A comment from Emily in one of the other evidence code related threads reminded me that I don't think the group has completely resolved the proposed usage of the with field for the NAS evidence code. Midori brought up a very good point that since authors don't generally make statements about the assumed roles of a gene in terms of GO terms, that it may not be appropriate to use GOids in the with field for NAS statements.
The text of the email discussion is below.
use of with field for NAS
> The Evidence Code Committee discussed the idea of making GO > annotations from Reactome entries. ... What does the full group feel > about the idea of allowing the ID for a database record, when such > exist, in the with field?
Midori (15 Jun 2007):
I'm all for including annotations based on Reactome entries -- they have a well-developed curation system that deeply involves expert biologists, so the statements in their records are very reliable.
I am not in favor of putting the Reactome ID in the with field for these annotations, however, because the Reactome entry does not modify or supplement the evidence; rather, the entry provides the evidence. GO would effectively be using a Recatome record as a source of information about a gene product, so it would make much more sense to put the Reactome ID in the reference field.
For the more general database record case, it may be that I don't sufficiently understand what might go in a GO_REF (or equivalent), so I don't understand the rationale for allowing 'with' for NAS.
For the case where the author infers one thing from another, using a GO ID in 'with' makes more sense, but I think it's not really necessary because the author (presumably) hasn't actually made any GO annotations, and hasn't stated observations or conclusions in terms of, well, GO terms. (Perhaps this will change some day!) Also, note that we have expressly disallowed the use of 'with' for NAS, so the script would have to be changed if the use of with-for-NAS is agreed.
Karen (9 Sept 2007):
Regarding the idea of allowing Reactome IDs in the with field, the thought was that it provided the specific information about which record in Reactome made the statement, but the idea was controversial even just with the Evidence Code Committee.
Regarding the idea of allowing GOids for NAS, I think you bring up a good point that this may not make sense since the author has typically not stated their statement in terms of a GOid from which an inference was made. Allowing this may just be more confusing than helpful, especially since deciding which GOid to put in the with field will almost always be a curator judgement.
However, I wasn't one of the proponents of this idea, so those who are may wish to defend it.
In any case, rather than adding yet another usage of the with column that is potentially confusing to users, I could personallyjust go with not allowing use of the with column at all for NAS.