POC Conf. Call 5-10-11

POC meeting, Webex Conference Call; Date: Tuesday May 10th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_5-06-11?

Status Report for Upcoming release:

Highlights and Major Accomplishments in this Release:

-Addition of XX terms requested by the physcomitrella group as well as xx associated terms that can be used for pteridophytes.

-Renamed PSO to PAO

-revised the In vitro plant structures branch and the embryonic plant structures branch

-Need to have a couple of weeks for users to review before release, especially Physco group.

-See the List of changes on our wiki which is available from the May_2011_Release_Page

-List of terms that have been obsoleted or merged: New_terms_and_obsolete_terms_for_May2011_release

Issues that still need to be dealt with:

gametophytic phase and sporophytic phase

sporophytic phase (PO:0028002)

Current definition: A plant life cycle phase that is the product of fertilization. [source: POC:rw]

Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis.

Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with fertilization or the division of a non-fertilized embryogenic cell.

Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis. A whole plant in the sporophytic phase usually has twice the chromosome complement of a plant in the gametophytic phase, but may not in the case of apogamy or in vitro culture of haploid embryos.

gametophytic phase (PO:0028003)

Current definition: A plant life cycle phase that arises through meiosis. [source: POC:rw]

Comment: During the gametophytic phase, a plant may produce gametes by mitosis.

Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with meiosis.

Comment: During the gametophytic phase, a plant may produce gametes by mitosis. In bryophytes and pteridophytes, a gametophytic phase may begin without meiosis by apospory. This usually occurs when damage to a plant in the sporophytic phase leads directly to the growth of a plant that is in the gametophytic phase but bears the chromosome complement that would normally be found in the sporophytic phase. A whole plant in the gametophytic phase usually has half the chromosome complement of a plant in the sporophytic phase, but not in the case of apospory.

Other Issues

*Review for OBO Foundry Acceptance

BS brought up the topic of review for OBO Foundry acceptance at the POC_Conf._Call_4-19-11. He suggested that the PO can be submitted for OBO Foundry membership within the next weeks

List of Foundry Principles:[Accepted] with a brief summary of each:

• FP 001 open:

The ontology must be open and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.

• FP 002 format:

The ontology is in, or can be expressed in, a common shared syntax. This may be either the OBO syntax, extensions of this syntax, or OWL.

• FP 003 URIs:

The ontology possesses a unique identifier space within the OBO Foundry. The identifier uniquely and persistently identifies a definition, which itself unambiguous identifies some type of biological entity. The identifier is for the definition: it is NOT the name and it is NOT an identifier for the name.

• FP 004 versioning:

The ontology provider has procedures for identifying distinct successive versions.

• FP 005 delineated content:

The ontology has a clearly specified and clearly delineated content. The ontology must be orthogonal to other ontologies already lodged within OBO.

• FP 006 textual definitions:

The ontologies include textual definitions for all terms.

• FP 007 relations:

The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.

• FP 008 documented:

The ontology is well documented.

• FP 009 users:

The ontology has a plurality of independent users.

• FP 010 collaboration:

The ontology will be developed collaboratively with other OBO Foundry members.

• FP 011 locus of authority:

single locus of authority, tracker (SOP), responsive help desk

• FP 012 naming conventions:

See naming conventions

• FP 016 maintenance

OBO is an open community and, by joining the initiative, the authors of an ontology commit to its maintenance in light of scientific advance and to working with other members to ensure the improvement of these principles over time

Upcoming meetings 2011:

Phenotype RCN Meeting: June 1-3rd, Boulder CO

Goals of the Plant Working Group at this meeting:

"Plants – Go through relevant parts of Plant Ontology in order to develop proofs of concept; explore how to make links to homology. Examine existing annotations and determine kinds of info can be extracted. Analyze quantitative data and look for ways to annotate them."

PJ will attend

More details TBA

2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.

Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.

-JE and JP will be attending

-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.

For more Workshop details: Semantic web.

* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- LC will attend and represent the PO. Invite other plant people?

*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Early-bird registration ends May 13.

Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.

For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details