POC-SoyBase Webex Conference Call 6-11-10, 2010

POC-SOYBase Webex Conference Call

Date: 6-11-10, 2010 8:30am (PDT)

In attendance: POC members: Laurel Cooper (OSU), Ramona Walls (NYBG)

SoyBase members: Rex Nelson,SoyBase USDA-ARS, Ames, Iowa

Discussion items:

1. Hands-on session of OBO-Edit to help Rex and David create separate namespaces in the SoyBase ontology RN: I can write a quick script to add a namespace tag to all of my records in the OBO file or I can use OBO edit? If I use OBO edit, will I have to go term by term and change the default namespace or can I do it globally? Rex sent the obo file and we opened it in OE to try the Namespace manager tool to create the three separate namespaces: Top level:

PJ (by email): It needs to be done whole scale by script.

2. Update on accessing the SVN repository?

3. Items from last meeting:

4. Other Items:

From Rex: The issues are:

1) What identifier should I use in col. 1 (I put SOY_QTL following the TAIR file)

2) We make our map symbols unique identifiers and such use them in our database, that's why Cols. 2 and 3 have the same value

3) Evidence codes. All of our QTL come from the literature so they are genetically mapped entities. The GO evidence codes don't seem to address genetic mapping directly. TAIR mostly used "IC" so that is what I used. It is not exactly correct but I don't know what other thing to put. Is there a better source for evidence codes?

4) Namespaces in the OBO file.