Posted: April 20th, 2009 | Author: shuly | Filed under: Uncategorized | No Comments »
Plant Ontology Consortium (POC) is excited to announce the release #0409 (April 2009) of the Plant Ontology Database.
In this release, we bring you 26625 gene annotations from TAIR, Gramene, SGN and MaizeGDB, 8558 QTL annotations from Gramene, 9832 germplasm associations from SGN, MaizeGDB and NASC.
The following number of annotations were added for the first time: 16016 gene annotations from TAIR, 3 gene annotations from Gramene, 2 gene annotations from SGN and 3928 germplasm annotations from MaizeGDB.
For genes curated by TAIR and SGN, you may also find links to their Gene Ontology (GO) pages through PO browser.
The new ontology files and the database dump are available for download.
To submit plant ontology term requests, we encourage researchers to use SourceForge PO tracker.
The Plant Ontology Consortium
web: http:www.plantontology.org
e-mail: po-dev at plantontology.org
The project is funded by National Science Foundation, USA, (Grant No. DBI-0703908)
Posted: December 2nd, 2008 | Author: shuly | Filed under: Uncategorized | 2 Comments »
…became an aunt to two beautiful twins, a girl and a boy, of my brother and his beautiful wife! Then on the next day I hear that my other brother’s girlfriend is pregnant too, and we’re all very excited – so I guess I can finally, somehow, in a way… be part of the “gramene babies” family…
Now back to business… These last couple weeks I’ve been working on several things. I’ll briefly discuss a few.
So, right after we’ve came out with the Plant Ontology data release on November 12 (yea!!!), I started setting up the Plant Ontology wiki. A decision was made, to convert all the documentation pages that are currently hosted on the plant ontology website in html format, onto the wiki, in order to simplify the task of editing documents and updating the website’s repository. To convert the html to wiki format I used the html2wiki converter, which helped quite a bit with the task, but required a few manual fixes to the pages.
The PO wiki access has been set up as read-only for everyone, and may be edited by registered users only. However, we also need an internal section that only registered users may read. Well, this is a bit tricky, since MediaWiki is not supporting per-page access restriction. According to MediaWiki documentations, there are two basic possibilities:
1. Set up separate wikis with a shared user database, configure one as viewable and one as unviewable, and make interwiki links between them.
2. Install a third-party hack or extension. You will have to reapply it every time you upgrade the software, and it may not be updated immediately when new security fixes or upgrades of MediaWiki are released. Almost all hacks or patches promising to add them will likely have flaws somewhere, which could lead to exposure of confidential data
A list of various extensions that restrict user access to specific pages or namespaces, and problems they may exhibit or, on the contrary, deal with, is found here.
In order to test the extensions for security problems, one may consult this page
Going over the above lists, I have chosen to test the Extension:Lockdown, which should allow us to use a custom namespace for our internal usage.
Using this extension, I’ve created a custom namespace, which only registered users may access. So far it seem to be working well. However, pages in this namespace do appear in search results, as well as on the “recent changes” page, yet the whole page is not accessible to anonymous users, and requires login to view. I intend to make some further testing to make sure no sensitive data is exposed, yet, I feel that we should eventually use two separate wikis with interwiki links between them (despite the fact that Pankaj is reluctant to maintain two wikis).
Another task I accomplished was to copy MySQL databases (all ensembl and markers dbs) from our live database server onto a new server, ‘filetta’, designated for web services, to be used by external users. These databases were created as compressed, read-only, using the ‘myisampack’ utility. This resulted in significant savings in space, and hopefully, better performance (that we’re still testing). To make my compression task simpler, and not to forget any step along the way (such as: locking the tables before packing, running myisamchk to check the tables for errors, rebuilding the indexes after packing and then flushing the tables) I wrote a simple shell script, which I can provide upon request (I intended to post it here, but encountered serious indentation problems).
Just to mention another MySQL database related work, is the “house cleaning” of “cabot”, our development database server, and changing the backup strategy from backing up all databases on a daily basis, which takes a huge amount of space and a long processing time (more than 12 hours), to selectively backing up some databases daily, and others on a weekly basis, as needed. Next thing would be to keep up with the performance tuning work as I discussed in my previous blog enrty.
One other thing I’ve been working on is semantic web services for the Plant Ontology using the SSWAP infrastructure. I’ve started off with composing a simple OWL-DL ontology, using the ontology editor protégé, to describe PO annotations. This first draft of the ontology is based on the PO database structure and the type of data we are aiming to provide, and is following the guidelines of similar ontologies hosted on the SSWAP ontologies page . The generated poAnnotation.owl ontology file may be best viewed by opening it with protege.
Well, that’s it for now…
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