Not much has happened research-wise (much gnashing of teeth) since the homologene results were computed. UMLS really is a bit of a monster to tackle, I’ll probably hold off on that. GO term analysis seems to be doable reasonable inside R – GOstats and GOsim seem to provide examples of how to put that all [...]
Archive for September, 2007
A little research depression
Posted in Uncategorized on September 28, 2007 | Leave a Comment »
Homologene Results are In!
Posted in R, SQL on September 14, 2007 | Leave a Comment »
Had to tweak the data dump scripts, but it looks like the homologene Human to mouse to disease is done.
Starting to get leery of evidence from low numbers of Pubmed articles. These tend to result in nice low p-values, but I’m guessing that they’re biased by low sample size. Then again, aren’t p-values supposed to [...]
Creating local UMLS repository
Posted in UMLS on September 13, 2007 | Leave a Comment »
Selected for the first pass the following subset of the UMLS: MeSH, ICD9-CM, ICD10, SNOMED CT, Gene Ontology and HUGO gene nomenclature. Ignored the non-english bits for now, and didn’t tinker with the suppressibility. After that…it seems that it’s off to the races.
Also currently running checks on the mysql databases. [...]
UMLS Confusion Fun
Posted in Uncategorized on September 13, 2007 | Leave a Comment »
Starting to look at the SQL code generated by the UMLS. Confusing set of tables (although it is documented) Need to figure out if it can be used “out of the box” (even though the table names are called things like MRCOC) or if it needs to be re-parsed into something more reasonable.
GO Term Analysis
Posted in GO, R on September 10, 2007 | Leave a Comment »
A little side-sojourn into analysis of GO terms, to help out with a paper. Tried out a R tool for computing GO term similarity – GOSim. However, the actual problem was evaluting the annotation level of particular genes, and the GO analysis is to compare the computed annotation level with [...]
