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Volumn 2014, Issue , 2014, Pages

Overview of the gene ontology task at BioCreative IV

(26)  Mao, Yuqing a   Van Auken, Kimberly b   Li, Donghui c   Arighi, Cecilia N d   McQuilton, Peter e   Hayman, G Thomas f   Tweedie, Susan e   Schaeffer, Mary L g   Laulederkind, Stanley J F f   Wang, Shur Jen f   Gobeill, Julien h,i   Ruch, Patrick h,i   Luu, Anh Tuan j   Kim, Jung Jae j   Chiang, Jung Hsien k   Chen, Yu De k   Yang, Chia Jung k,l   Liu, Hongfang m   Zhu, Dongqing d,m   Li, Yanpeng n   more..


Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGY; DATA MINING; GENE ONTOLOGY; HUMAN; MOLECULAR GENETICS; PROCEDURES; REPRODUCIBILITY;

EID: 84996554576     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau086     Document Type: Review
Times cited : (41)

References (67)
  • 1
    • 77950550898 scopus 로고    scopus 로고
    • Representing ontogeny through ontology: A developmental biologist's guide to the gene ontology
    • Hill, D.P., Berardini, T.Z., Howe, D.G. et al. (2010) Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology. Mol. Reprod. Dev., 77, 314-329.
    • (2010) Mol. Reprod. Dev. , vol.77 , pp. 314-329
    • Hill, D.P.1    Berardini, T.Z.2    Howe, D.G.3
  • 2
    • 84879394069 scopus 로고    scopus 로고
    • Use of gene ontology annotation to understand the peroxisome proteome in humans
    • Mutowo-Meullenet, P., Huntley, R.P., Dimmer, E.C. et al. (2013) Use of gene ontology annotation to understand the peroxisome proteome in humans. Database, 2013, bas062.
    • (2013) Database , vol.2013
    • Mutowo-Meullenet, P.1    Huntley, R.P.2    Dimmer, E.C.3
  • 3
    • 34547693374 scopus 로고    scopus 로고
    • Incorporation of gene ontology annotations to enhance micro-array data analysis
    • Ochs, M.F., Peterson, A.J., Kossenkov, A. et al. (2007) Incorporation of gene ontology annotations to enhance micro-array data analysis. Methods Mol. Biol., 377, 243-254.
    • (2007) Methods Mol. Biol. , vol.377 , pp. 243-254
    • Ochs, M.F.1    Peterson, A.J.2    Kossenkov, A.3
  • 4
    • 15944386344 scopus 로고    scopus 로고
    • GO molecular function terms are predictive of subcellular localization
    • Lu, Z. and Hunter, L. (2005) GO molecular function terms are predictive of subcellular localization. Pac. Symp. Biocomput., 2005, 151-161.
    • (2005) Pac. Symp. Biocomput , vol.2005 , pp. 151-161
    • Lu, Z.1    Hunter, L.2
  • 5
    • 84874253819 scopus 로고    scopus 로고
    • Gene ontology annotations and resources
    • Gene Ontology Consortium, Blake, J.A., Dolan, M. et al. (2013) Gene Ontology annotations and resources. Nucleic Acids Res., 41, D530-D535.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D530-D535
    • Blake, J.A.1    Dolan, M.2
  • 6
    • 84892683484 scopus 로고    scopus 로고
    • A guide to best practices for gene ontology (GO) manual annotation
    • Balakrishnan, R., Harris, M.A., Huntley, R. et al. (2013) A guide to best practices for Gene Ontology (GO) manual annotation. Database, 2013, bat054.
    • (2013) Database , vol.2013
    • Balakrishnan, R.1    Harris, M.A.2    Huntley, R.3
  • 7
    • 84876462011 scopus 로고    scopus 로고
    • Biocuration workflows and text mining: Overview of the BioCreative 2012 workshop track II
    • Lu, Z. and Hirschman, L. (2012) Biocuration workflows and text mining: overview of the BioCreative 2012 workshop track II. Database, 2012, bas043.
    • (2012) Database , vol.2012
    • Lu, Z.1    Hirschman, L.2
  • 8
    • 84876480423 scopus 로고    scopus 로고
    • Building an efficient curation workflow for the arabidopsis literature corpus
    • Li, D., Berardini, T.Z., Muller, R.J. et al. (2012) Building an efficient curation workflow for the Arabidopsis literature corpus. Database, 2012, bas047.
    • (2012) Database , vol.2012
    • Li, D.1    Berardini, T.Z.2    Muller, R.J.3
  • 9
    • 84876501269 scopus 로고    scopus 로고
    • BioCreative-2012 virtual issue
    • Wu, C.H., Arighi, C.N., Cohen, K.B. et al. (2012) BioCreative-2012 virtual issue. Database, 2012, bas049.
    • (2012) Database , vol.2012
    • Wu, C.H.1    Arighi, C.N.2    Cohen, K.B.3
  • 10
    • 84879330505 scopus 로고    scopus 로고
    • An overview of the BioCreative 2012 workshop track III: Interactive text mining task
    • Arighi, C.N., Carterette, B., Cohen, K.B. et al. (2013) An overview of the BioCreative 2012 workshop track III: interactive text mining task. Database, 2013, bas056.
    • (2013) Database , vol.2013
    • Arighi, C.N.1    Carterette, B.2    Cohen, K.B.3
  • 11
    • 84876499465 scopus 로고    scopus 로고
    • Accelerating literature curation with text-mining tools: A case study of using PubTator to curate genes in PubMed abstracts
    • Wei, C.H., Harris, B.R., Li, D. et al. (2012) Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database, 2012, bas041.
    • (2012) Database , vol.2012
    • Wei, C.H.1    Harris, B.R.2    Li, D.3
  • 12
    • 84864051137 scopus 로고    scopus 로고
    • Improving links between literature and biological data with text mining: A case study with GEO, PDB and MEDLINE
    • Neveol, A., Wilbur, W.J. and Lu, Z. (2012) Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. Database, 2012, bas026.
    • (2012) Database , vol.2012
    • Neveol, A.1    Wilbur, W.J.2    Lu, Z.3
  • 13
    • 84861878785 scopus 로고    scopus 로고
    • PubTator: A pubmed-like interactive curation system for document triage and literature curation
    • Washington, DC
    • Wei, C.-H., Kao, H.-Y. and Lu, Z. (2012) PubTator: a pubmed-like interactive curation system for document triage and literature curation. In: Proceedings of the BioCreative 2012 Workshop, Washington, DC, pp. 20-24.
    • (2012) Proceedings of the BioCreative 2012 Workshop , pp. 20-24
    • Wei, C.-H.1    Kao, H.-Y.2    Lu, Z.3
  • 14
    • 84883572716 scopus 로고    scopus 로고
    • PubTator: A web-based text mining tool for assisting biocuration
    • Wei, C.-H., Kao, H.-Y. and Lu, Z. (2013) PubTator: a web-based text mining tool for assisting Biocuration. Nucleic Acids Res., 41, W518-W522.
    • (2013) Nucleic Acids Res. , vol.41 , pp. W518-W522
    • Wei, C.-H.1    Kao, H.-Y.2    Lu, Z.3
  • 15
    • 82255163997 scopus 로고    scopus 로고
    • Extraction of data deposition statements from the literature: A method for automatically tracking research results
    • Neveol, A., Wilbur, W.J. and Lu, Z. (2011) Extraction of data deposition statements from the literature: a method for automatically tracking research results. Bioinformatics, 27, 3306-3312.
    • (2011) Bioinformatics , vol.27 , pp. 3306-3312
    • Neveol, A.1    Wilbur, W.J.2    Lu, Z.3
  • 16
  • 17
    • 34547831875 scopus 로고    scopus 로고
    • GeneRIF quality assurance as summary revision
    • Lu, Z., Cohen, K.B. and Hunter, L. (2007) GeneRIF quality assurance as summary revision. Pac. Symp. Biocomput. 2007, 269-280.
    • (2007) Pac. Symp. Biocomput , vol.2007 , pp. 269-280
    • Lu, Z.1    Cohen, K.B.2    Hunter, L.3
  • 18
    • 39049181601 scopus 로고    scopus 로고
    • Finding GeneRIFs via gene ontology annotations
    • Lu, Z., Cohen, K.B. and Hunter, L. (2006) Finding GeneRIFs via gene ontology annotations. Pac. Symp. Biocomput., 2006, 52-63.
    • (2006) Pac. Symp. Biocomput , vol.2006 , pp. 52-63
    • Lu, Z.1    Cohen, K.B.2    Hunter, L.3
  • 19
    • 84878376462 scopus 로고    scopus 로고
    • GeneRIF indexing: Sentence selection based on Machine learning
    • Jimeno-Yepes, A.J., Sticco, J.C., Mork, J.G. et al. (2013) GeneRIF indexing: sentence selection based on machine learning. BMC Bioinformatics, 14, 171.
    • (2013) BMC Bioinformatics , vol.14 , pp. 171
    • Jimeno-Yepes, A.J.1    Sticco, J.C.2    Mork, J.G.3
  • 20
    • 79952765434 scopus 로고    scopus 로고
    • Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction
    • Névéol, A., Islamaj Doǧan, R. and Lu, Z. (2011) Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. J. Biomed. Inform., 44, 310-318.
    • (2011) J. Biomed. Inform. , vol.44 , pp. 310-318
    • Névéol, A.1    Islamaj Doǧan, R.2    Lu, Z.3
  • 21
    • 70350455266 scopus 로고    scopus 로고
    • Semi-automated curation of protein subcellular localization: A text mining-based approach to gene ontology (GO) cellular component curation
    • Van Auken, K., Jaffery, J., Chan, J. et al. (2009) Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular component curation. BMC Bioinformatics, 10, 228.
    • (2009) BMC Bioinformatics , vol.10 , pp. 228
    • Van Auken, K.1    Jaffery, J.2    Chan, J.3
  • 22
  • 23
    • 33947311528 scopus 로고    scopus 로고
    • An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
    • Camon, E.B., Barrell, D.G., Dimmer, E.C. et al. (2005) An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics, 6(Suppl. 1), S17.
    • (2005) BMC Bioinformatics , vol.6 , pp. S17
    • Camon, E.B.1    Barrell, D.G.2    Dimmer, E.C.3
  • 24
    • 51049088875 scopus 로고    scopus 로고
    • Overview of the protein-protein interaction annotation extraction task of BioCreative II
    • Krallinger, M., Leitner, F., Rodriguez-Penagos, C. et al. (2008) Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome Biol., 9(Suppl. 2), S4.
    • (2008) Genome Biol. , vol.9 , pp. S4
    • Krallinger, M.1    Leitner, F.2    Rodriguez-Penagos, C.3
  • 25
    • 80052774027 scopus 로고    scopus 로고
    • The gene Normalization task in BioCreative III
    • Lu, Z., Kao, H.Y., Wei, C.H. et al. (2011) The gene normalization task in BioCreative III. BMC Bioinformatics, 12(Suppl. 8), S2.
    • (2011) BMC Bioinformatics , vol.12 , pp. S2
    • Lu, Z.1    Kao, H.Y.2    Wei, C.H.3
  • 26
    • 80053392951 scopus 로고    scopus 로고
    • Overview of BioCreative III gene Normalization
    • Bethesda, MD, USA
    • Lu, Z. and Wilbur, W.J. (2010) Overview of BioCreative III Gene Normalization. In: Proceedings of the BioCreative III Workshop, Bethesda, MD, USA, pp. 24-45.
    • (2010) Proceedings of the BioCreative III Workshop , pp. 24-45
    • Lu, Z.1    Wilbur, W.J.2
  • 27
    • 84876273527 scopus 로고    scopus 로고
    • Large-scale event extraction from literature with multi-level gene Normalization
    • Van Landeghem, S., Bjorne, J., Wei, C.H. et al. (2013) Large-scale event extraction from literature with multi-level gene normalization. PLoS One, 8, e55814.
    • (2013) PLoS One , vol.8
    • Van Landeghem, S.1    Bjorne, J.2    Wei, C.H.3
  • 28
    • 33750289197 scopus 로고    scopus 로고
    • The TREC 2004 genomics track categorization task: Classifying full text biomedical documents
    • Cohen, A.M. and Hersh, W.R. (2006) The TREC 2004 genomics track categorization task: classifying full text biomedical documents. J. Biomed. Discov. Collab., 1, 4.
    • (2006) J. Biomed. Discov. Collab. , vol.1 , pp. 4
    • Cohen, A.M.1    Hersh, W.R.2
  • 29
    • 37849005226 scopus 로고    scopus 로고
    • Text mining on GeneRIFs
    • Ph.D. Thesis. University of Colorado School of Medicine, Aurora, USA
    • Lu, Z. (2007) Text Mining on GeneRIFs. Computaitonal bioscience program. Ph.D. Thesis. University of Colorado School of Medicine, Aurora, USA.
    • (2007) Computaitonal Bioscience Program
    • Lu, Z.1
  • 32
    • 80053244362 scopus 로고    scopus 로고
    • Recommending MeSH terms for annotating biomedical articles
    • Huang, M., Neveol, A. and Lu, Z. (2011) Recommending MeSH terms for annotating biomedical articles. J. Am. Med. Inform. Assoc., 18, 660-667.
    • (2011) J. Am. Med. Inform. Assoc. , vol.18 , pp. 660-667
    • Huang, M.1    Neveol, A.2    Lu, Z.3
  • 33
    • 70349440994 scopus 로고    scopus 로고
    • A recent advance in the automatic indexing of the biomedical literature
    • Neveol, A., Shooshan, S.E., Humphrey, S.M. et al. (2009) A recent advance in the automatic indexing of the biomedical literature. J. Biomed. Inform., 42, 814-823.
    • (2009) J. Biomed. Inform. , vol.42 , pp. 814-823
    • Neveol, A.1    Shooshan, S.E.2    Humphrey, S.M.3
  • 34
    • 77956268182 scopus 로고    scopus 로고
    • Reflective random indexing for semi-automatic indexing of the biomedical literature
    • Vasuki, V. and Cohen, T. (2010) Reflective random indexing for semi-automatic indexing of the biomedical literature. J. Biomed. Inform., 43, 694-700.
    • (2010) J. Biomed. Inform. , vol.43 , pp. 694-700
    • Vasuki, V.1    Cohen, T.2
  • 39
    • 84892753494 scopus 로고    scopus 로고
    • BioC: A Minimalist approach to interoperability for biomedical text processing
    • Comeau, D.C., Islamaj Dogan, R., Ciccarese, P. et al. (2013) BioC: a minimalist approach to interoperability for biomedical text processing. Database, 2013, bat064.
    • (2013) Database , vol.2013
    • Comeau, D.C.1    Islamaj Dogan, R.2    Ciccarese, P.3
  • 42
    • 34248172904 scopus 로고    scopus 로고
    • Measures of semantic similarity and relatedness in the biomedical domain
    • Pedersen, T., Pakhomov, S.V., Patwardhan, S. et al. (2007) Measures of semantic similarity and relatedness in the biomedical domain. J. Biomed. Inform., 40, 288-299.
    • (2007) J. Biomed. Inform. , vol.40 , pp. 288-299
    • Pedersen, T.1    Pakhomov, S.V.2    Patwardhan, S.3
  • 44
    • 33645107704 scopus 로고    scopus 로고
    • Automatic assignment of biomedical categories: Toward a generic approach
    • Ruch, P. (2006) Automatic assignment of biomedical categories: toward a generic approach. Bioinformatics, 22, 658-664.
    • (2006) Bioinformatics , vol.22 , pp. 658-664
    • Ruch, P.1
  • 45
    • 84890551036 scopus 로고    scopus 로고
    • Answering gene ontology terms to proteomics questions by supervised macro reading in medline
    • Gobeill, J., Pasche, E., Teodoro, D. et al. (2012) Answering gene ontology terms to proteomics questions by supervised macro reading in Medline. EMBnet. J., 18, 29-31.
    • (2012) EMBnet. J. , vol.18 , pp. 29-31
    • Gobeill, J.1    Pasche, E.2    Teodoro, D.3
  • 46
    • 84885895986 scopus 로고    scopus 로고
    • Managing the data deluge: Data-driven GO category assignment improves while complexity of functional annotation increases
    • Gobeill, J., Pasche, E., Vishnyakova, D. et al. (2013) Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database, 2013, bat041.
    • (2013) Database , vol.2013
    • Gobeill, J.1    Pasche, E.2    Vishnyakova, D.3
  • 47
    • 84892722104 scopus 로고    scopus 로고
    • GOAssay: From gene ontology to assays identifiers-towards automatic functional annotation of pubchem bioassays
    • Guha, R., Gobeill, J. and Ruch, P. (2009) GOAssay: from gene ontology to assays Identifiers-towards automatic functional annotation of pubchem bioassays. Available from Nature Precedings .
    • (2009) Nature Precedings
    • Guha, R.1    Gobeill, J.2    Ruch, P.3
  • 48
    • 84883152491 scopus 로고    scopus 로고
    • The COMBREX project: Design, methodology, and initial results
    • Anton, B.P., Chang, Y.-C., Brown, P. et al. (2013) The COMBREX project: design, methodology, and initial results. PLoS Biol., 11, e1001638.
    • (2013) PLoS Biol. , vol.11
    • Anton, B.P.1    Chang, Y.-C.2    Brown, P.3
  • 49
    • 84987610788 scopus 로고    scopus 로고
    • Gene ontology concept recognition using cross-products and statistical methods
    • Bethesda, MD, USA
    • Luu, A.T., Kim, J.-J. and Ng, S.-K. (2013) Gene ontology concept recognition using cross-products and statistical methods. In: The Fourth BioCreative Challenge Evaluation Workshop, Vol. 1, Bethesda, MD, USA. pp. 174-181.
    • (2013) The Fourth BioCreative Challenge Evaluation Workshop , vol.1 , pp. 174-181
    • Luu, A.T.1    Kim, J.-J.2    Ng, S.-K.3
  • 50
    • 79952016835 scopus 로고    scopus 로고
    • Cross-product extensions of the gene ontology
    • Mungall, C.J., Bada, M., Berardini, T.Z. et al. (2011) Cross-product extensions of the gene ontology. J. Biomed. Inform., 44, 80-86.
    • (2011) J. Biomed. Inform. , vol.44 , pp. 80-86
    • Mungall, C.J.1    Bada, M.2    Berardini, T.Z.3
  • 51
    • 45749086922 scopus 로고    scopus 로고
    • Combining evidence, specificity, and proximity towards the Normalization of gene ontology terms in text
    • Gaudan, S., Yepes, A.J., Lee, V. et al. (2008) Combining evidence, specificity, and proximity towards the normalization of gene ontology terms in text. EURASIP J. Bioinform. Syst. Biol., 2008, 342746.
    • (2008) EURASIP J. Bioinform. Syst. Biol. , vol.2008
    • Gaudan, S.1    Yepes, A.J.2    Lee, V.3
  • 53
    • 0027621699 scopus 로고
    • Mining association rules between sets of items in large databases
    • Agrawal, R., Imieliński, T. and Swami, A. (1993) Mining association rules between sets of items in large databases. ACM SIGMOD Rec., 22, 207-216.
    • (1993) ACM Sigmod Rec. , vol.22 , pp. 207-216
    • Agrawal, R.1    Imieliński, T.2    Swami, A.3
  • 56
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Ashburner, M., Ball, C.A., Blake, J.A. et al. (2000) Gene Ontology: tool for the unification of biology. Nat. Genet, 25, 25-29.
    • (2000) Nat. Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3
  • 57
    • 77954310596 scopus 로고    scopus 로고
    • Document classification for mining host pathogen protein-protein interactions
    • Yin, L., Xu, G., Torii, M. et al. (2010) Document classification for mining host pathogen protein-protein interactions. Artif. Intell. Med., 49, 155-160.
    • (2010) Artif. Intell. Med. , vol.49 , pp. 155-160
    • Yin, L.1    Xu, G.2    Torii, M.3
  • 58
    • 84862957370 scopus 로고    scopus 로고
    • Learning from positive and unlabeled documents for automated detection of alternative splicing sentences in medline abstracts
    • Atlanta, GA, USA
    • Chen, Y., Torii, M., Lu, C.-T. et al. (2011) Learning from positive and unlabeled documents for automated detection of alternative splicing sentences in medline abstracts. In: Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference on. IEEE, Atlanta, GA, USA. pp. 530-537.
    • (2011) Bioinformatics and Biomedicine Workshops (BIBMW), 2011 IEEE International Conference On. IEEE , pp. 530-537
    • Chen, Y.1    Torii, M.2    Lu, C.-T.3
  • 60
    • 79952051431 scopus 로고    scopus 로고
    • The semantic vectors package: New algorithms and public tools for distributional semantics
    • Pittsburgh, PA, USA
    • Widdows, D. and Cohen, T. (2010) The semantic vectors package: new algorithms and public tools for distributional semantics. In: 2010 IEEE Fourth International Conference on Semantic Computing. IEEE, Pittsburgh, PA, USA, pp. 9-15.
    • (2010) 2010 IEEE Fourth International Conference on Semantic Computing. IEEE , pp. 9-15
    • Widdows, D.1    Cohen, T.2
  • 63
    • 84948481845 scopus 로고
    • An algorithm for suffix stripping
    • Porter, M.F. (1993) An algorithm for suffix stripping. Program, 14, 130-137.
    • (1993) Program , vol.14 , pp. 130-137
    • Porter, M.F.1
  • 65
    • 79551655977 scopus 로고    scopus 로고
    • A framework for semisuper-vised feature generation and its applications in biomedical literature mining
    • Li, Y., Hu, X., Lin, H. et al. (2011) A framework for semisuper-vised feature generation and its applications in biomedical literature mining. IEEE/ACM Trans. Comput. Biol. Bioinform., 8, 294-307.
    • (2011) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.8 , pp. 294-307
    • Li, Y.1    Hu, X.2    Lin, H.3


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