Very Important – medline baseline files are stored in a different directory than the updates. And here I thought they’d all gone away due to the end of year maintenance. Anyways, doing a high speed wget grab of all the baseline files…we’ll see how the processing goes.
On the flipside, all Pubmed articles with a [...]
Archive for November, 2007
Doh Moment
Posted in MeSH, PubMed on November 13, 2007 | Leave a Comment »
OMIM Gene-Disease to Entrez Gene-MeSH
Posted in Entrez, MeSH, OMIM on November 3, 2007 | 1 Comment »
OMIM Gene to OMIM Disease: The OMIM MorbidMap links loci to disease phenotypes
Entrez Gene mim2gene: Links Entrez Gene to genotype and phenotype OMIM entries
MeSH to OMIM: Doing this by converting to UMLS concepts (prototype in KNIME)
Fetch!
Posted in Entrez, PubMed on November 3, 2007 | Leave a Comment »
Wrote up code to grab all the Disease Heading terms in Pubmed. This set is pretty huge, so it’ll be a good workout for the “real” PubMed set – we’re looking at over 8 million entries in gigantic XML format (PubMed entire is more than double that, but we’re within an [...]
Recoding in XSL
Posted in PubMed, XML on November 3, 2007 | Leave a Comment »
Given that some of the weirdness I’ve been experiencing has involved XML parsing oddities, what better than to switch over to somebody else’s XML parsing system (and then point fingers at them!) This problem probably isn’t going away, given the ubiquitousness of XML as interface language (it would have to be the [...]
