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Volumn 12, Issue 1, 2015, Pages 17-29

RLIMS-P 2.0: A generalizable rule-based information extraction system for literature mining of protein phosphorylation information

Author keywords

Biology and genetics; Context Analysis and Indexing; Natural Language Processing; Text mining

Indexed keywords

ABSTRACTING; COMPUTATIONAL LINGUISTICS; ENZYMES; INDEXING (MATERIALS WORKING); INFORMATION ANALYSIS; INFORMATION RETRIEVAL; INFORMATION RETRIEVAL SYSTEMS; LINGUISTICS; NATURAL LANGUAGE PROCESSING SYSTEMS; PHOSPHORYLATION; SOCIAL NETWORKING (ONLINE); SUBSTRATES; TEXT PROCESSING;

EID: 84923261419     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2014.2372765     Document Type: Article
Times cited : (40)

References (51)
  • 1
    • 84865096530 scopus 로고    scopus 로고
    • Why nature chose phosphate to modify proteins
    • Sep.
    • T. Hunter, "Why nature chose phosphate to modify proteins," Philos. Trans. Royal Soc. London B. Biol. Sci., vol. 367, no. 1602, pp. 2513-2516, Sep. 2012.
    • (2012) Philos. Trans. Royal Soc. London B. Biol. Sci. , vol.367 , Issue.1602 , pp. 2513-2516
    • Hunter, T.1
  • 3
    • 84857047339 scopus 로고    scopus 로고
    • PhosphoSitePlus: A comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
    • Database issue Jan.
    • P. V. Hornbeck, J. M. Kornhauser, S. Tkachev, B. Zhang, E. Skrzypek, B. Murray, V. Latham, and M. Sullivan, "PhosphoSitePlus: A comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse," Nucleic Acids Res., vol. 40, no. Database issue, pp. D261-270, Jan. 2012.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D261-270
    • Hornbeck, P.V.1    Kornhauser, J.M.2    Tkachev, S.3    Zhang, B.4    Skrzypek, E.5    Murray, B.6    Latham, V.7    Sullivan, M.8
  • 4
    • 78651320816 scopus 로고    scopus 로고
    • Phospho.ELM: A database of phosphorylation sites-update 2011
    • Database issue Jan.
    • H. Dinkel, C. Chica, A. Via, C. M. Gould, L. J. Jensen, T. J. Gibson, and F. Diella, "Phospho.ELM: A database of phosphorylation sites-update 2011," Nucleic Acids Res., vol. 39, no. Database issue, pp. D261-D267, Jan. 2011.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D261-D267
    • Dinkel, H.1    Chica, C.2    Via, A.3    Gould, C.M.4    Jensen, L.J.5    Gibson, T.J.6    Diella, F.7
  • 5
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • The UniProt Consortium Database issue Jan.
    • The UniProt Consortium, "Reorganizing the protein space at the Universal Protein Resource (UniProt)," Nucleic Acids Res., vol. 40, no. Database issue, pp. D71-D75, Jan. 2012.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D71-D75
  • 6
    • 20744446607 scopus 로고    scopus 로고
    • Literature mining and database annotation of protein phosphorylation using a rule-based system
    • Jun.
    • Z. Z. Hu, M. Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, and C. H. Wu, "Literature mining and database annotation of protein phosphorylation using a rule-based system," Bioinformatics, vol. 21, no. 11, pp. 2759-2765, Jun. 2005.
    • (2005) Bioinformatics , vol.21 , Issue.11 , pp. 2759-2765
    • Hu, Z.Z.1    Narayanaswamy, M.2    Ravikumar, K.E.3    Vijay-Shanker, K.4    Wu, C.H.5
  • 8
    • 84860538817 scopus 로고    scopus 로고
    • Beyond the clause: Extraction of phosphorylation information from medline abstracts
    • Jun.
    • M. Narayanaswamy, K. E. Ravikumar, and K. Vijay-Shanker, "Beyond the clause: Extraction of phosphorylation information from medline abstracts," Bioinformatics, vol. 21, no. Suppl 1, pp. 1319-327, Jun. 2005.
    • (2005) Bioinformatics , vol.21 , pp. 1319-1327
    • Narayanaswamy, M.1    Ravikumar, K.E.2    Vijay-Shanker, K.3
  • 9
    • 84875129833 scopus 로고    scopus 로고
    • Application of text-mining for updating protein post-translational modification annotation in UniProtKB
    • Mar.
    • A.-L. Veuthey, A. Bridge, J. Gobeill, P. Ruch, J. R. McEntyre, L. Bougueleret, and I. Xenarios, "Application of text-mining for updating protein post-translational modification annotation in UniProtKB," BMC Bioinformatics, vol. 14, no. 1, p. 104, Mar. 2013.
    • (2013) BMC Bioinformatics , vol.14 , Issue.1 , pp. 104
    • Veuthey, A.-L.1    Bridge, A.2    Gobeill, J.3    Ruch, P.4    McEntyre, J.R.5    Bougueleret, L.6    Xenarios, I.7
  • 10
    • 81455143726 scopus 로고    scopus 로고
    • MinePhos: A literature mining system for protein phosphorylation information extraction
    • Apr.
    • Y. Xu, D. Teng, and Y. Lei, "MinePhos: A literature mining system for protein phosphorylation information extraction," IEEEACM Trans. Comput. Biol. Bioinformat., vol. 9, no. 1, pp. 311-315, Apr. 2011.
    • (2011) IEEEACM Trans. Comput. Biol. Bioinformat. , vol.9 , Issue.1 , pp. 311-315
    • Xu, Y.1    Teng, D.2    Lei, Y.3
  • 14
    • 84878105593 scopus 로고    scopus 로고
    • The functional genomics network in the evolution of biological text mining over the past decade
    • Mar.
    • C. Blaschke and A. Valencia, "The functional genomics network in the evolution of biological text mining over the past decade," New Biotechnol., vol. 30, no. 3, pp. 278-285, Mar. 2013.
    • (2013) New Biotechnol. , vol.30 , Issue.3 , pp. 278-285
    • Blaschke, C.1    Valencia, A.2
  • 15
    • 0037021472 scopus 로고    scopus 로고
    • Getting to the (c)ore of knowledge: Mining biomedical literature
    • Dec.
    • B. de Bruijn and J. Martin, "Getting to the (c)ore of knowledge: Mining biomedical literature," Int. J. Med. Inf., vol. 67, nos. 1-3, pp. 7-18, Dec. 2002.
    • (2002) Int. J. Med. Inf. , vol.67 , Issue.1-3 , pp. 7-18
    • De Bruijn, B.1    Martin, J.2
  • 16
    • 38949105955 scopus 로고    scopus 로고
    • Getting started in text mining
    • Jan.
    • K. B. Cohen and L. Hunter, "Getting started in text mining," PLoS Comput. Biol., vol. 4, no. 1, p. e20, Jan. 2008.
    • (2008) PLoS Comput. Biol. , vol.4 , Issue.1 , pp. e20
    • Cohen, K.B.1    Hunter, L.2
  • 18
    • 3943106585 scopus 로고    scopus 로고
    • Accomplishments and challenges in literature data mining for biology
    • Dec.
    • L. Hirschman, J. C. Park, J. Tsujii, L. Wong, and C. H. Wu, "Accomplishments and challenges in literature data mining for biology," Bioinformatica, vol. 18, no. 12, pp. 1553-1561, Dec. 2002.
    • (2002) Bioinformatica , vol.18 , Issue.12 , pp. 1553-1561
    • Hirschman, L.1    Park, J.C.2    Tsujii, J.3    Wong, L.4    Wu, C.H.5
  • 19
    • 51049110331 scopus 로고    scopus 로고
    • Linking genes to literature: Text mining, information extraction, and retrieval applications for biology
    • M. Krallinger, A. Valencia, and L. Hirschman, "Linking genes to literature: Text mining, information extraction, and retrieval applications for biology," Genome Biol., vol. 9, no. Suppl 2, p. S8, 2008.
    • (2008) Genome Biol. , vol.9 , pp. S8
    • Krallinger, M.1    Valencia, A.2    Hirschman, L.3
  • 20
    • 74549117176 scopus 로고    scopus 로고
    • Biomedical text mining and its applications
    • Dec.
    • R. Rodriguez-Esteban, "Biomedical text mining and its applications," PLoS Comput. Biol., vol. 5, no. 12, p. e1000597, Dec. 2009.
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.12 , pp. e1000597
    • Rodriguez-Esteban, R.1
  • 21
    • 46149102929 scopus 로고    scopus 로고
    • Seeking a new biology through text mining
    • Jul.
    • A. Rzhetsky, M. Seringhaus, and M. Gerstein, "Seeking a new biology through text mining," Cell, vol. 134, no. 1, pp. 9-13, Jul. 2008.
    • (2008) Cell , vol.134 , Issue.1 , pp. 9-13
    • Rzhetsky, A.1    Seringhaus, M.2    Gerstein, M.3
  • 22
    • 68249091561 scopus 로고    scopus 로고
    • Getting started in text mining: Part two
    • Jul.
    • A. Rzhetsky, M. Seringhaus, and M. B. Gerstein, "Getting started in text mining: Part two," PLoS Comput. Biol., vol. 5, no. 7, p. e1000411, Jul. 2009.
    • (2009) PLoS Comput. Biol. , vol.5 , Issue.7 , pp. e1000411
    • Rzhetsky, A.1    Seringhaus, M.2    Gerstein, M.B.3
  • 24
    • 84875865035 scopus 로고    scopus 로고
    • Biomedical text mining: A survey of recent progress
    • C. C. Aggarwal and C. Zhai, Eds. Boston, MA, USA: Springer
    • M. S. Simpson and D. Demner-Fushman, "Biomedical text mining: A survey of recent progress," in Mining Text Data, C. C. Aggarwal and C. Zhai, Eds. Boston, MA, USA: Springer, 2012, pp. 465-517.
    • (2012) Mining Text Data , pp. 465-517
    • Simpson, M.S.1    Demner-Fushman, D.2
  • 25
    • 36348990139 scopus 로고    scopus 로고
    • Frontiers of biomedical text mining: Current progress
    • Sep.
    • P. Zweigenbaum, D. Demner-Fushman, H. Yu, and K. B. Cohen, "Frontiers of biomedical text mining: current progress," Brief. Bioinformat., vol. 8, no. 5, pp. 358-375, Sep. 2007.
    • (2007) Brief. Bioinformat. , vol.8 , Issue.5 , pp. 358-375
    • Zweigenbaum, P.1    Demner-Fushman, D.2    Yu, H.3    Cohen, K.B.4
  • 26
    • 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, Z. Lu, J. Firby, W. A. Baumgartner Jr., H. L. Johnson, P. V. Ogren, and K. B. Cohen, "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, vol. 9, p. 78, 2008.
    • (2008) BMC Bioinformatics , vol.9 , pp. 78
    • Hunter, L.1    Lu, Z.2    Firby, J.3    Baumgartner, W.A.4    Johnson, H.L.5    Ogren, P.V.6    Cohen, K.B.7
  • 27
    • 84876760070 scopus 로고    scopus 로고
    • The potential of text mining in data integration and network biology for plant research: A case study on Arabidopsis
    • Mar.
    • S. Van Landeghem, S. De Bodt, Z. J. Drebert, D. Inz-e, and Y. Van de Peer, "The potential of text mining in data integration and network biology for plant research: A case study on Arabidopsis," Plant Cell, vol. 25, no. 3, pp. 794-807, Mar. 2013.
    • (2013) Plant Cell , vol.25 , Issue.3 , pp. 794-807
    • Van Landeghem, S.1    De Bodt, S.2    Drebert, Z.J.3    Inze, D.4    Peer De Y.Van5
  • 28
    • 33645104154 scopus 로고    scopus 로고
    • Extraction of regulatory gene/protein networks from Medline
    • Mar.
    • J. Saric, L. J. Jensen, R. Ouzounova, I. Rojas, and P. Bork, "Extraction of regulatory gene/protein networks from Medline," Bioinformatica, vol. 22, no. 6, pp. 645-650, Mar. 2006.
    • (2006) Bioinformatica , vol.22 , Issue.6 , pp. 645-650
    • Saric, J.1    Jensen, L.J.2    Ouzounova, R.3    Rojas, I.4    Bork, P.5
  • 29
    • 84874280242 scopus 로고    scopus 로고
    • The genia event and protein coreference tasks of the BioNLP shared task 2011
    • J.-D. Kim, N. Nguyen, Y. Wang, J. Tsujii, T. Takagi, and A. Yonezawa, "The genia event and protein coreference tasks of the BioNLP shared task 2011," BMC Bioinformat., vol. 13, no. Suppl 11, p. S1, 2012.
    • (2012) BMC Bioinformat. , vol.13 , pp. S1
    • Kim, J.-D.1    Nguyen, N.2    Wang, Y.3    Tsujii, J.4    Takagi, T.5    Yonezawa, A.6
  • 32
    • 84876264507 scopus 로고    scopus 로고
    • Biological event composition
    • H. Kilicoglu and S. Bergler, "Biological event composition," BMC Bioinformatics, vol. 13, no. Suppl 11, p. S7, 2012.
    • (2012) BMC Bioinformatics , vol.13 , pp. S7
    • Kilicoglu, H.1    Bergler, S.2
  • 33
    • 9544257285 scopus 로고    scopus 로고
    • Ipro LINK: An integrated protein resource for literature mining
    • Dec.
    • Z.-Z. Hu, I. Mani, V. Hermoso, H. Liu, and C. H. Wu, "iProLINK: An integrated protein resource for literature mining," Comput. Biol. Chem., vol. 28, nos. 5/6, pp. 409-416, Dec. 2004.
    • (2004) Comput. Biol. Chem. , vol.28 , Issue.5-6 , pp. 409-416
    • Hu, Z.-Z.1    Mani, I.2    Hermoso, V.3    Liu, H.4    Wu, C.H.5
  • 38
    • 84875589774 scopus 로고    scopus 로고
    • Literature mining of protein-residue associations with graph rules learned through distant supervision
    • Oct.
    • K. Ravikumar, H. Liu, J. D. Cohn, M. E. Wall, and K. Verspoor, "Literature mining of protein-residue associations with graph rules learned through distant supervision," J. Biomed. Semantics, vol. 3, no. Suppl 3, p. S2, Oct. 2012.
    • (2012) J. Biomed. Semantics , vol.3 , pp. S2
    • Ravikumar, K.1    Liu, H.2    Cohn, J.D.3    Wall, M.E.4    Verspoor, K.5
  • 40
    • 33646141828 scopus 로고    scopus 로고
    • Zone analysis in biology articles as a basis for information extraction
    • Jun.
    • Y. Mizuta, A. Korhonen, T. Mullen, and N. Collier, "Zone analysis in biology articles as a basis for information extraction," Int. J. Med. Inf., vol. 75, no. 6, pp. 468-487, Jun. 2006.
    • (2006) Int. J. Med. Inf. , vol.75 , Issue.6 , pp. 468-487
    • Mizuta, Y.1    Korhonen, A.2    Mullen, T.3    Collier, N.4
  • 41
    • 0040078056 scopus 로고    scopus 로고
    • Summarizing scientific articles: Experiments with relevance and rhetorical status
    • Dec.
    • S. Teufel and M. Moens, "Summarizing scientific articles: Experiments with relevance and rhetorical status," Comput. Linguistic, vol. 28, no. 4, pp. 409-445, Dec. 2002.
    • (2002) Comput. Linguistic , vol.28 , Issue.4 , pp. 409-445
    • Teufel, S.1    Moens, M.2
  • 43
    • 77957140630 scopus 로고    scopus 로고
    • The structural and content aspects of abstracts versus bodies of full text journal articles are different
    • K. B. Cohen, H. L. Johnson, K. Verspoor, C. Roeder, and L. E. Hunter, "The structural and content aspects of abstracts versus bodies of full text journal articles are different," BMC Bioinformatics, vol. 11, p. 492, 2010.
    • (2010) BMC Bioinformatics , vol.11 , pp. 492
    • Cohen, K.B.1    Johnson, H.L.2    Verspoor, K.3    Roeder, C.4    Hunter, L.E.5
  • 45
    • 84876494115 scopus 로고    scopus 로고
    • The eFIP system for text mining of protein interaction networks of phosphorylated proteins
    • C. O. Tudor, C. N. Arighi, Q. Wang, C. H. Wu, and K. Vijay-Shanker, "The eFIP system for text mining of protein interaction networks of phosphorylated proteins," Database J. Biol. Databases Curation, vol. 2012, p. bas044, 2012. doi:10.1093/database/bas044.
    • (2012) Database J. Biol. Databases Curation , vol.2012 , pp. bas044
    • Tudor, C.O.1    Arighi, C.N.2    Wang, Q.3    Wu, C.H.4    Vijay-Shanker, K.5
  • 47
    • 16644373279 scopus 로고    scopus 로고
    • Update on genome completion and annotations: Protein information resource
    • Mar.
    • C. Wu and D. W. Nebert, "Update on genome completion and annotations: Protein information resource," Human Genomics, vol. 1, no. 3, pp. 229-233, Mar. 2004.
    • (2004) Human Genomics , vol.1 , Issue.3 , pp. 229-233
    • Wu, C.1    Nebert, D.W.2
  • 48
    • 84891807550 scopus 로고    scopus 로고
    • Use of the protein ontology for multi-faceted analysis of biological processes: A case study of the spindle checkpoint
    • K. E. Ross, C. N. Arighi, J. Ren, D. A. Natale, H. Huang, and C. H. Wu, "Use of the protein ontology for multi-faceted analysis of biological processes: A case study of the spindle checkpoint," Front. Genetics, vol. 4, p. 62, 2013.
    • (2013) Front. Genetics , vol.4 , pp. 62
    • Ross, K.E.1    Arighi, C.N.2    Ren, J.3    Natale, D.A.4    Huang, H.5    Wu, C.H.6
  • 49
    • 84885901201 scopus 로고    scopus 로고
    • Construction of protein phosphorylation networks by data mining, text mining, and ontology integration: Analysis of the spindle checkpoint
    • K. E. Ross, C. N. Arighi, J. Ren, H. Huang, and C. H. Wu, "Construction of protein phosphorylation networks by data mining, text mining, and ontology integration: analysis of the spindle checkpoint," Database J. Biol. Databases Curation, vol. 2013, p. bat038. doi: 10.1093/database/bat038.
    • (2013) Database J. Biol. Databases Curation , pp. bat038
    • Ross, K.E.1    Arighi, C.N.2    Ren, J.3    Huang, H.4    Wu, C.H.5
  • 50
    • 78651296878 scopus 로고    scopus 로고
    • PhosphoGRID: A database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae
    • C. Stark, T.-C. Su, A. Breitkreutz, P. Lourenco, M. Dahabieh, B.-J. Breitkreutz, M. Tyers, and I. Sadowski, "PhosphoGRID: A database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae," Database J. Biol. Databases Curation, vol. 2010, p. bap026, 2010. doi: 10.1093/database/bap026.
    • (2010) Database J. Biol. Databases Curation , vol.2010 , pp. bap026
    • Stark, C.1    Su, T.-C.2    Breitkreutz, A.3    Lourenco, P.4    Dahabieh, M.5    Breitkreutz, B.-J.6    Tyers, M.7    Sadowski, I.8


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