POC Conf. Call 11-10-10

POC meeting, Webex Conference Call; Date: Wednesday Nov 10th, 2010 10am (PST)

In attendance:

POC members:

Absent:

Collaborators: none

Acceptance of the minutes from the 11-5-2010 and 11-6-2010 meeting?

Agenda: In progress...

Restructuring of PGDSO

On Nov. 5th, Barry gave a brief presentation of the structure of the Basic Formal Ontology (BFO), and how it is divided into occurants and continuants, with dependent and independent continuants. The PSO covers independent occurents. He suggested that the life cycle of a plant is a continuant that contains phases, and that the current structure, based on stages as continuants, was not correct.

There was some discussion of what is a whole plant, and we decided that zygote and spore were also whole plants, however, if we are going to remove other whole-plant phases of the plant life cycle (like seedling and gametophyte), it may be inconsistent to include structures like zygote, embryo or spore.

There was a discussion of splitting the PSO into adult and embryonic plant structures. Other anatomy ontologies (such as FMA) have dealt with the problem of embryonic or developing structures by only including adult structures. There are special problems with plants, in that the same plant can contain both adult and embryonic structures. We discussed the possibility of creating a separate branch of the PSO for reproductive plant structures and vegetative plant structures, but felt it might be better to leave those divisions at lower ontology levels, like we currently have for reproductive shoot system. Could add new terms like reproductive organ or reproductive cell. Still under consideration.

We discussed the possible need to include a term like whole plant collective structure (may not be best name) to deal with structures like seeds that contain parts of multiple individuals.

We need to add a category for embryonic growth stages to the PGDSO

There was a discussion of a major restructuring of the PGDSO:

The root term, plant growth and development stage, would be renamed plant life cycle process (a continuant).

The top level structure would have three branches, as below (this is an example, not a final, agreed-upon structure):

Plant life cycle process

>plant life cycle phase (phases in a plant life cycle)

>>gametophytic phase

>>sporphytic phase

>>>embryonic phase

>>>vegetative growth phase

>>>reproductive phase

>plant life cycle phase transition (the landmarks that mark the transitions from one phase to another)

>>>meiosis

>>>fertilization

>>>etc.

>plant structure development (these are biological processes, and may be better in GO, or maybe only put top level terms in GO with more detail in PO)

>>plant organ development (e.g. leaf or root development)

>>plant tissue development (maybe)

>>collective plant structure development (e.g. flower or inflorescence development)

>>whole plant development

>>>gametophyte development

>>>sporophyte development

(See also dev browser)

It should be possible to add corresponding phases for each of the developmental processes. For example, gametophytic phase corresponds to gametophyte development, and leave development phase could correspond to leaf development. Then it would be possible to move the developmental processes to GO, but keep the phases in PO.

Collaboration with Physco group to cover mosses in PO

Email from Stefan Rensing:

"We have now completely reworked the mapping of bryophyte terms to the new version of the PO. We would be happy to make this mapping available to you on the condition that we will be co-authoring the eventually resulting publication. Would that be ok for you?

Of course, we are willing and interested to continue discussion on this topic, e.g. on how to broaden term definitions that to our opinion are currently too narrow to accommodate bryophytes."

MossOntology wiki

How do we want to proceed? Should we set up a Webex or Skype meeting?

Next meeting

Weds Nov 10th- Barry cannot attend

Next meeting scheduled fro Nov. x 2010 at xx