How does one go looking up the features near a chromosomal location? At first pass, this seems pretty trivial – grab a genome browser of choice, then go look. But if I want to get the humans out of the loop, and do this automagically, it’s not so trivial.
First pass is to ask Google – [...]
Archive for the ‘Entrez’ Category
Searching the Genome…
Posted in Entrez on June 30, 2008 | Leave a Comment »
Gene2Pubmed
Posted in Entrez on January 25, 2008 | Leave a Comment »
Found another source of gene-pubmed links in Entrez Gene: There’s a gene2pubmed table! Turns out the pubmed citations you get in Entrez Gene are curated, and stored in their own table. Includes NCBI curated things as well as citations taken from public repositories. Anyways, this means more links for me to use – at the [...]
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 [...]
