메뉴 건너뛰기




Volumn 7, Issue 4, 2012, Pages

Context-specific protein network miner - an online system for exploring context-specific protein interaction networks from the literature

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER NETWORK; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION REGULATION; ONLINE SYSTEM; PREDICTION; PROTEIN DATABASE; PROTEIN INTERACTION; UPREGULATION; VALIDATION PROCESS; ALGORITHM; COMPUTER PROGRAM; DATA MINING; GENETIC DATABASE; GENETICS; HUMAN; INTERNET; MEDLINE; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION;

EID: 84859487766     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034480     Document Type: Article
Times cited : (21)

References (71)
  • 1
    • 46149102929 scopus 로고    scopus 로고
    • Seeking a new biology through text mining
    • Available:
    • Rzhetsky A, Seringhaus M, Gerstein M, (2008) Seeking a new biology through text mining. Cell 134: 9-13 Available:http://www.ncbi.nlm.nih.gov/pubmed/18614002.
    • (2008) Cell , vol.134 , pp. 9-13
    • Rzhetsky, A.1    Seringhaus, M.2    Gerstein, M.3
  • 2
    • 58149193222 scopus 로고    scopus 로고
    • Human Protein Reference Database-2009 update
    • Available:
    • Keshava P, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res 37: 767-772 Available:http://www.ncbi.nlm.nih.gov/pubmed/18988627.
    • (2009) Nucleic Acids Res , vol.37 , pp. 767-772
    • Keshava, P.1    Goel, R.2    Kandasamy, K.3    Keerthikumar, S.4    Kumar, S.5
  • 3
    • 75549083295 scopus 로고    scopus 로고
    • MINT, the molecular interaction database: 2009 update
    • Available:
    • Ceol A, Chatr AA, Licata L, Peluso D, Briganti L, et al. (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 38: 532-539 Available:http://www.ncbi.nlm.nih.gov/pubmed/19897547.
    • (2010) Nucleic Acids Res , vol.38 , pp. 532-539
    • Ceol, A.1    Chatr, A.A.2    Licata, L.3    Peluso, D.4    Briganti, L.5
  • 4
    • 33644873184 scopus 로고    scopus 로고
    • BioGRID: a general repository for interaction datasets
    • Available:
    • Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: 535-539 Available:http://www.ncbi.nlm.nih.gov/pubmed/16381927.
    • (2006) Nucleic Acids Res , vol.34 , pp. 535-539
    • Stark, C.1    Breitkreutz, B.J.2    Reguly, T.3    Boucher, L.4    Breitkreutz, A.5
  • 5
    • 20144387067 scopus 로고    scopus 로고
    • The MIPS mammalian protein-protein interaction database
    • Available:
    • Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-KI, et al. (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics 21: 832-834 Available:http://www.ncbi.nlm.nih.gov/pubmed/15531608.
    • (2005) Bioinformatics , vol.21 , pp. 832-834
    • Pagel, P.1    Kovac, S.2    Oesterheld, M.3    Brauner, B.4    Dunger-K, I.5
  • 6
    • 15944375458 scopus 로고    scopus 로고
    • PDZBase: a protein-protein interaction database for PDZ-domains
    • Available:
    • Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H, (2005) PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics 21: 827-828 Available:http://www.ncbi.nlm.nih.gov/pubmed/15513994.
    • (2005) Bioinformatics , vol.21 , pp. 827-828
    • Beuming, T.1    Skrabanek, L.2    Niv, M.Y.3    Mukherjee, P.4    Weinstein, H.5
  • 7
    • 75549087047 scopus 로고    scopus 로고
    • The IntAct molecular interaction database in 2010
    • Aranda B, Achuthan P, Alam-FY, Armean I, Bridge A, et al. (2010) The IntAct molecular interaction database in 2010. Nucleic Acids Res 38: 525-531 http://www.ncbi.nlm.nih.gov/pubmed/19850723.
    • (2010) Nucleic Acids Res , vol.38 , pp. 525-531
    • Aranda, B.1    Achuthan, P.2    Alam-F, Y.3    Armean, I.4    Bridge, A.5
  • 8
    • 38549130733 scopus 로고    scopus 로고
    • STITCH: interaction networks of chemicals and proteins
    • Available:
    • Kuhn M, Mering C, Campillos M, Jensen LJ, Bork P, (2008) STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res 36: 684-688 Available:http://www.ncbi.nlm.nih.gov/pubmed/18084021.
    • (2008) Nucleic Acids Res , vol.36 , pp. 684-688
    • Kuhn, M.1    Mering, C.2    Campillos, M.3    Jensen, L.J.4    Bork, P.5
  • 9
    • 33947321307 scopus 로고    scopus 로고
    • Overview of BioCreAtIvE task 1B: normalized gene lists
    • Available:
    • Hirschman L, Colosimo M, Morgan A, Yeh A, (2005) Overview of BioCreAtIvE task 1B: normalized gene lists. BMC Bioinformatics 6: S11 Available:http://www.ncbi.nlm.nih.gov/pubmed/15960823.
    • (2005) BMC Bioinformatics , vol.6
    • Hirschman, L.1    Colosimo, M.2    Morgan, A.3    Yeh, A.4
  • 10
    • 51049088874 scopus 로고    scopus 로고
    • Overview of BioCreative II gene mention recognition
    • Available:
    • Smith L, Tanabe LK, Ando RJ, Kuo CJ, Chung IF, et al. (2008) Overview of BioCreative II gene mention recognition. Genome Biology 9: S2 Available:http://www.ncbi.nlm.nih.gov/pubmed/18834493.
    • (2008) Genome Biology , vol.9
    • Smith, L.1    Tanabe, L.K.2    Ando, R.J.3    Kuo, C.J.4    Chung, I.F.5
  • 11
    • 41349103793 scopus 로고    scopus 로고
    • Overview of BioCreative II gene normalization
    • Available:
    • Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, et al. (2008) Overview of BioCreative II gene normalization. Genome Biology 9: S3 Available:http://www.ncbi.nlm.nih.gov/pubmed/18834494.
    • (2008) Genome Biology , vol.9
    • Morgan, A.A.1    Lu, Z.2    Wang, X.3    Cohen, A.M.4    Fluck, J.5
  • 12
    • 80053423937 scopus 로고    scopus 로고
    • The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
    • In Press. Available:
    • Krallinger M, Vazquez M, Leitner F, Salgado D, Aryamontri AC, et al. (2011) The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics In Press. Available:http://informatics.indiana.edu/rocha/ps/PPI_BC3.pdf.
    • (2011) BMC Bioinformatics
    • Krallinger, M.1    Vazquez, M.2    Leitner, F.3    Salgado, D.4    Aryamontri, A.C.5
  • 13
    • 33646502601 scopus 로고    scopus 로고
    • Developing a Robust Part-of-Speech Tagger for Biomedical Text, Advances in Informatics
    • 10th Panhellenic Conference on Informatics
    • Tsuruoka Y, Tateishi Y, Kim JD, Ohta T, McNaught J, et al. (2005) Developing a Robust Part-of-Speech Tagger for Biomedical Text, Advances in Informatics. pp. 382-392 10th Panhellenic Conference on Informatics Available:http://www-tsujii.is.s.u-tokyo.ac.jp/~tsuruoka/papers/pci05.pdf.
    • (2005) , pp. 382-392
    • Tsuruoka, Y.1    Tateishi, Y.2    Kim, J.D.3    Ohta, T.4    McNaught, J.5
  • 14
    • 40549140499 scopus 로고    scopus 로고
    • BANNER: an executable survey of advances in biomedical named entity recognition
    • []
    • Leaman R, Gonzalez G, (2008) BANNER: an executable survey of advances in biomedical named entity recognition. Pac Symp Biocomput pp. 652-663 [http://www.ncbi.nlm.nih.gov/pubmed/18229723].
    • (2008) Pac Symp Biocomput , pp. 652-663
    • Leaman, R.1    Gonzalez, G.2
  • 15
    • 84859507820 scopus 로고    scopus 로고
    • The gene normalization and intractive systems of the University of Tokyo in the BioCreative III challenge
    • Okazaki N, Cho HC, Sætre R, Pyysalo S, Ohta T, et al. (2010) The gene normalization and intractive systems of the University of Tokyo in the BioCreative III challenge. In the Proceedings of BioCreative III pp. 125-130.
    • (2010) In the Proceedings of BioCreative III , pp. 125-130
    • Okazaki, N.1    Cho, H.C.2    Sætre, R.3    Pyysalo, S.4    Ohta, T.5
  • 16
    • 49549120418 scopus 로고    scopus 로고
    • Inter-species normalization of gene mentions with GNAT
    • Available:
    • Hakenberg J, Plake C, Leaman R, Schroeder M, Gonzalez G, (2008) Inter-species normalization of gene mentions with GNAT. Bioinformatics 24: 126-132 Available:http://www.ncbi.nlm.nih.gov/pubmed/18689813.
    • (2008) Bioinformatics , vol.24 , pp. 126-132
    • Hakenberg, J.1    Plake, C.2    Leaman, R.3    Schroeder, M.4    Gonzalez, G.5
  • 17
    • 38349118307 scopus 로고    scopus 로고
    • Text processing through Web services: calling Whatizit
    • Available:
    • Rebholz-SD, Arregui M, Gaudan S, Kirsch H, Jimeno A, (2008) Text processing through Web services: calling Whatizit. Bioinformatics 24: 296-298 Available:http://www.ncbi.nlm.nih.gov/pubmed/18006544.
    • (2008) Bioinformatics , vol.24 , pp. 296-298
    • Rebholz-S, D.1    Arregui, M.2    Gaudan, S.3    Kirsch, H.4    Jimeno, A.5
  • 18
    • 33947258447 scopus 로고    scopus 로고
    • ProMiner: rule-based protein and gene entity recognition
    • Available:
    • Hanisch D, Fundel K, Mevissen HT, Zimmer R, Fluck J, (2005) ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 6: S14 Available:http://www.ncbi.nlm.nih.gov/pubmed/15960826.
    • (2005) BMC Bioinformatics , vol.6
    • Hanisch, D.1    Fundel, K.2    Mevissen, H.T.3    Zimmer, R.4    Fluck, J.5
  • 19
    • 34249717333 scopus 로고    scopus 로고
    • Gene symbol disambiguation using knowledge-based profiles
    • Available:
    • Xu H, Fan JW, Hripcsak G, Mendonça EA, Markatou M, et al. (2007) Gene symbol disambiguation using knowledge-based profiles. Bioinformatics 23: 1015-1022 Available:http://www.ncbi.nlm.nih.gov/pubmed/17314123.
    • (2007) Bioinformatics , vol.23 , pp. 1015-1022
    • Xu, H.1    Fan, J.W.2    Hripcsak, G.3    Mendonça, E.A.4    Markatou, M.5
  • 20
    • 84864074911 scopus 로고    scopus 로고
    • Gene mention normalization in full texts using GNAT and LINNAEUS
    • Available:
    • Solt I, Gerner M, Thomas P, Nenadic G, Bergman CM, et al. (2010) Gene mention normalization in full texts using GNAT and LINNAEUS. BioCreative III Workshop pp. 143-148 Available:http://personalpages.manchester.ac.uk/postgrad/martin.gerner/pdf/gnat-paper.pdf.
    • (2010) BioCreative III Workshop , pp. 143-148
    • Solt, I.1    Gerner, M.2    Thomas, P.3    Nenadic, G.4    Bergman, C.M.5
  • 21
    • 62549162626 scopus 로고    scopus 로고
    • High-performance gene name normalization with GENO
    • Available:
    • Wermter J, Tomanek K, Hahn U, (2009) High-performance gene name normalization with GENO. Bioinformatics 25: 815-821 Available:http://www.ncbi.nlm.nih.gov/pubmed/19188193.
    • (2009) Bioinformatics , vol.25 , pp. 815-821
    • Wermter, J.1    Tomanek, K.2    Hahn, U.3
  • 22
    • 77952310847 scopus 로고    scopus 로고
    • Moara: a Java library for extracting and normalizing gene and protein mentions
    • Available:
    • Neves ML, Carazo JM, Pascual-MA, (2010) Moara: a Java library for extracting and normalizing gene and protein mentions. BMC Bioinformatics 11: 157 Available:http://www.ncbi.nlm.nih.gov/pubmed/20346105.
    • (2010) BMC Bioinformatics , vol.11 , pp. 157
    • Neves, M.L.1    Carazo, J.M.2    Pascual-MA3
  • 23
    • 70449565738 scopus 로고    scopus 로고
    • Normalizing Biomedical Name Entities by Similarity-Based Inference Network and De-ambiguity Mining, 2009 Ninth IEEE International Conference on Bioinformatics and Bioengineering
    • Wei CH, Huang IC, Hsu YY, Kao HY, (2009) pp. 461-466 Normalizing Biomedical Name Entities by Similarity-Based Inference Network and De-ambiguity Mining, 2009 Ninth IEEE International Conference on Bioinformatics and Bioengineering Available:http://www.computer.org/portal/web/csdl/doi/10.1109/BIBE.2009.41.
    • (2009) , pp. 461-466
    • Wei, C.H.1    Huang, I.C.2    Hsu, Y.Y.3    Kao, H.Y.4
  • 24
    • 79953325924 scopus 로고    scopus 로고
    • GeneTUKit: a software for document-level gene normalization
    • Available:
    • Huang M, Liu J, Zhu X, (2011) GeneTUKit: a software for document-level gene normalization. Bioinformatics 27: 1032-1033 Available:http://www.ncbi.nlm.nih.gov/pubmed/21303863.
    • (2011) Bioinformatics , vol.27 , pp. 1032-1033
    • Huang, M.1    Liu, J.2    Zhu, X.3
  • 25
    • 80053441509 scopus 로고    scopus 로고
    • The GNAT library for local and remote gene mention normalization
    • Available:
    • Hakenberg J, Gerner M, Haeussler M, Solt I, Plake C, et al. (2011) The GNAT library for local and remote gene mention normalization. Bioinformatics 27: 2769-2771 Available:http://www.ncbi.nlm.nih.gov/pubmed/21813477.
    • (2011) Bioinformatics , vol.27 , pp. 2769-2771
    • Hakenberg, J.1    Gerner, M.2    Haeussler, M.3    Solt, I.4    Plake, C.5
  • 26
    • 3242881967 scopus 로고    scopus 로고
    • NLProt: extracting protein names and sequences from papers
    • Available:
    • Mika S, Rost B, (2004) NLProt: extracting protein names and sequences from papers. Nucleic Acids Res 32: W634-W637 Available:http://www.ncbi.nlm.nih.gov/pubmed/15215466.
    • (2004) Nucleic Acids Res , vol.32
    • Mika, S.1    Rost, B.2
  • 27
    • 66349121774 scopus 로고    scopus 로고
    • Bayesian inference of protein-protein interactions from biological literature
    • Available:
    • Chowdhary R, Zhang J, Liu JS, (2009) Bayesian inference of protein-protein interactions from biological literature. Bioinformatics 25: 1536-1542 Available:http://www.ncbi.nlm.nih.gov/pubmed/19369495.
    • (2009) Bioinformatics , vol.25 , pp. 1536-1542
    • Chowdhary, R.1    Zhang, J.2    Liu, J.S.3
  • 28
    • 80053429575 scopus 로고    scopus 로고
    • Syntactic features for protein-protein interaction extraction
    • Proceedings of the 2nd International Symposium on Languages in Biology and Medicine
    • Saetre R, Sagae K, Tsujii J, (2008) Syntactic features for protein-protein interaction extraction. pp. 6.1-6.14 Proceedings of the 2nd International Symposium on Languages in Biology and Medicine Available:http://www.cs.cmu.edu/~sagae/docs/saetre-lbm2007.pdf.
    • (2008) , pp. 1-14
    • Saetre, R.1    Sagae, K.2    Tsujii, J.3
  • 29
    • 41349107398 scopus 로고    scopus 로고
    • OpenDMAP: An open source, ontology-driven concept analysis engine, with application to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression
    • Available:
    • Hunter L, Lu Z, Firby J, Baumgartner WA, Johnson HL, et al. (2008) OpenDMAP: An open source, ontology-driven concept analysis engine, with application to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics 9: 78 Available:http://www.ncbi.nlm.nih.gov/pubmed/18237434.
    • (2008) BMC Bioinformatics , vol.9 , pp. 78
    • Hunter, L.1    Lu, Z.2    Firby, J.3    Baumgartner, W.A.4    Johnson, H.L.5
  • 30
    • 73449147335 scopus 로고    scopus 로고
    • Looking at cerebellar malformations through text-mined interactomes of mice and humans
    • Available:
    • Iossifov I, Rodriguez ER, Mayzus I, Millen KJ, Rzhetsky A, (2009) Looking at cerebellar malformations through text-mined interactomes of mice and humans. PLoS Comput Biol 5: e1000559 Available:http://www.ncbi.nlm.nih.gov/pubmed/19893633.
    • (2009) PLoS Comput Biol , vol.5
    • Iossifov, I.1    Rodriguez, E.R.2    Mayzus, I.3    Millen, K.J.4    Rzhetsky, A.5
  • 31
    • 1342330525 scopus 로고    scopus 로고
    • Knowledge discovery by automated identification and ranking of implicit relationships
    • Available:
    • Wren JD, Bekeredjian R, Stewart JA, Shohet RV, Garner HR, (2004) Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics 20: 389-398 Available:http://www.ncbi.nlm.nih.gov/pubmed/14959466.
    • (2004) Bioinformatics , vol.20 , pp. 389-398
    • Wren, J.D.1    Bekeredjian, R.2    Stewart, J.A.3    Shohet, R.V.4    Garner, H.R.5
  • 32
    • 77955465839 scopus 로고    scopus 로고
    • Extracting protein interactions from text with the unified AkaneRE event extraction system
    • Available:
    • Saetre R, Yoshida K, Miwa M, Matsuzaki T, Kano Y, et al. (2010) Extracting protein interactions from text with the unified AkaneRE event extraction system. IEEE/ACM Trans Comput Biol Bioinform 7: 442-453 Available:http://www.ncbi.nlm.nih.gov/pubmed/20671316.
    • (2010) IEEE/ACM Trans Comput Biol Bioinform , vol.7 , pp. 442-453
    • Saetre, R.1    Yoshida, K.2    Miwa, M.3    Matsuzaki, T.4    Kano, Y.5
  • 34
    • 75749099276 scopus 로고    scopus 로고
    • Protein interactome analysis for countering pathogen drug resistance
    • Available:
    • Wong L, Liu G, (2010) Protein interactome analysis for countering pathogen drug resistance. J Comp Sci Tech 25: 124-130 Available:http://www.comp.nus.edu.sg/~wongls/psZ/jcst-5631proof.pdf.
    • (2010) J Comp Sci Tech , vol.25 , pp. 124-130
    • Wong, L.1    Liu, G.2
  • 35
    • 78651423600 scopus 로고    scopus 로고
    • A hybrid approach to extract protein-protein interactions
    • Available:
    • Bui QC, Katrenko S, Sloot PM, (2011) A hybrid approach to extract protein-protein interactions. Bioinformatics 27: 259-265 Available:http://www.ncbi.nlm.nih.gov/pubmed/21062765.
    • (2011) Bioinformatics , vol.27 , pp. 259-265
    • Bui, Q.C.1    Katrenko, S.2    Sloot, P.M.3
  • 36
    • 78049245506 scopus 로고    scopus 로고
    • A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature
    • Available:
    • Tikk D, Thomas P, Palaga P, Hakenberg J, Leser U, (2010) A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature. PLoS Comput Biol 6: e1000837 Available:http://www.ncbi.nlm.nih.gov/pubmed/20617200.
    • (2010) PLoS Comput Biol , vol.6
    • Tikk, D.1    Thomas, P.2    Palaga, P.3    Hakenberg, J.4    Leser, U.5
  • 37
    • 84908464360 scopus 로고    scopus 로고
    • An Exploration of Mining Gene Expression Mentions and their Anatomical Locations from Biomedical Text
    • Proceedings of the 2010 Workshop on Biomedical Natural Language Processing
    • Gerner M, Nenadic G, Bergman CM, (2010) An Exploration of Mining Gene Expression Mentions and their Anatomical Locations from Biomedical Text. pp. 72-80 Proceedings of the 2010 Workshop on Biomedical Natural Language Processing Available:http://personalpages.manchester.ac.uk/postgrad/martin.gerner/pdf/getm-paper.pdf.
    • (2010) , pp. 72-80
    • Gerner, M.1    Nenadic, G.2    Bergman, C.M.3
  • 38
    • 77949510039 scopus 로고    scopus 로고
    • LAITOR-Literature Assistant for Identification of Terms co-Occurrences and Relationships
    • Available:
    • Barbosa-Silva A, Soldatos TG, Magalhães IL, Pavlopoulos GA, Fontaine JF, et al. (2010) LAITOR-Literature Assistant for Identification of Terms co-Occurrences and Relationships. Bioinformatics 11: 70 Available:http://www.ncbi.nlm.nih.gov/pubmed/20122157.
    • (2010) Bioinformatics , vol.11 , pp. 70
    • Barbosa-Silva, A.1    Soldatos, T.G.2    Magalhães, I.L.3    Pavlopoulos, G.A.4    Fontaine, J.F.5
  • 39
    • 48449105927 scopus 로고    scopus 로고
    • PIE: an online prediction system for protein-protein interactions from text
    • Available:
    • Kim S, Shin SY, Lee IH, Kim SJ, Sriram R, et al. (2008) PIE: an online prediction system for protein-protein interactions from text. Nucleic Acids Res 36: W411-W415 Available:http://www.ncbi.nlm.nih.gov/pubmed/18508809.
    • (2008) Nucleic Acids Res , vol.36
    • Kim, S.1    Shin, S.Y.2    Lee, I.H.3    Kim, S.J.4    Sriram, R.5
  • 40
    • 80053425479 scopus 로고    scopus 로고
    • Identifying protein-protein interactions in biomedical text articles
    • Dogan R, Yang Y, Neveol A, Huang M, Lu Z, (2010) Identifying protein-protein interactions in biomedical text articles. BioCreative III pp. 61-66.
    • (2010) BioCreative III , pp. 61-66
    • Dogan, R.1    Yang, Y.2    Neveol, A.3    Huang, M.4    Lu, Z.5
  • 41
    • 84859498649 scopus 로고    scopus 로고
    • Machine learning based approaches for Biocreative III tasks
    • Available:
    • Agarwal S, Liu F, Li Z, Yu H, (2010) Machine learning based approaches for Biocreative III tasks. BioCreative III pp. 46-51 Available:https://pantherfile.uwm.edu/agarwal/www/pdfs/biocreativ3.pdf.
    • (2010) BioCreative III , pp. 46-51
    • Agarwal, S.1    Liu, F.2    Li, Z.3    Yu, H.4
  • 42
    • 84874759009 scopus 로고    scopus 로고
    • Fast classification of scientific abstracts related to protein-protein interaction using a Naive Bayesian linear classifier
    • Fontaine JF, Navarro MA, (2010) Fast classification of scientific abstracts related to protein-protein interaction using a Naive Bayesian linear classifier. BioCreative III pp. 67-72.
    • (2010) BioCreative III , pp. 67-72
    • Fontaine, J.F.1    Navarro, M.A.2
  • 43
    • 80053419124 scopus 로고    scopus 로고
    • Improving protein-protein interaction article classification performance by utilizing grammatical relations
    • Available:
    • Kim S, Wilbur WJ, (2010) Improving protein-protein interaction article classification performance by utilizing grammatical relations. BioCreative III pp. 83-88 Available:http://www.mendeley.com/research/improving-proteinprotein-interaction-article-classification-performance-utilizing-grammatical-relations/.
    • (2010) BioCreative III , pp. 83-88
    • Kim, S.1    Wilbur, W.J.2
  • 44
    • 84859504689 scopus 로고    scopus 로고
    • A top-down approach for finding interaction detection methods
    • Available:
    • Leaman R, Sullivan R, Gonzalez G, (2010) A top-down approach for finding interaction detection methods. BioCreative III pp. 99-104 Available:http://www.mendeley.com/research/topdown-approach-finding-interaction-detection-methods/.
    • (2010) BioCreative III , pp. 99-104
    • Leaman, R.1    Sullivan, R.2    Gonzalez, G.3
  • 45
    • 80053408501 scopus 로고    scopus 로고
    • Testing Extensive Use of NER tools in Article Classification and a Statistical Approach for Method Interaction Extraction in the Protein-Protein Interaction Literature
    • Available:
    • Lourenco A, Conover M, Wong A, Pan F, Abi-Haidar A, et al. (2010) Testing Extensive Use of NER tools in Article Classification and a Statistical Approach for Method Interaction Extraction in the Protein-Protein Interaction Literature. BioCreative III pp. 113-118 Available:http://informatics.indiana.edu/rocha/ps/BC3_workshop.pdf.
    • (2010) BioCreative III , pp. 113-118
    • Lourenco, A.1    Conover, M.2    Wong, A.3    Pan, F.4    Abi-Haidar, A.5
  • 46
    • 80053405517 scopus 로고    scopus 로고
    • Vector-space models and terminologies in gene normalization and document classification
    • Matos S, Campos D, Oliveira JL, (2010) Vector-space models and terminologies in gene normalization and document classification. BioCreative III pp. 119-124.
    • (2010) BioCreative III , pp. 119-124
    • Matos, S.1    Campos, D.2    Oliveira, J.L.3
  • 47
    • 78651324347 scopus 로고    scopus 로고
    • The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
    • Available:
    • Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: 561-568 Available:http://www.ncbi.nlm.nih.gov/pubmed/21045058.
    • (2011) Nucleic Acids Res , vol.39 , pp. 561-568
    • Szklarczyk, D.1    Franceschini, A.2    Kuhn, M.3    Simonovic, M.4    Roth, A.5
  • 48
    • 3042786293 scopus 로고    scopus 로고
    • A gene network for navigating the literature
    • Available:
    • Hoffmann R, Valencia A, (2004) A gene network for navigating the literature. Nature Genetics 36: 664 Available:http://www.ncbi.nlm.nih.gov/pubmed/15226743.
    • (2004) Nature Genetics , vol.36 , pp. 664
    • Hoffmann, R.1    Valencia, A.2
  • 49
    • 75549088687 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • Available:
    • Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, et al. (2010) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 38: 5-16 Available:http://www.ncbi.nlm.nih.gov/pubmed/19910364.
    • (2010) Nucleic Acids Res , vol.38 , pp. 5-16
    • Sayers, E.W.1    Barrett, T.2    Benson, D.A.3    Bolton, E.4    Bryant, S.H.5
  • 50
    • 35948989284 scopus 로고    scopus 로고
    • The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
    • Available:
    • Smith B, Ashburner M, Rosse C, Bard J, Bug W, et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25: 1251-1255 Available:http://www.ncbi.nlm.nih.gov/pubmed/17989687.
    • (2007) Nat Biotechnol , vol.25 , pp. 1251-1255
    • Smith, B.1    Ashburner, M.2    Rosse, C.3    Bard, J.4    Bug, W.5
  • 51
    • 66349132579 scopus 로고    scopus 로고
    • From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations
    • Available:
    • Du P, Feng G, Flatow J, Song J, Holko M, et al. (2009) From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinformatics 25: 63-68 Available:http://www.ncbi.nlm.nih.gov/pubmed/19478018.
    • (2009) Bioinformatics , vol.25 , pp. 63-68
    • Du, P.1    Feng, G.2    Flatow, J.3    Song, J.4    Holko, M.5
  • 53
    • 0034069495 scopus 로고    scopus 로고
    • Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Available:
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet 25: 25-29 Available:http://www.ncbi.nlm.nih.gov/pubmed/10802651.
    • (2000) Nature Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 54
    • 78651302604 scopus 로고    scopus 로고
    • The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
    • Available:
    • Gremse M, Chang A, Schomburg I, Grote A, Scheer M, et al. (2011) The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res 39: 507-513 Available:http://www.ncbi.nlm.nih.gov/pubmed/21030441.
    • (2011) Nucleic Acids Res , vol.39 , pp. 507-513
    • Gremse, M.1    Chang, A.2    Schomburg, I.3    Grote, A.4    Scheer, M.5
  • 55
    • 33846056843 scopus 로고    scopus 로고
    • Entrez Gene: gene-centered information at NCBI
    • Available:
    • Maglott D, Ostell J, Pruitt KD, Tatusova T, (2007) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 35: 26-31 Available:http://www.ncbi.nlm.nih.gov/pubmed/17148475.
    • (2007) Nucleic Acids Res , vol.35 , pp. 26-31
    • Maglott, D.1    Ostell, J.2    Pruitt, K.D.3    Tatusova, T.4
  • 57
    • 30344472426 scopus 로고    scopus 로고
    • BioThesaurus: a web-based thesaurus of protein and gene names
    • Available:
    • Liu H, Hu ZZ, Zhang J, Wu C, (2006) BioThesaurus: a web-based thesaurus of protein and gene names. Bioinformatics 22: 103-105 Available:http://www.ncbi.nlm.nih.gov/pubmed/16267085.
    • (2006) Bioinformatics , vol.22 , pp. 103-105
    • Liu, H.1    Hu, Z.Z.2    Zhang, J.3    Wu, C.4
  • 58
    • 9144232912 scopus 로고    scopus 로고
    • UniProt: the Universal Protein knowledgebase
    • Available:
    • Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, et al. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32: 115-119 Available:http://www.ncbi.nlm.nih.gov/pubmed/14681372.
    • (2004) Nucleic Acids Res , vol.32 , pp. 115-119
    • Apweiler, R.1    Bairoch, A.2    Wu, C.H.3    Barker, W.C.4    Boeckmann, B.5
  • 59
    • 77956548953 scopus 로고    scopus 로고
    • Cytoscape Web: an interactive web-based network browser
    • Available:
    • Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, et al. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26: 2347-2348 Available:http://www.ncbi.nlm.nih.gov/pubmed/20656902.
    • (2010) Bioinformatics , vol.26 , pp. 2347-2348
    • Lopes, C.T.1    Franz, M.2    Kazi, F.3    Donaldson, S.L.4    Morris, Q.5
  • 60
    • 16244423656 scopus 로고    scopus 로고
    • Comparative experiments on learning information extractors for proteins and their interactions
    • Available:
    • Bunescu R, Ge R, Kate RJ, Marcotte EM, Mooney RJ, et al. (2005) Comparative experiments on learning information extractors for proteins and their interactions. Artificial Intelligence in Medicine 33: 139-155 Available:http://www.ncbi.nlm.nih.gov/pubmed/15811782.
    • (2005) Artificial Intelligence in Medicine , vol.33 , pp. 139-155
    • Bunescu, R.1    Ge, R.2    Kate, R.J.3    Marcotte, E.M.4    Mooney, R.J.5
  • 61
    • 84859498694 scopus 로고    scopus 로고
    • hiPathDB: a human-integrated pathway database with facile visualization
    • Available:
    • Yu N, Seo J, Rho K, Jang Y, Park J, et al. (2012) hiPathDB: a human-integrated pathway database with facile visualization. Nucleic Acids Research 40: D797-D802 Available:http://www.ncbi.nlm.nih.gov/pubmed/22123737.
    • (2012) Nucleic Acids Research , vol.40
    • Yu, N.1    Seo, J.2    Rho, K.3    Jang, Y.4    Park, J.5
  • 62
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Available:
    • Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M, (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Research 40: D109-D114 Available:http://www.ncbi.nlm.nih.gov/pubmed/2022080510.
    • (2012) Nucleic Acids Research , vol.40
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 64
    • 78651275182 scopus 로고    scopus 로고
    • Reactome: a database of reactions, pathways and biological processes
    • Available:
    • Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Research 39: D691-D697 Available:http://www.ncbi.nlm.nih.gov/pubmed/21067998.
    • (2011) Nucleic Acids Research , vol.39
    • Croft, D.1    O'Kelly, G.2    Wu, G.3    Haw, R.4    Gillespie, M.5
  • 65
    • 34250797912 scopus 로고    scopus 로고
    • Filaggrin null mutations are associated with increased asthma severity in children and young adults
    • Available:
    • Palmer CNA, Ismail T, Lee SP, Terron-Kwiatkowski A, Zhao Y, et al. (2007) Filaggrin null mutations are associated with increased asthma severity in children and young adults. Journal of Allergy and Clinical Immunology 120: 64-68 Available:http://www.ncbi.nlm.nih.gov/pubmed/17531295.
    • (2007) Journal of Allergy and Clinical Immunology , vol.120 , pp. 64-68
    • Palmer, C.N.A.1    Ismail, T.2    Lee, S.P.3    Terron-Kwiatkowski, A.4    Zhao, Y.5
  • 66
    • 79951991731 scopus 로고    scopus 로고
    • Filaggrin Gene Defects Are Independent Risk Factors for Atopic Asthma in a Polish Population: A Study in ECAP Cohort
    • Available:
    • Poninska J, Samolinski B, Tomaszewska A, Raciborski F, Samel-Kowalik P, et al. (2011) Filaggrin Gene Defects Are Independent Risk Factors for Atopic Asthma in a Polish Population: A Study in ECAP Cohort. PLoS ONE 6: e16933 Available:http://www.ncbi.nlm.nih.gov/pubmed/2021365004.
    • (2011) PLoS ONE , vol.6
    • Poninska, J.1    Samolinski, B.2    Tomaszewska, A.3    Raciborski, F.4    Samel-Kowalik, P.5
  • 67
    • 70449085067 scopus 로고    scopus 로고
    • Filaggrin mutations in the onset of eczema, sensitization, asthma, hay fever and the interaction with cat exposure
    • Available:
    • Schuttelaar MLA, Kerkhof M, Jonkman MF, Koppelman GH, Brunekreef B, et al. (2009) Filaggrin mutations in the onset of eczema, sensitization, asthma, hay fever and the interaction with cat exposure. Allergy 64: 1758-1765 Available:http://www.ncbi.nlm.nih.gov/pubmed/19839980.
    • (2009) Allergy , vol.64 , pp. 1758-1765
    • Schuttelaar, M.L.A.1    Kerkhof, M.2    Jonkman, M.F.3    Koppelman, G.H.4    Brunekreef, B.5
  • 70
    • 79952145156 scopus 로고    scopus 로고
    • Gastrin-releasing peptide blockade as a broad-spectrum anti-inflammatory therapy for asthma
    • Available:
    • Zhou S, Potts EN, Cuttitta F, Foster WM, Sunday ME, (2011) Gastrin-releasing peptide blockade as a broad-spectrum anti-inflammatory therapy for asthma. Proceedings of the National Academy of Sciences 108: 2100-2105 Available:http://www.ncbi.nlm.nih.gov/pubmed/21252304.
    • (2011) Proceedings of the National Academy of Sciences , vol.108 , pp. 2100-2105
    • Zhou, S.1    Potts, E.N.2    Cuttitta, F.3    Foster, W.M.4    Sunday, M.E.5
  • 71
    • 33645406090 scopus 로고    scopus 로고
    • Gene expression profiling of human alveolar macrophages of phenotypically normal smokers and nonsmokers reveals a previously unrecognized subset of genes modulated by cigarette smoking
    • Available:
    • Heguy A, O'Connor T, Luettich K, Worgall S, Cieciuch A, et al. (2006) Gene expression profiling of human alveolar macrophages of phenotypically normal smokers and nonsmokers reveals a previously unrecognized subset of genes modulated by cigarette smoking. Journal of Molecular Medicine 84: 318-328 Available:http://www.ncbi.nlm.nih.gov/pubmed/16520944.
    • (2006) Journal of Molecular Medicine , vol.84 , pp. 318-328
    • Heguy, A.1    O'Connor, T.2    Luettich, K.3    Worgall, S.4    Cieciuch, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.