Seems like the homologene mouse route (human gene to mouse gene to generif to pubmed to MeSH) worked OK – need to put together the baseline (how many articles are related via generif in general if we go by mouse) then combine this (and compare to human results). Hypothesis is that there will be more [...]
Archive for August, 2007
Partial Success?
Posted in Uncategorized on August 29, 2007 | Leave a Comment »
OMIM diseases and genes
Posted in Uncategorized on August 28, 2007 | Leave a Comment »
Time to start mapping out how I will extract OMIM references to brain diseases and TF genes from the existing databases. For TF genes, this should be easy, just extract the OMIM references from Entrez Gene itself. This should map both OMIM disease and OMIM gene entries to genes
This leaves mapping the OMIM disease names [...]
Reloaded…and then???
Posted in SQL on August 28, 2007 | Leave a Comment »
After the reload, jumped right in and tried the big query. And no error…but no result?! Starting to get frustrated, says my brain. But turns out that the mesh table was incorrectly loaded – darn difference between a comma and semi-colon! Trying to re-run now with corrected results.
Also [...]
This Week’s TODO list
Posted in todo on August 27, 2007 | Leave a Comment »
Look at extracting TFs and brain diseases from OMIM
parsing OMIM, look for existing OMIM-to-MeSH binding
Do first order separation database query
sonoma back online, databases reloaded
write auto-reload database script
date stamp older versions, automatically invoke parsers as needed
skeleton of scripts and directories for rapid deployment on server
Web Version
Posted in SQL, rails, ruby on August 24, 2007 | Leave a Comment »
Starting to look at what will be needed to make a web accessible version of the database live. Ruby on Rails looks promising – OO scripting language, automagic linking to databases and building webpages. What’s not to like?
Downsides – looks like it needs new-style MySQL password hashing – it looks like the [...]
Reloaded!
Posted in SQL on August 24, 2007 | Leave a Comment »
Concatenated all the loading commands into a script. The reloading went off without a hitch last night, so here’s crossing my fingers hoping that first order related articles will work out.
Things to consider doing while I’m in the reloading frame of mind: writing scripts to automatically download newer versions of all the [...]
SQL Woes
Posted in SQL on August 23, 2007 | Leave a Comment »
Currently suffering from SQL limitation setbacks – hitting situation where temporary tables are getting big (then again, we’re in the millions or billions or records…maybe there’s temp file limitations).
On the upside, I’m happy to discover that MySQL text client has tab completion…
Current status – I’ve loaded homologene, and I’ve crafted queries for related articles. [...]
Back to the Research!
Posted in todo on August 10, 2007 | Leave a Comment »
Finally – it’s time to get back to research. A couple things currently on the plate as extra-curricular:
journal version of the n-SIFT paper. I should set up experiments to correlate angle of rotation with point match error
finish testing for the shape-based ChIP on chip expression peak modelling
Back to my actual research!
Speaking of [...]
