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MEDLINE tools
Automatic retrieval of MEDLINE citations from a list of PubMed IDs (PMIDs)

The following perl tool retrieves PubMed citations in XML format from a list of PubMed IDs (pmids). It is based on the demonstration program eutils_example.pl available from PubMed Programming Utilities.

• prepareIDlist.pl takes the full list of pmids to process and breaks it in batches of 215, which is about the maximum number of PMIDs eFetch will process in one call.

• eutils_AN.pl uses the files prepared above to produce the XML file.
  

• the resulting XML file can be used as an input for this Medline Categorization Tool, described in this paper.

• Alternatively, post_fetch_pubmed.pl [PMIDs] [MEDLINE] takes a list of PMIDs and returns the corresponding citations in MEDLINE format. It uses the perl package NCBI_PowerScripting distributed with Powerscripting course material.

• eutils_RelatedCitation.pl takes a list of PMIDs and returns the MEDLINE citations retrieved for each PMID by the PubMed Related Citations algorithm.

Acknowledgements: This work was supported by an appointment of A. Névéol to the NLM Postdoctoral Program sponsored by the National Library of Medicine and administered by the Oak Ridge Institute for Science and Education.

 

Mar. 2006, revised Jul'08