NDLI: Use of figures in literature mining for biomedical digital libraries

Content Provider	IEEE Xplore Digital Library
Author	Nawei Chen Shatkay, H. Blostein, D.
Copyright Year	2006
Description	Author affiliation: Sch. of Comput., Queen's Univ., Kingston, Ont. (Nawei Chen; Shatkay, H.; Blostein, D.)
Abstract	The maintenance of biomedical digital libraries (including organism databases and protein databases) involves analysis of a large number of documents. Much work is done manually: curators study large numbers of biomedical documents while updating and annotating organism databases such as MGI (mouse genome informatics) and Flybase (a database of the fruit-fly genome). We summarize the annotation process in organism databases, and describe some of the roles played by the gene ontology and by document databases such as PubMed. Efforts are ongoing to automate parts of the annotation process. Biomedical text mining contests, such as the TREC Genomics Track (Hersh et al., 2004, 2005), define annotation subtasks, and provide training and test data. So far, these efforts have focused on the analysis of the text content of documents. We are investigating the analysis of figures in biomedical documents; the information derived from figure analysis may later be combined with the information derived from text analysis. We present an algorithm for using figures in document triage; triage involves determining which documents are relevant to a given annotation task. In our triage algorithm, we segment figures into subfigures and classify the subfigures as graphical, gel, fluorescence microscopy, and other microscopy. A secondary classification into subcategories is performed by clustering, using clusters created from the subfigures in the labeled training data. The classifications of all subfigures in a document are combined to form a document descriptor. The document descriptor is then classified using a naive Bayes classifier, as either relevant or irrelevant to the given annotation task
Starting Page	18
Ending Page	197
File Size	2042937
Page Count	180
File Format	PDF
ISBN	0769525318
DOI	10.1109/DIAL.2006.45
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2006-04-27
Publisher Place	France
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Software libraries Data analysis Databases Microscopy Genomics Clustering algorithms Organisms Bioinformatics Information analysis
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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