#413 PomBase specific "extensions"

[Valerie Wood]

This is a place holder ticket.

It is likely that PomBase with have a set of annotation qualifiers which will be excluded from GO because they extend the information about the annotated gene product rather than the term (they are really a qualifier with a "relation')

Curators will go through the deprecated terms in the New Year and decide if they are useful, if we can capture any other way to define a set which we wish to keep.

We will not export these in the GO file

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In addition, we would like to use the "PomBase specific" relations to create an annotation extension with the relation "binds" for the interacting partner of the GO "protein binding" annotations with IPI evidence and the interacting PomBase gene in the 'with' field

These will also not be exported in the GO file

[Kim Rutherford]

I had forgotten that we already load and allow several extension relation ontologies, including this one:
pombe-embl/mini-ontologies/gene_ex_extension_relations.obo

So we could put extra terms there (or create a new OBO file).

The loader will need modification to store the "with" from the contig files, Canto and GAF files as a "binds" where appropriate (protein binding/IPI).

The GAF exporter will need changing too.

[Valerie Wood]

At the moment it seems that the pombase specific GO extensions will be

29 | dependent_on (consider to be in-house extension)
46 | independent_of (consider to be in-house extension)
and the negated extensions
6 | not_exists_during
1 | not_happens_during

but we will raise the priority of this ticket when GO decides to boot them out