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Tagging Pubmed With Umls

Tagging with MetaMap seems to be very computational intensive and hard to do for the full corpus of Pubmed. Is there a way to do tagging faster with less accuracy or is there maybe a source where I can download Pubmed tagged with UMLS terms?

pubmed text
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updated by Ram Ram • written by Christiank • Christiank

The UMLS Metathesaurus is actually a collection of dictionaries, and MeSH is just a subset of UMLS. So you have to choose first which dictionary of the UMLS Metathesaurus you want to use.

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written by Michael Kuhn Michael Kuhn

Are you looking for tagged PubMed/Medline abstracts, or article full text? I can't tell from your question and comments.

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written by Heather Piwowar • Heather Piwowar

3 answers

I think that the MESH terms of pubmed are tightly related to UMLS.

So you can use the NCBI eutils to download your papers.

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

Yes, that would be my answer too.

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written by Paulo Nuin Paulo Nuin

yes, but MeSH is just a subset of UMLS. You also have other dictionaries in UMLS, like COSTART, MedDRA, SNOMED, ...

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written by Michael Kuhn Michael Kuhn

If I understand it right this allows me to ask NCBI to get pubmed article IDs for a given MESH concept. I don't see where that webservice provides me with information about all the concept contained in a single pubmed article and where they appear.

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written by Christiank • Christiank

But then I still don't have a tagged version of the article but the article in plain text.

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written by Christiank • Christiank

how are you accessing the article ? Are you using the NCBI-Eutilities ?

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written by Pierre Lindenbaum Pierre Lindenbaum

The Medline demo at Lingpipe might help: http://alias-i.com/lingpipe/demos/tutorial/medline/read-me.html and a specialized version, LingMed, at http://alias-i.com/lingpipe/web/sandbox.html

I can't see a Lingpipe example of tagging with the UMLS per se, but you could probably make it work.

Or, you could do a quick and dirty tagging (via NLTK/Lingpipe?/other) with terms and synonyms related to the task you're working on, perhaps derived from the Metathesaurus? http://www.nlm.nih.gov/research/umls/new_users/online_learning/Meta_004.htm

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updated by Ram Ram • written by Heather Piwowar • Heather Piwowar

Try bioLabeler. BioLabeler extracts UMLS concepts from Biomedical texts such as scientific paper abstracts, experiments descriptions or medical notes and can be use to automatically curate and annotate BioMedical Literature or to index large documents databases and improve searches or discover relationships between them.

http://www.biolabeler.com

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written by Joselu • Joselu

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