final PAMGO proposal now on SourceForge

[Candace Collmer]

Dear Pathogenesis Interest Group --

           I want to alert you to the posting on Sourceforge (965023) of 
the revised-yet-again PAMGO (Plant-Associated Microbe Gene Ontology) 
proposal, which has taken into account relevant discussion at the GO 
content meeting held in California in August, 2004, at the GO meeting held 
in Chicago in October, 2004, and via email since then. The most recent 
addition accommodates the process of biofilm formation in or on a host, 
which required a further development of terms related to biofilm formation. 
We believe that this final proposal accommodates all comments and concerns 
and represents consensus.

          The original PAMGO proposal offered terms for annotating gene 
products in microbes that are involved in various types of symbiosis, 
including pathogenesis as one type of symbiosis involving interaction with 
a host organism.  We specifically proposed general terms that we hoped 
would serve communities studying both plant and animal pathogens, as well 
as microbes (and nematodes) involved in mutualism, commensalism and other 
types of symbiosis. This final proposal achieves that goal, as "symbiosis" 
is now specifically defined with a broad definition that includes 
relationships along a continuum from mutualism through parasitism. The term 
"pathogenesis" is also present in the tree as a child of symbiosis, and as 
a sibling to all of the original general terms (e.g. "recognition of 
host,"  "entry into host," etc.) The idea is that a gene product involved 
in recognition of a host by a pathogen would be annotated to both the 
general term "recognition of host" and the term "pathogenesis". A gene 
product involved in recognition of a host by a microbe about to initiate a 
mutualistic relationship would be annotated to the general term only (as 
that term is a child of "symbiosis"). Specific process terms such as 
"mutualism" could be added later, if desirable, to be siblings of 
"pathogenesis" and children of "symbiosis."

           This posting includes two word documents (attached also to this 
email) -- one with the revised tree of GO terms (GO-PAMGO-fnlfnl-tree.doc), 
the other with the definitions for those terms (GO-PAMGO-fnlfnl-def.doc) as 
well as proposed obsoletions of existing GO terms, modifications of 
definitions of existing GO terms, and remaining questions.

                 Thanks for all the work everyone did on this 
proposal.  Candace Collmer
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Candace W. Collmer
Professor of Biology
Wells College
Aurora, NY 13026
    phone: 315-364-3271
    fax: 315-364-3464
    email: ccollmer at wells.edu