[go] finishing up Evidence Code Issues
Harold Drabkin
hjd at informatics.jax.org
Tue Sep 11 06:25:30 PDT 2007
We are still not happy at all with the ISS, so I'd like it added to the
potential discussion if it hasn't been done already.
hjd;
> Hi,
>
> Since I'm due on September 20th and will be going on maternity leave
> shortly before the GO meeting, Mike asked me to send these remaining
> items to finish up the Evidence Code documentation directly to the
> list to at least get the discussion started. Some issues may need to
> be discussed at the GO meeting as well.
>
> This email will contain some responses to Midori's last email and a
> few other email comments to resolve some minor comments on the current
> draft of the new Evidence Code documentation. I will send separate
> emails to deal with each of these specific issues:
>
> 1. Restriction that all unknowns MUST use ND
>
> 2. IMP vs IGI for single gene mutations, regardless of gene being
> annotated
>
> 3. How to put program or method names in the with column for ISS
>
> 4. Scope of the RCA evidence code
>
> For both issues 2 and 4, I think that the recommendations I've made
> will help make it possible to create a decision tree/flowchart that is
> fairly simple and clear. I'll send a very rough draft of a flowchart
> separately as well.
>
> Note that for both #s 3 and 4, I have put some supplemental info into
> html docs in my personal space. I did not spend much time doing html
> formatting for these docs, on the thought that people might prefer to
> move them to the GOC wiki. However, as the Evidence Code Committee was
> not designated as a Working Group, I have no idea where to put them
> within the wiki structure. If a spot is designated for them, they can
> be moved to the wiki.
>
> -Karen
>
>
>
> Responses and comments on things in red on this page:
>
> http://www-dev.yeastgenome.org/draftGO/go/www/GO.evidence.new.shtml
>
>
> 1. GO_REF documentation
>
>> We should have documentation that explains GO_REF's and links to it
>> when we refer to them.
>
> Midori (15 Jun 2007):
> Links can go to the existing GO References page:
>
> http://www.geneontology.org/cgi-bin/references.cgi
>
> I can write up a description (which will be brief; there's not an
> enormous amount to say) and give it to Amelia to be added to the blurb
> at the top of this page. The plain text file from which the web page
> is generated contains a brief description of the format, which could
> be HTMLified and also added to the blurb if it would be useful.
>
> Karen (9 Sept 2007):
>
> Please do. It would also be good if the page for the GO_REFs is made
> easier to find in general in our documentation.
>
>
> 2. ChEBI IDs in with field?
>
>> Do we allow things like ChEBI IDs in the with field?
>
> Midori (15 Jun 2007):
> I would say yes.
>
> Karen (9 Sept 2007):
>
> Perhaps we should make this a quick agenda item for the next GO
> meeting, so that people can ratify this face to face, unless we get an
> overwhelming response via email to proceed with allowing this new ID
> for the with field.
>
> 3. IMP examples
>
>> any more positive examples for IMP?, e.g. phenotypic similarity
>
> Midori (15 Jun 2007):
> Dredged up from email from January 2002 ...
>
> Erich Schwarz needed to know which code to use for "other mutations
> sharing a complex mutant phenotype syndrome with [a well-characterized
> mutant]." My comment at the time was: "The situation you've described
> is IMP, not IGI, because (if I understand correctly) you're looking at
> one mutation at a time. Comparing the phenotype of one mutation to
> that of another helps you interpret the meaning, but is not a kind of
> genetic interaction."
>
> I think this still holds. Erich provided some details of an example,
> which I can forward if you want.
>
> Karen (9 Sept 2007):
>
> We can certainly include it, the more examples the better in my
> opinion, but don't send it to me. I'll be going on maternity leave
> soon and don't want to be responsible for this getting added.
>
>
> 4. 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.
>
>
> 5. Representation of examples for with/from:
>
> Susan (14 Jun 2007):
>
> IPI examples
>
> Looks good but there something odd about the IPI example,
> assuming I am looking at the latest version ok.
>
> Firstly, the paper is about mouse proteins not Drosophila so could we
> change FB to MGI please. Also, I am confused as to why there are three
> lines shown - MGI just list the middle one:
>
> FB:gene_1_ID Abcd3 GO:0005515 PMID:10551832 IPI
> UniProt:protein_2_ID ...
> FB:gene_1_ID Abcd3 GO:0005515 PMID:10551832 IPI
> UniProt:protein_2_ID|UniProt:protein_3_ID ...
> FB:gene_1_ID Abcd3 GO:0005515 PMID:10551832 IPI
> FB:gene_2_ID
>
> So unless I'm missing something I suggest we lose the extra lines and
> have either:
>
> MGI:1349216 Abcd3 GO:0005515 PMID:10551832 IPI
> UniProt:P33897|UniProt:Q61285
>
> OR
>
> MGI:gene_1_ID Abcd3 GO:0005515 PMID:10551832 IPI
> UniProt:protein_2_ID|UniProt:protein_3_ID
>
> I'd prefer to include the real identifiers so it isn't a mix of 'real'
> and 'example'.
>
> Similarly there seems to be a mix of FB and SGD db identifiers in the
> IGI examples. A possible alternative for IGI is:
>
> In PMID:9043060, flies simultaneously mutant for three genes: klingon
> (klg), sevenless (sev) and Son of sevenless (Sos) are used to show that
> klingon participates in R7 photoreceptor fate commitment. This leads to
> the annotation:
>
> FB:FBgn0017590 klg GO:0045466 PMID:9043060 IGI
> FB:FBgn0003366|FB:FBgn0001965
>
>
> Karen (9 Sept 2007):
>
> I'm all for real examples, but I don't have time to dig them up for
> every evidence code. Perhaps we could distribute this task around, so
> that we have multiple real examples for each evidence code. It would
> be good to have at least one example with one entry in the with
> column, as well as the one with multiple. It would also be good if
> they showed various IDs in the with field.
>
> This would be a reasonable task if there was one person for each
> evidence code to find some real examples, and then hopefully it would
> be easy for Amelia to put them in the right format if she was given
> all the specific info that should be in the table.
>
> 6. ISS & with col:
>> Note that there should be good evidence that the gene product(s)
>> placed in the with/from column actually has the activity, process,
>> etc. being annotated.
>
> Midori (15 Jun 2007):
> Do we want to specifically say the "good evidence" should be
> *experimental* evidence? Would be consistent with the Ref Genome
> requirement, and good practice generally ...
>
> Karen (9 Sept 2007):
> We do have to remember that this Evidence Code document is not just
> for the use of the Reference Genomes. While did agree that ISS should
> not be made from pairwise BLAST unless the gene to be placed in the
> with column has been experimentally characterized, the ISS code covers
> more situations than just that. The with field may also contain Pfams,
> Prosite, TIGRFAMS, CBS, COG, PANTHER, and we also have to determine
> how to include method names here for stuff like tRNAscan and my
> specific question about snoRNAs. Michelle Gwinn may wish to comment
> on this too.
>
>
> Typos, other trivial fixes:
> -------------------------------------------------------
>
> 1. IGI
>
>> Should we add a statement in the paragraph above to IGI, similar to
>> the one in IMP, about care in making annotations from gain of
>> function mutations ...?
>
> Midori (15 Jun 2007):
> Sounds reasonable to me.
>
> Karen (9 Sept 2007):
>
> OK, added to first paragraph of IGI.
>
> 2. Last paragraph of Introduction:
>
> Midori (15 Jun 2007):
> Change "effect" to "affect" in "... will also effect the quality of
> the resulting annotation."
>
> Karen (9 Sept 2007):
> done
>
> 3. IDA & IMP:
>
> Midori (15 Jun 2007):
> Does "over-expression" really need to be hyphenated? I've seen it
> unhyphenated more frequently; also, there's one unhyphenated
> occurrence in the document.
>
> Karen (9 Sept 2007):
> changed to unhyphenated
>
> 4. IGI examples:
>
> Midori (15 Jun 2007):
> The statements "For this type of experiment, use the IGI Code" could
> be deleted -- they're redundant with the fact that the description
> appears in a list headed "where the IGI code should be used."
>
> Karen (9 Sept 2007):
>
> done
>
>
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