POC Conf. Call 3-1-11

POC meeting, Webex Conference Call; Date: Tuesday Mar 1st, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_2-22-11?

Report from the Phenotype Ontology RCN Summit

The Phenotype Ontology RCN

February 25-27, 2010 at the National Evolutionary Synthesis Center in Durham, NC,

Laurel and Pankaj will be attending.

From RW: -What is official PO strategy for dealing with phenotypes?

-Should it differ between description of mutant phenotypes and descriptions needed for systematic studies?

-Should PO develop a list of terms to be submitted to PATO (rather than our current piecemeal suggestions)?

-Possible case study: description of inflorescence types.

Continuing User requests: for PSO

- Deal with and complete the list of user requests on SourceForge, continued from last week

TraitNet requests

corm

proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.

child of stem (PO:0009047).

podarium

Their comment: is synonym to Tubercle

podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.

tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).

proposed def:

pneumatophore

definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves

proposed def: A root that is erect and protrudes above the soil, found in trees that live in flooded habitats such as mangroves. Comment: Pneumatophores may provide oxygen to below ground roots growing in flooded soils.

diaspore

definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.

We could add this term as a kind of upper level bin term (similar to trichome)

cone

Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?

sorus

from Crum (2001): a cluster of fern sporangia from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.

Proposed definition: A cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.

Part_of vascular leaf, has_part sporangium

tendril

Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.

tendrils can derived from multiple types of structures. Suggest we make separate terms:

branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.

leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.

leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.

leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.

Can add other types of tendrils if they come up or users need them.

root terms

submitted by Rich Zobel (Nov 2009)

User requests still open on Source Forge; PGDSO

tuber growth and development stages

This item has been open on SF since 6/2009

I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).

Suggested stages:

-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)

-tuber initiation

-tuber growth

-tuber maturation

How we work these in will depend on restructuring of PGDSO

l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926

terms for seed development stages

This is a fairly new request for terms for cotton

Upcoming meetings 2011:

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

ICBO

CALL FOR WORKSHOP AND TUTORIAL PROPOSALS: Melissa, Alan and Chris are organizing an anatomy ontology workshop.

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

-BS suggested we might want to submit a short paper which could be published in longer form later- see above

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme.

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

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