final PAMGO proposal submitted to GO

[Jane Lomax]

Hi Candace - okay - the chnages are all now live - hooray! Have a look 
through, and if you spot any problems let me know and I'll fix asap (the 
nesting of the terms in the word file you attched was a bit hard for me 
to figure out sometimes, and while i think everything now has the correct 
parentage, you'd better check!).

I've left that term definition-less for the time being - let me know when 
you have a def and I'll add.

Great work guys!

Jane


On Fri, 28 Jan 2005, ccollmer wrote:

> 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
> 
>