Modelling of annotation extensions

"Annotation extensions" are an increasingly important component of GO annotation because this is how we capture connections between terms (I.e the actual biology, and form the basis of our causal modelling

For example
**cdc2** (protein kinase) [[phosphorylates **cdc15**] [during mitotic S-phase] ]
**clp1** (protein phosphatase) [[dephsophorylates **cdc2**] [during mitotic M phase]]

This is the type of data we would really need to be able to interrogate but, because the terms are curated (and thus represented here) as a single extension it is not possible to separate out the datatypes to query independently.

This is what we see

So we cannot extract either
I) the biological targets of a specific gene/protein (i.e all of the targets of a kinase, or a transcription factor)
Or
ii) query on the phase of the cell cycle at which these occur.

An extension is actually often a compound annotation comprising numerous relations and datatypes stored in a single field of the GO-GAF.

I have a proposal to make these accessible in PomBeMine. First, I don't think it is practical within the time-constraints of the project to include all annotation extensions types we have used:
i.e.
168 coincident_with
180 existence_overlaps
669 happens_during
1834 has_input
218 occurs_in
702 part_of

so I suggest that we try to model the 3 most useful, namely
has_input (to give access to targets)
happens during (to give access to phases)
part of (to link molecular functions to processes)

This would require loading each gene list into a field describing it's extensions type. In PomBemine, instead of

it would need to look like:

Gene DB identifier | Ontology term Identifier | Extension (during) | Extension (target) | Extension (Part of process)
-- | -- | -- | -- | --
SPBC11B10.09 | GO:0004693 | GO:0000084| SPAC17A5.07c| NO DATA
SPBC11B10.09 | GO:0004693 | GO:0000084| SPAC18G6.10 | NO DATA
SPBC11B10.09 | GO:0004693 | GO:0000084| SPAC20G8.05c | NO DATA
SPBC11B10.09 | GO:0004693 | GO:0000080| SPAC22E12.19) | NO DATA
SPBC11B10.09 | GO:0004693 | GO:0000084 |SPAC22H10.11c | NO DATA
SPBC11B10.09 | GO:0004693 | GO:0000089 |SPCC736.14 | GO:0090307