final PAMGO proposal submitted to GO

[ccollmer]

Hi Jane --
   All of your suggested changes look fine to me.  However, I was not able to 
look at the complete set of terms related to symbiosis using the link below -- 
I got the complete set of GO terms (I think) and was uable to find our 
particular ones within those. However, it's difficult for me to look today 
because I'm using a dial-up connection.
   I'll have to get back to you on that last definition -- perhaps Michelle 
will have a good suggestion there, as it's now a bit outside of my area of 
expertise.  But we'll come up with one soon.
   Thanks so much for all your owrk, Jane -- can't wait to see these all live 
after Monday.  -Candace


   >===== Original Message From Jane Lomax <jane at ebi.ac.uk> =====
>Okay - it's pretty much finished. You can download it from here to have a
>look (load into DAG-Edit):
>
>http://www.ebi.ac.uk/~jane/gene_ontology.obo
>
>I'll send out a final email now warning people that I'll merge the
>changes in on Monday, and listing the terms that will be made obsolete.
>
>A few final things to suggest/check:
>
>Another couple of name changes (just for consistency of term names really,
>and making names clearer):
>
>host cell invasion -> entry into host cell (old name as exact synonym)
>
>(sorry - I know I already suggested changing that one once already!)
>
>viral entry -> viral entry into host cell
>
>I've also made 'viral entry' a child of 'host cell invasion' like this:
>
>entry into host cell
>---[i] viral entry into host cell
>
>This is because the definition of 'viral entry' is 'The process by which a
>virion enters a host cell, including virion attachment and penetration'.
>Let me know if that definition's wrong and I can change it back.
>
>
>Could the definition of 'interaction between organisms' be changed
>slightly from:
>
>The processes by which an organism has an observable effect on an organism
>of a different species.
>
>to
>
>The processes by which an organism affects an organism of a different
>species.
>
>?
>(we don't like to include experimental references like 'observe')
>
>And Candace, could you come up with a definition for the new term
>'symbiotic interaction with other, non-host organism' do you think? It'll be
>much better than mine!
>
>thanks,
>
>Jane

----------------------------
Candace W. Collmer, Ph.D.
Professor of Biology
Wells College
Aurora, NY 13026
  phone: 315-364-3271
  email: ccollmer at wells.edu