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Volumn 12, Issue 3, 2013, Pages 173-181

PPIExtractor: A protein interaction extraction and visualization system for biomedical literature

Author keywords

Feature coupling generalization; information extraction; multiple kernels learning; protein protein interaction

Indexed keywords

BIOMEDICAL LITERATURE; EXPERIMENTAL EVALUATION; FEATURE COUPLING; FUNCTIONAL ORGANIZATION; MULTIPLE KERNELS; PROTEIN-PROTEIN INTERACTIONS; SIMILARITY-BASED METHODS; STATE-OF-THE-ART PERFORMANCE;

EID: 84883377947     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2013.2263837     Document Type: Article
Times cited : (15)

References (41)
  • 1
    • 0037138406 scopus 로고    scopus 로고
    • Mint: A molecular interaction database
    • A. Zanzoni et al Mint: A molecular interaction database FEBS Lett., vol. 513, pp. 135-140, 2002.
    • (2002) FEBS Lett , vol.513 , pp. 135-140
    • Zanzoni, A.1
  • 2
    • 0037245913 scopus 로고    scopus 로고
    • BIND-The biomolecular interaction network database
    • G. Bader, D. Betel, and C. Hogue, "BIND-The biomolecular interaction network database Nucl. Acids Res., Vol. 31, Pp. 248-250, 2003.
    • (2003) Nucl. Acids Res , vol.31 , pp. 248-250
    • Bader, G.1    Betel, D.2    Hogue, C.3
  • 3
    • 0033971642 scopus 로고    scopus 로고
    • DIP: The database of interacting proteins
    • I. Xenarios et al DIP: The database of interacting proteins Nucl. Acids. Res., vol. 28, pp. 289-291, 2000.
    • (2000) Nucl. Acids. Res , vol.28 , pp. 289-291
    • Xenarios, I.1
  • 4
    • 0036522638 scopus 로고    scopus 로고
    • The frame-based module of the SUISEKI information extraction system
    • C. Blaschke and A. Valencia, "The frame-based module of the SUISEKI information extraction system IEEE Intell. Syst., Vol. 17, Pp. 14-20, 2002.
    • (2002) IEEE Intell. Syst , vol.17 , pp. 14-20
    • Blaschke, C.1    Valencia, A.2
  • 5
    • 0033655017 scopus 로고    scopus 로고
    • Biobibliometrics: Information retrieval and visualization from co-occurrence of gene names in Medline abstracts
    • B. J. Stapley and G. Benoit, "Biobibliometrics: Information retrieval and visualization from co-occurrence of gene names in Medline abstracts In Proc. Pac. Symp. Biocomput., 2000, Pp. 526-537.
    • (2000) Proc. Pac. Symp. Biocomput. , pp. 526-537
    • Stapley, B.J.1    Benoit, G.2
  • 6
    • 10244245424 scopus 로고    scopus 로고
    • BioRAT: Extracting biological information from full-length papers
    • D. P. Corney, B. F.Buxton, W. B. Langdon, andD. T. Jones, "BioRAT: Extracting biological information from full-length papers Bioinformatics, Vol. 17, Pp. 3206-3213, 2004.
    • (2004) Bioinformatics , vol.17 , pp. 3206-3213
    • Corney, D.P.1    Buxton, B.F.2    Langdon, W.B.3    Jones, D.T.4
  • 7
    • 48449105927 scopus 로고    scopus 로고
    • PIE: An online prediction system for protein-Protein interactions from text
    • S. Kim et al PIE: An online prediction system for protein-Protein interactions from text Nucl. Acids Res, vol. 36, pp. W411-W415, 2008.
    • (2008) Nucl. Acids Res , vol.36
    • Kim, S.1
  • 8
    • 41349107398 scopus 로고    scopus 로고
    • OpenDMAP: An open source ontology-driven concept analysis engine with applications to capturing knowledge regarding protein transport protein interactions and cell-type-specific gene expression
    • L. Hunter et al OpenDMAP: An open source ontology-driven concept analysis engine with applications to capturing knowledge regarding protein transport protein interactions and cell-type-specific gene expression BMC Bioinformatics, 2008, 10.1186/1471- 2105-9-78.
    • (2008) BMC Bioinformatics , vol.10
    • Hunter, L.1
  • 9
    • 77954850017 scopus 로고    scopus 로고
    • PPLook: An automated data mining tool for protein-protein interaction
    • S. W. Zhang, Y. J. Li, L. Xia, and Q. Pan, "PPLook: An automated data mining tool for protein-protein interaction BMC Bioinformatics, 2010, 10.1186/1471-2105-11-326.
    • (2010) BMC Bioinformatics , vol.10
    • Zhang, S.W.1    Li, Y.J.2    Xia, L.3    Pan, Q.4
  • 10
    • 77955465839 scopus 로고    scopus 로고
    • Extracting protein interactions from text with the unified AkaneRE event extraction system
    • R. Saetre et al Extracting protein interactions from text with the unified AkaneRE event extraction system IEEE/ACM Trans. Comput. Biol. Bioinform., vol. 7, pp. 442-453, 2010.
    • (2010) IEEE/ACM Trans. Comput. Biol. Bioinform , vol.7 , pp. 442-453
    • Saetre, R.1
  • 11
    • 68949148714 scopus 로고    scopus 로고
    • Incorporating rich background knowledge for gene named entity classification and recognition
    • Y. P. Li, H. F. Lin, and Z. H. Yang, "Incorporating rich background knowledge for gene named entity classification and recognition BMC Bioinformatics, 2009, 10.1186/1471-2105-10-223.
    • (2009) BMC Bioinformatics , vol.10 , pp. 11861471-210510223
    • Li, Y.P.1    Lin, H.F.2    Yang, Z.H.3
  • 13
    • 33947398303 scopus 로고    scopus 로고
    • Biomedical named entity recognition using conditional random fields and rich feature sets
    • Geneva, Switzerland
    • B. Settles, "Biomedical named entity recognition using conditional random fields and rich feature sets in Proc. COLING 2004 Int. Joint Workshop Nat. Lang. Process. Biomed. Its Appl., Geneva, Switzerland, 2004, pp. 107-110.
    • (2004) Proc. COLING 2004 Int. Joint Workshop Nat. Lang. Process. Biomed. Its Appl. , pp. 107-110
    • Settles, B.1
  • 14
    • 80053254837 scopus 로고    scopus 로고
    • Bidirectional inference with the easiestfirst strategy for tagging sequence data
    • Vancouver, BC, Canada
    • Y. Tsuruoka and T. Tsujii, "Bidirectional inference with the easiestfirst strategy for tagging sequence data in Proc. Hum. Lang. Technol. EmpiricalMethods Nat. Lang. Process., Vancouver, BC, Canada, 2005, pp. 467-474.
    • (2005) Proc. Hum. Lang. Technol. EmpiricalMethods Nat. Lang. Process. , pp. 467-474
    • Tsuruoka, Y.1    Tsujii, T.2
  • 15
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • M. Ashburner et al Gene ontology: Tool for the unification of biology Nat. Genet., vol. 25, pp. 25-29, 2000.
    • (2000) Nat. Genet , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 16
    • 41349103793 scopus 로고    scopus 로고
    • Overview of BioCreative II gene normalization
    • 10 1186/gb-2008-9-s2-s3
    • A. Morgan et al Overview of BioCreative II gene normalization Genome Biol., 2008, 10.1186/gb-2008-9-s2-s3.
    • (2008) Genome Biol.
    • Morgan, A.1
  • 17
    • 51049088875 scopus 로고    scopus 로고
    • Overview of the protein-protein interaction annotation extraction task of BioCreative II
    • 10.1186/gb-2008-9-s2-s4
    • M. Krallinger, F. Leitner, C. Rodriguez-Penagos, and A. Valencia, "Overview of the protein-protein interaction annotation extraction task of BioCreative II Genome Biol., 2008, 10.1186/gb-2008-9-s2-s4.
    • (2008) Genome Biol.
    • Krallinger, M.1    Leitner, F.2    Rodriguez-Penagos, C.3    Valencia, A.4
  • 18
    • 68649115793 scopus 로고    scopus 로고
    • A realistic assessment of methods for extracting gene/protein interactions from free text
    • 10.1186/1471-2105-10-233
    • R. Kabiljo, A. B. Clegg, and A. J. Shepherd, "A realistic assessment of methods for extracting gene/protein interactions from free text BMC Bioinformatics, 2009, 10.1186/1471-2105-10-233.
    • (2009) BMC Bioinformatics
    • Kabiljo, R.1    Clegg, A.B.2    Shepherd, A.J.3
  • 19
    • 0033664385 scopus 로고    scopus 로고
    • Protein networks-built by association
    • M. L. Mayer and P. Hieter, "Protein networks-built by association Nat. Biotechnol., vol. 18, pp. 1242-1243, 2000.
    • (2000) Nat. Biotechnol , vol.18 , pp. 1242-1243
    • Mayer, M.L.1    Hieter, P.2
  • 20
    • 13444256580 scopus 로고    scopus 로고
    • Gene name ambiguity of eukaryotic nomenclatures
    • L. Chen, H. Liu, and C. Friedman, "Gene name ambiguity of eukaryotic nomenclatures Bioinformatics, vol. 21, pp. 248-256, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 248-256
    • Chen, L.1    Liu, H.2    Friedman, C.3
  • 23
    • 56649091413 scopus 로고    scopus 로고
    • All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning
    • 10.1186/1471-2105-9-S11-S2
    • A. Airola et al All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning BMC Bioinformatics, 2008, 10.1186/1471-2105-9-S11-S2.
    • (2008) BMC Bioinformatics
    • Airola, A.1
  • 24
    • 37549050918 scopus 로고    scopus 로고
    • Kernel approaches for genic interaction extraction
    • S. Kim, J. Yoon, and J. Yang, "Kernel approaches for genic interaction extraction Bioinformatics, vol. 24, pp. 118-126, 2008.
    • (2008) Bioinformatics , vol.24 , pp. 118-126
    • Kim, S.1    Yoon, J.2    Yang, J.3
  • 25
    • 71549135535 scopus 로고    scopus 로고
    • Protein-protein interaction extraction by leveraging multiple kernels and parsers
    • M. Miwa, R. Saetre, Y. Miyao, and J. Tsujii, "Protein-protein interaction extraction by leveraging multiple kernels and parsers Int. J.Med. Inform., vol. 78, pp. e39-e46, 2009.
    • (2009) Int. J.Med. Inform , vol.78
    • Miwa, M.1    Saetre, R.2    Miyao, Y.3    Tsujii, J.4
  • 26
    • 79954589221 scopus 로고    scopus 로고
    • Multiple kernel learning in protein-protein interaction extraction from biomedical literature
    • Z. H. Yang et al Multiple kernel learning in protein-protein interaction extraction from biomedical literature Artif. Intell. Med., vol. 51, pp. 163-173, 2011.
    • (2011) Artif. Intell. Med , vol.51 , pp. 163-173
    • Yang, Z.H.1
  • 29
    • 0031191630 scopus 로고    scopus 로고
    • The use of the area under the ROC curve in the evaluation of machine learning algorithms
    • A. P. Bradley, "The use of the area under the ROC curve in the evaluation of machine learning algorithms Pattern Recogn., vol. 30, pp. 1145-1159, 1997.
    • (1997) Pattern Recogn , vol.30 , pp. 1145-1159
    • Bradley, A.P.1
  • 30
    • 84874277359 scopus 로고    scopus 로고
    • Combining multiple layers of syntactic information for protein-protein interaction extraction
    • Turku, Finland
    • M. Miwa, R. Sætre, Y.Miyao, T. Ohta, and J. Tsujii, "Combining multiple layers of syntactic information for protein-protein interaction extraction in Proc. 3rd Int. Symp. SemanticMining Biomed., Turku, Finland, 2008, pp. 101-108.
    • (2008) Proc. 3rd Int. Symp. SemanticMining Biomed. , pp. 101-108
    • Miwa, M.1    Sætre, R.2    Miyao, Y.3    Ohta, T.4    Tsujii, J.5
  • 31
    • 59549091756 scopus 로고    scopus 로고
    • Evaluating contributions of natural language parsers to protein-protein interaction extraction
    • Y. Miyao, R. Sætre, K. Sagae, T. Matsuzaki, and J. Tsujii, "Evaluating contributions of natural language parsers to protein-protein interaction extraction Bioinformatics, vol. 25, pp. 394-400, 2009.
    • (2009) Bioinformatics , vol.25 , pp. 394-400
    • Miyao, Y.1    Sætre, R.2    Sagae, K.3    Matsuzaki, T.4    Tsujii, J.5
  • 32
    • 0034868773 scopus 로고    scopus 로고
    • Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study
    • C. Blaschke and A. Valencia, "Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study Comp. Funct. Genom., vol. 2, pp. 196-206, 2001.
    • (2001) Comp. Funct. Genom , vol.2 , pp. 196-206
    • Blaschke, C.1    Valencia, A.2
  • 33
    • 74649083091 scopus 로고    scopus 로고
    • BioPPISVMExtractor: A proteinprotein interaction extractor for biomedical literature using SVM and rich feature sets
    • Z. H. Yang, H. F. Lin, and Y. P. Li, "BioPPISVMExtractor: A proteinprotein interaction extractor for biomedical literature using SVM and rich feature sets J. Biomed. Inform., vol. 43, pp. 88-96, 2010.
    • (2010) J. Biomed. Inform , vol.43 , pp. 88-96
    • Yang, Z.H.1    Lin, H.F.2    Li, Y.P.3
  • 34
    • 56649105092 scopus 로고    scopus 로고
    • BioPPIExtractor: A proteinprotein interaction extraction system for biomedical literature
    • Z. H. Yang, H. F. Lin, and B. D. Wu, "BioPPIExtractor: A proteinprotein interaction extraction system for biomedical literature Expert Syst. Appl., vol. 36, pp. 2228-2233, 2009.
    • (2009) Expert Syst. Appl , vol.36 , pp. 2228-2233
    • Yang, Z.H.1    Lin, H.F.2    Wu, B.D.3
  • 35
    • 84872980656 scopus 로고    scopus 로고
    • IntEx: A syntactic role driven protein-protein interaction extractor for bio-medical text
    • Ontologies, Databases: Mining Biol. Semantics, Detroit, MI, USA
    • S. T. Ahmed, D. Chidambaram, H. Davulcu, and C. Baral, "IntEx: A syntactic role driven protein-protein interaction extractor for bio-medical text in Proc. ACL-ISMB Workshop Linking Biol. Literature, Ontologies, Databases: Mining Biol. Semantics, Detroit, MI, USA, 2005.
    • (2005) Proc. ACL-ISMB Workshop Linking Biol. Literature
    • Ahmed, S.T.1    Chidambaram, D.2    Davulcu, H.3    Baral, C.4
  • 36
    • 33847608309 scopus 로고    scopus 로고
    • BioInfer: A corpus for information extraction in the biomedical domain
    • 10.1186/1471-2105-8-50
    • S. Pyysalo et al BioInfer: A corpus for information extraction in the biomedical domain BMC Bioinformatics, vol. 8, no. 50, 2007, 10.1186/1471-2105-8- 50.
    • (2007) BMC Bioinformatics , vol.8 , Issue.50
    • Pyysalo, S.1
  • 37
    • 33847294345 scopus 로고    scopus 로고
    • RelEx-Relation extraction using dependency parse trees
    • K. Fundel, R. Küffner, and R. Zimmer, "RelEx-Relation extraction using dependency parse trees Bioinformatics, vol. 23, pp. 365-371, 2007.
    • (2007) Bioinformatics , vol.23 , pp. 365-371
    • Fundel, K.1    Küffner, R.2    Zimmer, R.3
  • 39
    • 33847253112 scopus 로고    scopus 로고
    • Learning language in logic-genic interaction extraction challenge
    • Bonn, Germany
    • C. Nédellec, "Learning language in logic-genic interaction extraction challenge in Proc. 4th Learn. Lang. Logic Workshop, Bonn, Germany, 2005, pp. 31-37.
    • (2005) Proc. 4th Learn. Lang. Logic Workshop , pp. 31-37
    • Nédellec, C.1
  • 40
    • 10744224197 scopus 로고    scopus 로고
    • Development of human protein reference database as an initial platform for approaching systems biology in humans
    • S. Peri et al Development of human protein reference database as an initial platform for approaching systems biology in humans Genome Res., vol. 13, pp. 2363-2371, 2003.
    • (2003) Genome Res , vol.13 , pp. 2363-2371
    • Peri, S.1
  • 41
    • 33644873184 scopus 로고    scopus 로고
    • BioGRID: A general repository for interaction datasets
    • C. Stark et al BioGRID: A general repository for interaction datasets Nucl. Acids Res., vol. 34, pp. 535-539, 2006.
    • (2006) Nucl. Acids Res , vol.34 , pp. 535-539
    • Stark, C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.