MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations
Open Access
- 27 October 2004
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 21 (5) , 694-695
- https://doi.org/10.1093/bioinformatics/bti087
Abstract
Summary: 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. Availability:http://metnetdb.gdcb.iastate.edu/medkit Contact:berleant@iastate.eduKeywords
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