#243 Load PAINT annotations for checking (but not into chado release version!)

[Valerie Wood]

When we eventually load the PAINT annotations we need to exclude the NOT annotations.
The PAINT annotations use NOT differently...and the consequence is annotations with NOTS which you would not expect to be true in the first place.

Longer term, there might be a place for comprehensive NOT annotation in the database, but not yet....

I'll update here
https://sourceforge.net/apps/trac/pombase/wiki/ExternalGOData

[Valerie Wood]

I'm upping the priority of this ticket as it seems that these annotation will go into GOA soon, and so we will need to deal with them anyway.

I'd like to assess them first out and weed out any clearly erroneous ones.
Therefore, for the next month or two It would be good if we could include them in interim builds (for assessment and weeding), but omit from the final build.

Step 1.
Get the PomBase PAINT gaf from
http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/gene-associations/submission/paint/pre-submission/

Filter out anything which is:
1 GeneDB_Spombe as source
or
2 Does not have a PomBase systematic ID in column 2 (I have reported both of these errors)
3. Any negative (NOT) annotations. These are slightly different for PAINT and negative annotations are made that we would not curate.

Step 2

Import the data, but filter anything with the PAINT evidence codes * which is provided already by experimental or ISS annotation.

• I will add the PAINT evidence codes shortly.... I can't access the PAINT files at the moment they are empty so I'll come back to this....

Once this part is done I will assess the annotations and then decide whether we can load them yet, or not...

v