Manager 25Aug10

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M. Tuberculosis annotations

The GOA group have received a request to incorporate some manual
annotations to M. tuberculosis from a user in Germany.

We would like to discuss this at the next Managers call. Here is a summary
of our findings.

There are almost 6000 annotations to 886 unique references, approximately
3000 of these annotations are from high-throughput papers. I've spoken to
Rama about these and we have both spot-checked quite a few of the
annotations and we generally think they are of high quality and overall he
has picked the correct GO terms. There are a couple of mistakes he has
made with evidence codes and use of the 'with' column, such as completing
the 'with' column when using the IEP or IDA evidence codes. One example of
this is this annotation line;

UniProt        UniProt:P71814        P71814_MYCTU               
GO:0045941        PMID:16573683        IEP        UniProt:O50436        P 
             phoP|Rv0757        protein        taxon:1773        20100623

So, the annotation he is trying to make is that P71814 is involved in
positive regulation of transcription and it's target is O50436. So the
annotation should be using the IDA code and putting the target accession
in column 16. Rama and I feel that these mistakes could be corrected
pretty easily and I'm sure the user would be happy to do these corrections
himself. However, maybe the column 16 entries should be left out for now
until such a time as we are ready to incorporate them?

The user is happy to update the file on a yearly basis, he appears to be
unaffiliated and working on this on his own, therefore the entry in the
assigned_by field would need to be changed from UniProt to a source chosen
by the user.

I have attached the email exchange between the user and myself so far,
together with the GAF file he sent us.

What next? These are the first manual annotations we have for M.
tuberculosis so it would be good if we could incorporate as many of these
as possible.


  • Agreed to include the data in GO through the GOA file, and attributed will be by that person.
  • The Annotation group will report that at the GOC meeting in the 'progress report' so that everyone is aware that we are trying to take those annotations from external groups.

Monthly Annotation Conference call

Until now we have used the ref.genome calls to discuss annotation related issues. Not many curators attend these calls, and we would like to hold a monthly call to discuss broader annotation related issues. This will free up some time during the ref.genome call and we can limit the ref.genome call to issues pertaining to ref.genome curation. The first Annotation will be on the Transcription over haul.


  • Distinction between ref genome and annotation calls:
    • Rama: some topics, like the wnt signaling issue we discussed last time, was more annotation-related, and maybe some other people would have been interested who didn't attend
    • Pascale: The focus of the reference genome calls is not only annotation; it's also PAINT, sequence files, where files should be saved, etc. So, interest are overlapping but different.
    • Generally from everyone: Good idea to have those calls