From cherry at genome.Stanford.EDU Wed Dec 1 16:57:06 2004 From: cherry at genome.Stanford.EDU (Mike Cherry) Date: Wed, 1 Dec 2004 16:57:06 -0800 Subject: PATHOGENESIS/CELL KILLING/IMMUNOLOGY interest list is open Message-ID: <1670652E-43FD-11D9-A1A3-000A9599D30C@genome.stanford.edu> Hello, You are subscribed to the PATHOGENESIS at GENEONTOLOGY.ORG mailing list. Posting to this list is limited to the list's subscribers. -Mike From cherry at genome.Stanford.EDU Wed Dec 1 17:22:29 2004 From: cherry at genome.Stanford.EDU (Mike Cherry) Date: Wed, 1 Dec 2004 17:22:29 -0800 Subject: You are subscribed to the PATHOGENESIS list Message-ID: Hello, Sorry about the previous message. There was a problem and I had included the GO list in this interest list. You are really subscribed to the PATHOGENESIS at GENEONTOLOGY.ORG mailing list. -Mike From ccollmer at wells.edu Wed Dec 15 12:35:40 2004 From: ccollmer at wells.edu (Candace Collmer) Date: Wed, 15 Dec 2004 15:35:40 -0500 Subject: final PAMGO proposal now on SourceForge Message-ID: <5.2.1.1.2.20041215153118.02f46138@henry.wells.edu> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://fafner.stanford.edu/pipermail/pathogenesis/attachments/20041215/2ba19435/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: GO-PAMGO-fnlfnl-tree.doc Type: application/msword Size: 29696 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/pathogenesis/attachments/20041215/2ba19435/attachment.doc -------------- next part -------------- A non-text attachment was scrubbed... Name: GO-PAMGO-fnlfnl-def.doc Type: application/msword Size: 46080 bytes Desc: not available Url : http://fafner.stanford.edu/pipermail/pathogenesis/attachments/20041215/2ba19435/attachment-0001.doc -------------- next part -------------- --------------------------- Candace W. Collmer Professor of Biology Wells College Aurora, NY 13026 phone: 315-364-3271 fax: 315-364-3464 email: ccollmer at wells.edu