PAMGO conference calls

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PAMGO Conference Call-March 18, 2008

Update on association files submitted to GOC:
              gene_association.PAMGO_Atumefaciens.gz
              gene_association.PAMGO_Oomycetes.gz
              gene_association.PAMGO_Magnaporthe grisea.gz


Issues arising from proposed terms on infection processes in fungi and oomycetes, under discussion by the fungal and oomycete groups. (Credit to Shaowu for taking the initiative on the term development

The set of new terms (about 50) will be sent out after the two groups have finished working on it but there are some general issues which we thought we could bring up at the conference call for discussion.

One of the terms in the proposal is "lesion development" We would want to hear other views on how to deal with cellular and tissue damage. Is "cell killing" the only appropriate term? What if you are looking at chlorotic or water-soaked lesions.

The second issue is whether we need child terms of pathogenesis viz regulation of pathogenesis, positive and negative regulation of pathogenesis. Is that a possibility or we are all convinced that pathogenesis should have no child terms


Changing wording in some host terms

At the last conference call, I mentioned I was rewording some of the host terms already incorporated in the GO. Attached is a file of the original host terms and the changes I made to some of these terms, based on an earlier discussion and comments sent by some members of the group. Please look at the terms again, confirm that they should remain in the ontology and correct wording where necessary. Send corrected files to me by e-mail (trudy@vbi.vt.edu). Unresolved issues will be discussed at the conference call. File:ChecK Host terms.xls



"Induction" and "Up-regulated" terms

At the last meeting, there was a consensus on making the "induction" and "up-regulation" terms synonyms of the parent term "positive regulation" Find attached, a list of the terms tagged to be collapsed into the respective parent terms. File:Induction Upregulation.doc

PAMGO Conference Call-February 15 2008

Update on association files submitted to GOC:

               gene_association.PAMGO_Atumefaciens.gz
               gene_association.PAMGO_Oomycetes.gz



Update on association files for:

                 P. syringae
                 Erwinia sp
                 M. grisea


GOC announcement: Regulation terms

                 "For some time now, the GO content developers have been aware that
                   regulatory processes are not necessarily integral to the processes (as
                   previously indicated by the use of the 'part_of' relation) that they
                   regulate. Nevertheless, regulatory processes have been represented as
                   part_of the processes they regulate. We have long intended to replace
                   these part_of relationships with a new relationship type called
                   'regulates'. We are now in a position to make this replacement" 
                   See entire e-mail:  File:New relationship types in GO.doc
                   Most of the modulation/regulation terms have a is_a relationship to parents
                   Few with part_of relationships, which  should still be fine if "part_of" is replaced with "regulates"
                   See examples: File:Regulates relationship.doc


Induction and Upregulation terms

                    Induction and Up-regulation of........ are currently child terms of positive regulation. Should this be merged into positive
                    regulation?  Many of the induction and upregulation terms are synonyms of their respective "positive regulation" parent terms.    
                   
                    See examples:   File:Merge into positive reg.doc


Changing wording in some host terms

                    Will put a list on the wiki soon for your comments


Mini Reviews


Report

                      Use of PAMGO terms by virulence community-Michelle


PAMGO workshop July 14-16 2008

                     Please print out attached brochure and distribute at meetings/conferences you plan on attending before July
                     We need to attract a diverse group of people this year.
                     Download brochure: File:Workshop Brochure.pdf


Others

PAMGO Conference Call-November 15 2007

Test set of annotations sent to Chris Mungall (GOC) File:PAMGO test assoc.xls

New "Properties" column in the association file

Updated Evidence Code documentation. http://www.geneontology.org/GO.evidence.shtml New children codes under ISS (still under review)


Topic for discussion: Hypersensitive response (HR) and Programmed cell death (PCD) tree

See "PAMGO SUMMARY_2007" for Candace's proposal on this subject