Finally managed to finish the VarCrawler (sub)application for WAVe.
Deploy calls Creator and then Builder.
Creator for starting up and loading default values, Builder will read variants from all the web and load information from GeNS.
It is running now… for 6 hours and is at COLA63…
(Re)Started developing the variant reader. IDbases and other general databases are almost there. More on tomorrow!
MySQL is OK so far!
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!
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.
Updated DiseaseCard database to fit the new GeneCards link. And this was accomplished before UniProt!
(note: first post from MacJournal)
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!
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!
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.
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
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!
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