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Ticket Resolution Summary Owner Reporter
#4 duplicate check ISS outliers/stale ISS somebody gomidori
Description

There are a LARGE number of ISS annotations which are "unsupported" i.e the with column target does not have the annotation

A few may need removing but I think most probably need more granular at SGD. In some cases it is possible that the original annotation was removed from SGD (It would be great if there was some alerting for this!)

There is a Goose MySQL query to get the numbers.

Maybe this should link to a wiki page with a link to the query where we periodically check the total?

I don't really intend to do this as a task, but in general the numbers should obviously decrease.

It also might be a nice training exercise for Antonia (or us) to check a few of these and either

i) ask SGD if the annotation should be moved down

or

ii) find other supporting evidence

or

iii) remove if incorrect

#3 duplicate annotate overlapping protein coding genes somebody gomidori
Description

I want to annotate all of the protein coding genes which overlap with each other (as the overlaps are usually small, only a few amino acids), but it is useful to users to know.

I think this is most of them: http://old.genedb.org/genedb/Curation?organism=pombe&action=search&search=warning%2C+protein+coding+overlap+with+adjacent+gene

We can identify these in Artemis, and check that all are flagged (the new gene structures may have added or removed some)

#2 duplicate Post translational modifications, move to ontology val_wood gomidori
Description

I had a tracker item to standardise the post-translational modification annotation (Which I think I have pretty much done, see below), so these are probably ready to map to an ontology.

I was intending to do this as my "obo edit" training exercise, so you can issign this issue to me. I might pass it to Antonia and do something else as I think this is pretty straightforward.

modification, acetylated (11)

modification, biotinylated (2)

modification, carboxymethylated (1)

modification, disulphide bond (2)

modification, farnesylated (10)

modification, gerenylgerenylated (3) correct spelling

modification, glycosylated (84)

modification, GPI attachment site (42)

modification, hypusination (1)

modification, lipidated (1)

modification, lipoylated (4)

modification, mannosylated (1)

modification, methylated (10)

modification, N-myristoylated (2)

modification, neddylated (3)

modification, palmitoylated (3)

modification, phosphatidylethanolominated (1) correct spelling

modification, phosphopantetheine attachment site (1)

modification, phosphorylated (1254)

modification, prenylated (4)

modification, proteolytic cleavage (11)

modification, trimethylguanosine capped (1)

S-thiolated (1)

modification, sulfinic acid formation (1)

modification, sumoylated (8)

modification, ubiquitinated (18)

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