[Gusdev-gusdev] Re: proposed modifications to GO Schema for GUS3.0

[Arnaud K. <ax...@sa...>]

Hi Sharon

I had a discussion with Matt and from our point of view, the design 
you're proposing sounds sensible.

Just two clarifications about evidences:

    (1) for an evidence attached to a GOAssociationInstance, it can be:
        *  Similarity data,
        * a AAMotifGORule,
        * a DB Reference, stored in an ExternalDBEntry if it's external,
        * if it's a pubmed_id, we may want to store the whole reference 
into a reference entry. But I guess it can be done with the schema 
you're proposing, is that right ?

    (2) for an evidence attached to a GOAssocInstEvidenceCode as it may 
be an "internal DB link", e.g. a protein_id for example, the DB name 
prefix will be GeneDB in our case, or if it's a GO_id, it will be GO as 
a prefix. Will it be generated on the fly ?

Also re. the GOTerm table, would it be possible to add a comment field ?

cheers
Arnaud

Sharon Diskin wrote:

> Hi Arnaud,
>
> I've attached the new GO schema and documentation that Jonathan Schug 
> and I have come up. We believe that this new schema addresses your 
> concern about the association date and also provides a better way of 
> tracking multiple instances/sources of the same association (see 
> description of GOAssociationInstance table).
>
>
> Regarding your other question concerning the 'DB:Ref' and 'from or 
> with', we see these being tracked using the generic Evidence table.   
> The 'from or with' would be Evidence for the GOAssocInstEvidCode entry 
> as it is connected to a specific evidence code that is assigned to the 
> association.  The 'DB:Ref' (such as in the PubMed example you 
> mentioned) would be Evidence for the GOAssociationInstance entry as it 
> is _not_ connected to a specific evidence code, but rather the 
> association as a whole.  More details can be found in the attached 
> documentation.
>
>
> Any feedback is welcome.  Also, if any of this is unclear, just let us 
> know.
>
> Cheers,
> Sharon
>
>