Plant Tech Tonics

Recently, we decided to migrate our entire codebase from CVS to Subversion (SVN). Ken did most of the groundwork. I am really excited about our new version control setup, and have been dreaming about this for a long time. But to butcher a biblical metaphor, I only played Aaron to Ken’s Moses.

Read the rest of this entry »

It’s Halloween and hot in Texas, and I’m blogging. Read the rest of this entry »

Gramene uses GO terms to annotate proteins and genes. I am familiar with GO terms since I am responsible for developing and maintaining the ontology database and loading all kinds of ontology terms and annotations. I knew little about the GO slim terms. Doreen asked me to generate the GO and GO slim annotations for rice and arabidopsis in this summer. Until then I began to touch the GO slim terms.

GO slim terms are subset of GO terms. It is still a ontology and a DAG. Initially I thought GO slim terms are bunch of ancestor terms without relationship among them. But they are not. Because the GO ontology is a DAG and the GO slim is also a DAG, one term used in annotation may map to several slim terms via different paths. When I looked at the slim example graph It is quite interesting for node 9 and 10. Node 9 seems mapping to slim node 3 and 4. But node 3 is not because it is a parent term of the slim node 4. Node 4 is the most pertinent term of node 9 comparing to node 3. Node 10 can get to slim node 2 and node 3 via two paths( 10->5->2 or 10->8->6->3) . Since slim node 2 and node 3 have no hierarchical relationship, node 10 can map to both slim node 2 and node 3.

Gramene ontology database stores the GO terms and the relationship of these terms. It does not store the slim terms and relationships. I can’t use the gramene ontology database to do the GO slim mapping. I find Chris Mungall already has one script map2slim to do the work. It is easy now since Shuly has already installed the go-perl package for amigo on our machine, and I have the ontology cvs which contains the GO ontology and GO slim ontology terms. The map2slim need the input file in specific GO annotation format. What I have to do is to write a generic script to get the ensembl gene annotations from ensembl databases and generate the result in the GO annotation format. My work is done ! Later I’d like to look into the map2slim codes to see what the code does when the relationships in the slim ontology is not consistent with the relationships of the GO ontology, e.g. a slim term becomes obsolete in the GO ontology. Now the script just fails.

This weekend I’ve been working on tuning the MySQL server parameters, In order to optimize MySQL on our production environment, so called ‘flume’. Read the rest of this entry »

It’s late on stormy Friday night in mid October, probably a good time for my inaugural post to this blog. In particular as I have done very little in the way of plant informatics work recently.

So; what has been on my plate? I’ve contributed a chunk of web code to the (long delayed) Ensembl 51 release. This is a page for displaying gene trees. I’ve been promising various Ensembl-ites that I would work this up to for many years, so this is my special gift for their half-century. I’m not going to try to explain what it looks like, or provide a link (it’s not released yet), sorry. I am, however, quite pleased by the end result!

But most of my time recently has been taken up with writing the ‘WormMart’ paper in the last few weeks that I have working on that project (WormBase is off to Canada without me). WormMart, for those not intimately familiar with resources for the study of the biology of nematodes, is my (BioMart-based) data warehouse for WormBase and is, as such, similar to GrameneMart. So I’ve been buried in bioinformatics database papers in an effort to absorb sufficient of their nuances for me produce a decent forgery.

I missed posting last Friday because I was out, Read the rest of this entry »

Now that Gramene’s 28 release is mostly done (I’m rebuilding CMap with UniGenes and need to figure out the stacked maps still), I’ve been on a modernization and reorganization kick. Read the rest of this entry »

Build 28 of Gramene is finally out Read the rest of this entry »