User Advocacy - February 2008: Difference between revisions

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[[Category:Advocacy and Outreach]]
== Virulence Factor Ontology ==
== Virulence Factor Ontology ==



Latest revision as of 16:58, 16 July 2014

Virulence Factor Ontology

From Michelle Gwinn-Giglio:

I think I told you already about the virulence group I met with. Can't remember if I gave you all the details.

Here are some more:

I met with a group of people (most from a company called MITRE, a non-profit that works a lot with the government, others from some national labs, and then me and my colleague Lynn Schryml from IGS) interested in developing a virulence factor ontology. They asked me to come for my knowledge of GO and PAMGO.

After discussing the concepts they want to capture, and after I informed them a bit about the content of PAMGO terms and GO in general, it became clear that almost everything they want to capture is already in GO (and often in the PAMGO section.) There are only two areas on their list that are not currently covered in GO: toxin activity and antibiotic resistance.

Both of these are concepts that used to be in GO but which were obsoleted at one time or another. During this meeting I really started feeling like I should perhaps raise the issue of bringing back these terms in some form. I'm still thinking about that. (and fighting to keep the response to toxin term from getting obsoleted!)

In the meantime, the virulence group has decided to try to annotate some toxins to GO and see where existing terms can be used and if there are any places where new terms might be needed. In addition, we are thinking about ways to capture the toxin activity concepts outside of GO and devising some trees of controlled vocabularies to capture the toxins.

We are also now exploring the use of CheBI and other ontologies to make the kinds of annotations we want to make.


EBI Roadshow Ghent, Belgium

By Jennifer Deegan

This roadshow included a 2 hour tutorial on GO. The users present were about half and half first year PhD students, and postdocs. There were two group leaders. The meeting was organised by Wouter van Gool at VIB, which is predominantly an Arabidopsis research institute, but there were some medical researchers present too.

General GO concepts were presented, followed by a hands-on training in browsing GO on AmiGO and the TAIR website. The users tried the current AmiGO, and the beta version. They also tried Goose. Some users were very perplexed by Goose, while others found it extremely useful. It seemed to be a real eye opener though, and intrigued people. After this, all users tried making their own custom GO slim. We had the usual problems with getting OBO-Edit onto the computers in the room (local rules on installation of applications), which slowed things down. However the users were all very technically able and all had started to add GO terms to their slim by the time the session ended. They were all given a complete tutorial sheet to take away, showing how they could complete the slim and use the GO Slimmer tool on AmiGO.