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

From Plant Ontology Wiki
Jump to navigationJump to search

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 create separate namespaces in the SoyBase ontology SoyBase Ontology page

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?

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

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: should be "Soybean_Ontology" New namespaces:

  • soybean_structure
  • soybean_trait
  • soybean_whole_plant_growth_stages

See comments from 5-27-10 meeting about the renumbering of the top level term: "SOY:0000001:Soybean_Ontology" that number is currently used for germination.

Rex can post a question on the OBO-Edit working group list to see if anyone has an easier way to do this or a script they already hav tried. Send questions to: OBO-Edit Working Group <Geneontology-oboedit-working-group@lists.sourceforge.net>


2. Update on accessing the SVN repository? Laurel has created a folder on the PO SVN repository: SoyBase SVN


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.

Retrieved from "http://wiki.plantontology.org/index.php?title=POC-SoyBase_Webex_Conference_Call_6-11-10,_2010&oldid=1382"