POC Conf. Call 9-29-10

POC meeting, Webex Conference Call; Date: Sept 29th, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 9-22-10 meeting?

Updating and Fixing the Annotations

We need to formalize the procedures in place for making updates to the annotation files on the SVN and in our ontologies.

Current status:

• TAIR- Would like us to set up an script to automatically retrieve the files from their FTP site. They are updated weekly- do we want to reload the files between releases to keep the annotations more up-to-date?

• MaizeGDB-

• Gramene-

• Solanaceae Genomics network (SGN)

Other Items

• We have been contacted by Stefan Rensing, University of Freiburg, Germany re: setting up an ontology for bryophytes with a focus on the model moss Physcomitrella patens.

Ramona and Dennis will respond to him. Issues arising from this:

• Setting the AmiGO browser to display terms that have been obsoleted.

Laurel posted a message on the AmiGO SF tracker and has been discussing this possibility with Seth Carbon at the Berkeley Bioinformatics group.

In summary, it appears there may* be a variable in the config.pl file that can be set before installation or reinstsllstion.

$ENV{AMIGO_OBSOLETE_BEHAVIOUR}

The options are: 'ignore','include_commented', and 'include_all'.

However, Seth was not sure how much of this is in the current version of AmiGO. Chris- Perhaps you know better??

• Status of BSA announcement for bulletin? Did it ever get sent?

• Mailing lists

We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal. I think po-announce, po-internal are fine, but what are the other 2 supposed to be for?

In mid-August the new list po-discuss@plantontology was set up and the members of po-internal were added to it. This is the address that will be used in the letters to the reviewers.

We all agreed that these need to be reviewed and we need to deal with the spam problem as well.

PO slims

GO includes reduced versions of their ontologies (Go slims) for some user groups. The slims are developed and maintained by the users, but publicly accessable as part of the GO flat file. We have one user group (TraitNet) that is interested in creating a PO slim. We should decide if we want to include that in the PO flat file, and if we want to have any other policies regarding slims. For example, GO also maintains a generic slim. Should we make something similar (especially as the PO gets more detailed and adds more taxon specific terms)?

Upcoming meetings 2010-2011:

• Latin American Congress of Botany

LACB. La Serena, Chile, October 4-10;

Dennis is attending LACB. We will consider having a presentation at this meeting. Alejandra will not be able to attend.

• Infectious Disease Ontology Workshop

Dallas, Dec. 8th and 9th, 2010

Organized by Lindsay Cowall (Duke University) and others, under the auspices of the National Center for Biomedical Ontology. IDO Workshop December 2010. Note that relations between the IDO and other ontologies is one of their provisional goals.

Pankaj will represent the PO with regard to plant infectious diseases. This is especially relevant to the PO as infectious disease agents (viruses and bacteria) are widely used in plant genetic research.

For additional information on the IDO see http://www.infectiousdiseaseontology.org/Home.html

• Plant and Animal Genome XIX Conference

January 15-19, 2011 PAG 2011

Registration is open, abstract deadline Nov 1, 2010.

Lol and Ramona should plan on attending and meeting with collaborators. Set up a computer demonstration, and possibly a Phenote workshop. Perhaps Dennis and Alejandra could also attend, and we could all meet there. PJ is not attending as he is teaching.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open- deadline for abstracts: 31 October 2010, Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.

Ramona contacted the organizers about whether or not it is possible to get a room with Internet for outreach activities, but hasn't gotten a response yet. Is this something we still want to pursue?

Pankaj, Ramona, and Angelica Cibrian (Harvard and ANMH, Genomics of Seed Plants) are scheduled to give talks and must submit abstracts by October 31st. Three additional speakers will be chosen from abstracts that are submitted.

Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology.