Literature DB >> 17238458

Towards answering biological questions with experimental evidence: automatically identifying text that summarize image content in full-text articles.

Hong Yu1.   

Abstract

Images (i.e., figures) are important experimental evidence that are typically reported in bioscience full-text articles. Biologists need to access images to validate research facts and to formulate or to test novel research hypotheses. We propose to build a biological question answering system that provides experimental evidences as answers in response to biological questions. As a first step, we develop natural language processing techniques to identify sentences that summarize image content.

Mesh:

Year:  2006        PMID: 17238458      PMCID: PMC1839512     

Source DB:  PubMed          Journal:  AMIA Annu Symp Proc        ISSN: 1559-4076


  7 in total

1.  A hierarchical unsupervised growing neural network for clustering gene expression patterns.

Authors:  J Herrero; A Valencia; J Dopazo
Journal:  Bioinformatics       Date:  2001-02       Impact factor: 6.937

2.  Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules.

Authors:  J L Sussman; D Lin; J Jiang; N O Manning; J Prilusky; O Ritter; E E Abola
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1998-11-01

3.  GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.

Authors:  C Friedman; P Kra; H Yu; M Krauthammer; A Rzhetsky
Journal:  Bioinformatics       Date:  2001       Impact factor: 6.937

4.  Linking molecular imaging terminology to the gene ontology (GO).

Authors:  P K Tulipano; W S Millar; J J Cimino
Journal:  Pac Symp Biocomput       Date:  2003

5.  The Gene Ontology (GO) database and informatics resource.

Authors:  M A Harris; J Clark; A Ireland; J Lomax; M Ashburner; R Foulger; K Eilbeck; S Lewis; B Marshall; C Mungall; J Richter; G M Rubin; J A Blake; C Bult; M Dolan; H Drabkin; J T Eppig; D P Hill; L Ni; M Ringwald; R Balakrishnan; J M Cherry; K R Christie; M C Costanzo; S S Dwight; S Engel; D G Fisk; J E Hirschman; E L Hong; R S Nash; A Sethuraman; C L Theesfeld; D Botstein; K Dolinski; B Feierbach; T Berardini; S Mundodi; S Y Rhee; R Apweiler; D Barrell; E Camon; E Dimmer; V Lee; R Chisholm; P Gaudet; W Kibbe; R Kishore; E M Schwarz; P Sternberg; M Gwinn; L Hannick; J Wortman; M Berriman; V Wood; N de la Cruz; P Tonellato; P Jaiswal; T Seigfried; R White
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

6.  Multiple sequence alignment with hierarchical clustering.

Authors:  F Corpet
Journal:  Nucleic Acids Res       Date:  1988-11-25       Impact factor: 16.971

7.  Exploring supervised and unsupervised methods to detect topics in biomedical text.

Authors:  Minsuk Lee; Weiqing Wang; Hong Yu
Journal:  BMC Bioinformatics       Date:  2006-03-16       Impact factor: 3.169

  7 in total
  16 in total

Review 1.  Frontiers of biomedical text mining: current progress.

Authors:  Pierre Zweigenbaum; Dina Demner-Fushman; Hong Yu; Kevin B Cohen
Journal:  Brief Bioinform       Date:  2007-10-30       Impact factor: 11.622

2.  Automated semantic indexing of figure captions to improve radiology image retrieval.

Authors:  Charles E Kahn; Daniel L Rubin
Journal:  J Am Med Inform Assoc       Date:  2009-03-04       Impact factor: 4.497

3.  Figure summarizer browser extensions for PubMed Central.

Authors:  Shashank Agarwal; Hong Yu
Journal:  Bioinformatics       Date:  2011-04-14       Impact factor: 6.937

4.  Evaluating the Importance of Image-related Text for Ad-hoc and Case-based Biomedical Article Retrieval.

Authors:  Matthew S Simpson; Dina Demner-Fushman; George R Thoma
Journal:  AMIA Annu Symp Proc       Date:  2010-11-13

5.  Degree centrality for semantic abstraction summarization of therapeutic studies.

Authors:  Han Zhang; Marcelo Fiszman; Dongwook Shin; Christopher M Miller; Graciela Rosemblat; Thomas C Rindflesch
Journal:  J Biomed Inform       Date:  2011-05-08       Impact factor: 6.317

6.  FigSum: automatically generating structured text summaries for figures in biomedical literature.

Authors:  Shashank Agarwal; Hong Yu
Journal:  AMIA Annu Symp Proc       Date:  2009-11-14

7.  Automatically extracting information needs from complex clinical questions.

Authors:  Yong-gang Cao; James J Cimino; John Ely; Hong Yu
Journal:  J Biomed Inform       Date:  2010-07-27       Impact factor: 6.317

Review 8.  Overview of the First Natural Language Processing Challenge for Extracting Medication, Indication, and Adverse Drug Events from Electronic Health Record Notes (MADE 1.0).

Authors:  Abhyuday Jagannatha; Feifan Liu; Weisong Liu; Hong Yu
Journal:  Drug Saf       Date:  2019-01       Impact factor: 5.606

9.  Automatic figure ranking and user interfacing for intelligent figure search.

Authors:  Hong Yu; Feifan Liu; Balaji Polepalli Ramesh
Journal:  PLoS One       Date:  2010-10-07       Impact factor: 3.240

10.  Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension.

Authors:  Hong Yu; Shashank Agarwal; Mark Johnston; Aaron Cohen
Journal:  J Biomed Discov Collab       Date:  2009-01-06
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