메뉴 건너뛰기




Volumn 7, Issue 3, 2010, Pages 454-461

An IR-aided machine learning framework for the biocreative II.5 challenge

Author keywords

Bioinformatics (genome or protein) databases; information search and retrieval; systems and software; text mining

Indexed keywords

BIOINFORMATICS (GENOME OR PROTEIN) DATABASE; EXTERNAL KNOWLEDGE; INFORMATION SEARCH AND RETRIEVAL; MACHINE-LEARNING; ORTHOLOGS; TEXT MINING; TRAINING DATA; UNIVERSITY OF WISCONSIN-MILWAUKEE;

EID: 77955473893     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2010.56     Document Type: Article
Times cited : (3)

References (41)
  • 1
    • 33748372941 scopus 로고    scopus 로고
    • Automatic document classification of biological literature
    • D. Chen, H.M. Müller, and P.W. Sternberg, "Automatic Document Classification of Biological Literature," BMC Bioinformatics, vol.7, p. 370, 2006.
    • (2006) BMC Bioinformatics , vol.7 , pp. 370
    • Chen, D.1    Müller, H.M.2    Sternberg, P.W.3
  • 3
    • 8444226721 scopus 로고    scopus 로고
    • Biomedical named entity recognition using two-phase model based on SVMs
    • K.J. Lee, Y.S. Hwang, S. Kim, and H.C. Rim, "Biomedical Named Entity Recognition Using Two-Phase Model Based on SVMs," J. Biomedical Informatics, vol.37, pp. 436-447, 2004.
    • (2004) J. Biomedical Informatics , vol.37 , pp. 436-447
    • Lee, K.J.1    Hwang, Y.S.2    Kim, S.3    Rim, H.C.4
  • 6
    • 6344229209 scopus 로고    scopus 로고
    • Molecular triangulation: Bridging linkage and molecular-network information for identifying candidate genes in alzheimer's disease
    • Oct.
    • M. Krauthammer, C.A. Kaufmann, T.C. Gilliam, and A. Rzhetsky, "Molecular Triangulation: Bridging Linkage and Molecular-Network Information for Identifying Candidate Genes in Alzheimer's Disease," Proc. Nat'l Academy of Sciences USA, vol.101, pp. 15148- 15153, Oct. 2004.
    • (2004) Proc. Nat'l Academy of Sciences USA , vol.101 , pp. 15148-15153
    • Krauthammer, M.1    Kaufmann, C.A.2    Gilliam, T.C.3    Rzhetsky, A.4
  • 7
    • 0033655017 scopus 로고    scopus 로고
    • Biobibliometrics: Information retrieval and visualization from co-occurrences of gene names in medline abstracts
    • B.J. Stapley and G. Benoit, "Biobibliometrics: Information Retrieval and Visualization from Co-Occurrences of Gene Names in Medline Abstracts," Proc. Pacific Symp. Biocomputing, pp. 529-540, 2000.
    • (2000) Proc. Pacific Symp. Biocomputing , pp. 529-540
    • Stapley, B.J.1    Benoit, G.2
  • 8
    • 70349571707 scopus 로고    scopus 로고
    • Mining protein-protein interactions from published literature using linguamatics i2e
    • (Clifton, NJ)
    • J. Bandy, D. Milward, and S. McQuay, "Mining Protein-Protein Interactions from Published Literature Using Linguamatics I2E," Methods in Molecular Biology (Clifton, NJ), vol.563, pp. 3-13, 2009.
    • (2009) Methods in Molecular Biology , vol.563 , pp. 3-13
    • Bandy, J.1    Milward, D.2    McQuay, S.3
  • 9
    • 0002284942 scopus 로고    scopus 로고
    • Identifying the interaction between genes and gene products based on frequently seen verbs in medline abstracts
    • T. Sekimizu, H. Park, and J. Tsujii, "Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts," Proc. Workshop Genome Informatics, vol.9, pp. 62-71, 1998.
    • (1998) Proc. Workshop Genome Informatics , vol.9 , pp. 62-71
    • Sekimizu, T.1    Park, H.2    Tsujii, J.3
  • 11
    • 0347724100 scopus 로고    scopus 로고
    • GIS: A biomedical text-mining system for gene information discovery
    • Jan.
    • J. Chiang, H. Yu, and H. Hsu, "GIS: A Biomedical Text-Mining System for Gene Information Discovery," Bioinformatics, vol.20, pp. 120-121, Jan. 2004.
    • (2004) Bioinformatics , vol.20 , pp. 120-121
    • Chiang, J.1    Yu, H.2    Hsu, H.3
  • 13
    • 33947304181 scopus 로고    scopus 로고
    • Overview of BioCreAtIvE: Critical assessment of information extraction for biology
    • L. Hirschman, A. Yeh, C. Blaschke, and A. Valencia, "Overview of BioCreAtIvE: Critical Assessment of Information Extraction for Biology," BMC Bioinformatics, vol.6, suppl 1, pp. S1-S10, 2005.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • Hirschman, L.1    Yeh, A.2    Blaschke, C.3    Valencia, A.4
  • 14
    • 51049088875 scopus 로고    scopus 로고
    • Overview of the protein-protein interaction annotation extraction task of biocreative II
    • M. Krallinger, F. Leitner, C. Rodriguez-Penagos, and A. Valencia, "Overview of the Protein-Protein Interaction Annotation Extraction Task of Biocreative II," Genome Biology, vol.9, suppl 2, pp. S4- S22, 2008.
    • (2008) Genome Biology , vol.9 , Issue.SUPPL. 2
    • Krallinger, M.1    Leitner, F.2    Rodriguez-Penagos, C.3    Valencia, A.4
  • 15
    • 75249101080 scopus 로고    scopus 로고
    • Evaluation of linguistic features useful in extraction of interactions from pubmed; Application to annotating known, high-throughput and predicted interactions in i2d
    • Jan.
    • Y. Niu, D. Otasek, and I. Jurisica, "Evaluation of Linguistic Features Useful in Extraction of Interactions from PubMed; Application to Annotating Known, High-Throughput and Predicted Interactions in I2D," Bioinformatics, vol.26, pp. 111-119, Jan. 2010.
    • (2010) Bioinformatics , vol.26 , pp. 111-119
    • Niu, Y.1    Otasek, D.2    Jurisica, I.3
  • 16
  • 17
    • 0742321913 scopus 로고    scopus 로고
    • Mining the biomedical literature in the genomic era: An overview
    • H. Shatkay and R. Feldman, "Mining the Biomedical Literature in the Genomic Era: An Overview," J. Computational Biology, vol.10, pp. 821-855, 2003.
    • (2003) J. Computational Biology , vol.10 , pp. 821-855
    • Shatkay, H.1    Feldman, R.2
  • 22
    • 0035236048 scopus 로고    scopus 로고
    • GENIES: A natural-language processing system for the extraction of molecular pathways from journal articles
    • (Oxford, England)
    • C. Friedman, P. Kra, H. Yu, M. Krauthammer, and A. Rzhetsky, "GENIES: A Natural-Language Processing System for the Extraction of Molecular Pathways from Journal Articles," Bioinformatics (Oxford, England), vol.17, pp. 74-82, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 74-82
    • Friedman, C.1    Kra, P.2    Yu, H.3    Krauthammer, M.4    Rzhetsky, A.5
  • 23
    • 1842559914 scopus 로고    scopus 로고
    • Extracting human protein interactions from MEDLINE using a full-sentence parser
    • Mar.
    • N. Daraselia, A. Yuryev, S. Egorov, S. Novichkova, A. Nikitin, and I. Mazo, "Extracting Human Protein Interactions from MEDLINE Using a Full-Sentence Parser," Bioinformatics, vol.20, pp. 604-611, Mar. 2004.
    • (2004) Bioinformatics , vol.20 , pp. 604-611
    • Daraselia, N.1    Yuryev, A.2    Egorov, S.3    Novichkova, S.4    Nikitin, A.5    Mazo, I.6
  • 25
    • 1842765629 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using support vector machines
    • Feb.
    • A. Koike and T. Takagi, "Prediction of Protein-Protein Interaction Sites Using Support Vector Machines," Protein Eng., Design and Selection, vol.17, pp. 165-173, Feb. 2004.
    • (2004) Protein Eng., Design and Selection , vol.17 , pp. 165-173
    • Koike, A.1    Takagi, T.2
  • 26
    • 33947305118 scopus 로고    scopus 로고
    • Identifying gene and protein mentions in text using conditional random fields
    • R. McDonald and F. Pereira, "Identifying Gene and Protein Mentions in Text Using Conditional Random Fields," BMC Bioinformatics, vol.6, suppl 1, pp. S6-S12, 2005.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 1
    • McDonald, R.1    Pereira, F.2
  • 27
    • 33645106979 scopus 로고    scopus 로고
    • Automatic term list generation for entity tagging
    • T. Sandler, A.I. Schein, and L.H. Ungar, "Automatic Term List Generation for Entity Tagging," Bioinformatics, vol.22, pp. 651-657, 2006.
    • (2006) Bioinformatics , vol.22 , pp. 651-657
    • Sandler, T.1    Schein, A.I.2    Ungar, L.H.3
  • 31
    • 0036579940 scopus 로고    scopus 로고
    • Mapping abbreviations to full forms in biomedical articles
    • May
    • H. Yu, G. Hripcsak, and C. Friedman, "Mapping Abbreviations to Full Forms in Biomedical Articles," J. Am. Medical Informatics Assoc., vol.9, pp. 262-272, May 2002.
    • (2002) J. Am. Medical Informatics Assoc. , vol.9 , pp. 262-272
    • Yu, H.1    Hripcsak, G.2    Friedman, C.3
  • 32
    • 1242349373 scopus 로고    scopus 로고
    • Extracting synonymous gene and protein terms from biological literature
    • (Oxford, England)
    • H. Yu and E. Agichtein, "Extracting Synonymous Gene and Protein Terms from Biological Literature," Bioinformatics (Oxford, England), vol.19, suppl 1, pp. i340-i349, 2003.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Yu, H.1    Agichtein, E.2
  • 33
    • 84976825385 scopus 로고
    • Algorithms for the longest common subsequence problem
    • D.S. Hirschberg, "Algorithms for the Longest Common Subsequence Problem," J. ACM, vol.24, pp. 664-675, 1977.
    • (1977) J. ACM , vol.24 , pp. 664-675
    • Hirschberg, D.S.1
  • 34
    • 0012866045 scopus 로고    scopus 로고
    • The state of record linkage and current research problems
    • Statistical Research Division, United States Census Bureau
    • W.E. Winkler, "The State of Record Linkage and Current Research Problems," Technical Report RR99-04, Statistical Research Division, United States Census Bureau, 1999.
    • (1999) Technical Report RR99-04
    • Winkler, W.E.1
  • 36
    • 33749588452 scopus 로고    scopus 로고
    • A large scale, corpus-based approach for automatically disambiguating biomedical abbreviations
    • H. Yu, W. Kim, V. Hatzivassiloglou, and J. Wilbur, "A Large Scale, Corpus-Based Approach for Automatically Disambiguating Biomedical Abbreviations," ACM Trans. Information Systems, vol.24, pp. 380-404, 2006.
    • (2006) ACM Trans. Information Systems , vol.24 , pp. 380-404
    • Yu, H.1    Kim, W.2    Hatzivassiloglou, V.3    Wilbur, J.4
  • 37
    • 33847616032 scopus 로고    scopus 로고
    • Using MEDLINE as a knowledge source for disambiguating abbreviations and acronyms in full-text biomedical journal articles
    • H. Yu, W. Kim, V. Hatzivassiloglou, and W.J. Wilbur, "Using MEDLINE as a Knowledge Source for Disambiguating Abbreviations and Acronyms in Full-Text Biomedical Journal Articles," J. Biomedical Informatics, vol.40, pp. 150-159, 2007.
    • (2007) J. Biomedical Informatics , vol.40 , pp. 150-159
    • Yu, H.1    Kim, W.2    Hatzivassiloglou, V.3    Wilbur, W.J.4
  • 38
    • 4944229711 scopus 로고    scopus 로고
    • GENIA corpus- semantically annotated corpus for bio-textmining
    • J. Kim, T. Ohta, Y. Tateisi, and J. Tsujii, "GENIA Corpus- Semantically Annotated Corpus for Bio-Textmining," Bioinformatics, vol.19, suppl 1, pp. i180-i182, 2003.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Kim, J.1    Ohta, T.2    Tateisi, Y.3    Tsujii, J.4
  • 39
    • 25144520247 scopus 로고    scopus 로고
    • ABNER: An open source tool for automatically tagging genes, proteins and other entity names in text
    • July
    • B. Settles, "ABNER: An Open Source Tool for Automatically Tagging Genes, Proteins and Other Entity Names in Text," Bioinformatics, vol.21, pp. 3191-3192, July 2005.
    • (2005) Bioinformatics , vol.21 , pp. 3191-3192
    • Settles, B.1
  • 41
    • 33747886579 scopus 로고    scopus 로고
    • Accessing bioscience images from abstract sentences
    • H. Yu and M. Lee, "Accessing Bioscience Images from Abstract Sentences," Bioinformatics, vol.22, pp. e547-e556, 2006.
    • (2006) Bioinformatics , vol.22
    • Yu, H.1    Lee, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.