Back on builder
(Re)Started developing the variant reader. IDbases and other general databases are almost there. More on tomorrow!
MySQL is OK so far!
LSDB list final
Finalized the LSDB-Gene list with verification against IDBases, LOVD and UMD datbases.
Plenty more genes now (also removed lots of “dead” genes and other erroneous links! Sent it to Adam at Leicester… ask him to share with the world?
On other news, tomorrow time to migrate the system to MySQL!
Gene-LSDB list
Finished Stage 1 of the list containing LSDB and Gene relations. I won’t leave it like it is.
Next step will include careful verifications for each IDbases, UMD and LOVD (include version number) and a normalization of the list.
One file with all the lists will be easier to maintain.
Then, send it to Leicester.
DiseaseCard GeneCards Update
Updated DiseaseCard database to fit the new GeneCards link. And this was accomplished before UniProt!
(note: first post from MacJournal)
WAVe: jQuery Tree online
WAVe finally has a Javascript tree. There are many many issues with the data… PubMed ID values are being passed to OMIM addresses… don’t know what’s wrong!
Still have to rewrite the xmlCard methods and re-test (and comment) all the tree functions!
Semantic Web in 20 minutes – Part 2
Full morning presenting “Semantic Web in 20 minutes”. Several questions but I guess I’ve managed to explain everything… don’t really know what the general opinion from “upstairs” but we’ll see…
The afternoon was lost trying to install PHP and OpenConf in CICUA’s bioserver!
Semantic Web in 20 Minutes
And today I’ve finished the keynote regarding Semantic Web due tomorrow.
Also created a new mockup for EU-ADR Web Platform and was given a new one to do. Tomorrow it is. Also JLO has greenlit my attendance to the EBI Summer School in June. Hope I can get in.
750 genes on WAVe
Finally finished LOVD importer based on their REST Atom Feeds API. It takes a long time to import everything and even more time to get the PubMed publications associated with each gene (only genes with variants: 91 minutes).
Also started preparing the “Semantic Web in 20 minutes” keynote. Due on tuesday.
Current WAVe status: 232 diseases, 750 genes, 27570 publications, 802390 variants
Pedrolopes.net with Clean URLs
Some new updates on Pedrolopes.net also.
Included header and footer (.php) in the various files to easy the update process. Added .htaccess rules to enable pretty URLs. No more about.php, just about!
Stripes & jQuery -> =(
Spent most of the day trying to put Stripes working with jQuery for an autocomplete search box… The idea is to show autocomplete when searching for genes! It was really complex and it is not working. The main problem are the autocomplete plugins who usually search by appending a “q=
I guess I really need to spend more time planning the application.
On a success note: all LOVD 2.0.24 installations variants where added to the WAVe database. Current status: 750 genes with variant data.
