 , pp. 261-270
    • Leroy, G.1    Chen, H.2
  • 24
    • 1542332887 scopus 로고    scopus 로고
    • Evaluation of WordNet as a source of lay knowledge for molecular biology and genetic diseases: A feasibility study
    • Bodenreider, O., Burgun, A. & Mitchell, J. A. Evaluation of WordNet as a source of lay knowledge for molecular biology and genetic diseases: a feasibility study. Stud. Health Technol. Inform. 95, 379-384 (2003). Maps GO terms and NCBl's LocusUnk terms to WordNet to determine the overlap between molecular biological and lay knowledge.
    • (2003) Stud. Health Technol. Inform. , vol.95 , pp. 379-384
    • Bodenreider, O.1    Burgun, A.2    Mitchell, J.A.3
  • 26
    • 0035234673 scopus 로고    scopus 로고
    • A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems
    • RESEARCH0012
    • Cook, D. L., Farley, J. F. & Tapscott, S. J. A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems. Genome Biol. 2, RESEARCH0012 (2001). Provides a lexicon of icons to graphically represent molecular biology information.
    • (2001) Genome Biol. , vol.2
    • Cook, D.L.1    Farley, J.F.2    Tapscott, S.J.3
  • 27
    • 0037022306 scopus 로고    scopus 로고
    • Global organization of the WordNet lexicon
    • Sigman, M. & Cecchi, G. A. Global organization of the WordNet lexicon. Proc. Natl Acad. Sci. USA 99, 1742-1747 (2002). Applies graph theoretical calculations to analyse the organization of WordNet.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1742-1747
    • Sigman, M.1    Cecchi, G.A.2
  • 28
    • 0034667776 scopus 로고    scopus 로고
    • A heunstic graph comparison algorithm and its application to detect functionally related enzyme clusters
    • Ogata, H., Fujibuchi, W., Goto, S. & Kanehisa, M. A heunstic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Res. 28, 4021-4028 (2000). Uses graph comparison methods to correlate the genome locations of microbial genes and these organisms' metabolic pathways.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4021-4028
    • Ogata, H.1    Fujibuchi, W.2    Goto, S.3    Kanehisa, M.4
  • 29
    • 0037880376 scopus 로고    scopus 로고
    • Ontologies: Formalising biological knowledge for bioinformatics
    • Bard, J. Ontologies: formalising biological knowledge for bioinformatics. Bioessays 25, 501-506 (2003).
    • (2003) Bioessays , vol.25 , pp. 501-506
    • Bard, J.1
  • 30
    • 0031968567 scopus 로고    scopus 로고
    • Motivation and organizational principles for anatomical knowledge representation: The digital anatomist symbolic knowledge base
    • Rosse, C. et al. Motivation and organizational principles for anatomical knowledge representation: the digital anatomist symbolic knowledge base. J. Am. Med. Inform. Assoc. 5, 17-40 (1998), Proposes a human anatomy ontology that accommodates both the systemic and regional (topographical) views of anatomy.
    • (1998) J. Am. Med. Inform. Assoc. , vol.5 , pp. 17-40
    • Rosse, C.1
  • 31
    • 18344415387 scopus 로고    scopus 로고
    • GALEN: A third generation terminology tool to support a multipurpose national coding system for surgical procedures
    • Trombert-Paviot, B. et al. GALEN: a third generation terminology tool to support a multipurpose national coding system for surgical procedures. Int. J. Med. Inf. 58-59, 71-85 (2000). Provides an information-management architecture for handling all types of clinical data in language-independent ways.
    • (2000) Int. J. Med. Inf. , vol.58-59 , pp. 71-85
    • Trombert-Paviot, B.1
  • 32
    • 0346801873 scopus 로고    scopus 로고
    • The Gene Ontology (GO) database and informatics resource
    • Harris, M. A. et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-D261 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Harris, M.A.1
  • 33
    • 9144253908 scopus 로고    scopus 로고
    • The mouse Gene Expression Database (GXD): Updates and enhancements
    • Hill, D. P. et al. The mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res. 32, D568-D571 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Hill, D.P.1
  • 34
    • 1542332886 scopus 로고    scopus 로고
    • Protege-2000: An open-source ontology-development and knowledge-acquisition environment
    • Noy, N. P. et al. Protege-2000: an open-source ontology-development and knowledge-acquisition environment. Proc. AMIA Symp. 953 (2003).
    • (2003) Proc. AMIA Sym. , pp. 953
    • Noy, N.P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.