MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations | Zendy

Jing Ding | Zendy; Daniel Berleant | Zendy

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MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations

Author(s) -

Jing Ding,

Daniel Berleant

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti087

Subject(s) - computer science , medline , information retrieval , data science , world wide web , biology , biochemistry

MEDLINE/PubMed is one of the most important information sources for bioinformatics text mining. However, there remain limitations in working with MEDLINE/PubMed citations. For example, PubMed imposes an upper limit of 10,000 for downloading PMID list or citations; and MEDLINE files are too large for most off-the-shelf XML parsers. We developed a Java package, MedKit, to work-around the limitations, as well as provide other useful functionalities, e.g. random sampling. Its four modules (querier, sampler, fetcher and parser) can work independently, or be pipelined in various combinations. It can be used as a stand-alone GUI application, or integrated into other text-mining systems. Text mining researchers and others may download and use the toolkit free for non-commercial purposes.

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