Notes on PGDSO revisions fall 2011

This is the working page for making notes on changes to the PGDSO as we go along.

Plan for revising the PGDSO, fall 2011

The current PGDSO is a mixture of processes and phases (although it was intended to be all stages/phases), and was designed with angiosperms in mind.

We need to correct some specific problems with the PGDSO, and to make it applicable to all plants, as we have done withe PAO.

Open SourceForge trackers for the PGDSO

See Items_for_future_meetings#User_requests_still_open_on_Source_Forge.3B_PGDSO for a complete list.

PGDSO terms without is_a parents

imbibition (PO:0007022)

seedling growth (PO:0007131)

shoot emergence (PO:0007130)

'plant life' ('life of whole plant')

Barry suggested that we need a term like "life of whole plant", of which all phases would form parts.

Previous proposal

See POC_Conf._Call_12-15-10#Restructuring_PGDSO_for_Occurents for a description of a proposal that BS, LC and RW worked on in December.

Also see: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/branches/PGDSO_2011/plant_ontology_test.obo?view=log for a copy of the test ontology file and changes in new PGDSO version for a summary of changes that were made to the test file.

In that proposal, the root term, plant growth and development stage, would be replaced by 'plant life cycle process' (an "Occurrent"). The top level structure would have three branches, as below:

The proposal described here is simpler than December's (does not include biological processes, which could be in GO), but follow many of the same principals.

New relations linking the PAO and the PGDSO

These still need to be discussed/worked on.

derives_from

At the POC meeting on 7-19-11, we agreed to create a new relation in the PO called derives_by_manipulation_from (see POC_Conf._Call_7-19-11#derives_from_relations_in_PO:). This would be a special case of the RO relation derives_from.

participates_in and has_participant

See POC_Conf._Call_7-19-11#participates_in_relation

Chris asked: "will you add temporal relations to the stages?"

other

We may want to add temporal relations such as preceded_by, precedes and follows, or perhaps more precisely, immediately_preceded_by, immediately_precedes. This would be comparable to the adjacent_to relation.