POC Conf. Call 2-22-11

POC meeting, Webex Conference Call; Date: Tuesday Feb 22th, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_2-15-11?

Phenotype RCN Meeting this week

• LC submitted a short description of our project and what the goals are.

"The Plant Ontology (PO: http://www.plantontology.org) is a structured vocabulary and database resource that consists of a hierarchical tree of rigorously-defined, interrelated terms that describe plant structures as well as plant growth and developmental stages and encompasses terms and annotations from all plants. The overall goal of the PO is to establish a framework for meaningful cross-species/ taxon queries and for annotating phenotypes and gene expression datasets. We are developing a platform for cross product composition of ontology terms to describe qualitative and quantitative phenotypes of plants. For example, the phenotype descriptor; ‘leaf color’ is the product of pre/post-composition of the terms ‘leaf’(PO:0025034) and ‘color’ (PATO:0000014).”

This will be printed this out along with your name, affiliation, email, etc. and distributed it at the meeting. The purpose is to help everyone learn names and get to know each attendee.

• LC is preparing a ‘lightning talk’ for the first day (Friday). Suggestions are welcome!

Specs: "This should be a 5 minute (maximum), 5 slide (maximum) talk where you cover the points below. The point of these talks is to familiarize you with others, and to spark discussions and collaborations."

Lightning talks (no more than 5 slides, 5 minutes): 1. Who you are (ontology developer/contributor, ontology consumer)? 2. Why are you making or using ontologies or why do you want to use ontologies? What are you doing with them? 3. What tools are you using? A little nitty gritty here... obo-edit, protege, excel,... 4. Biggest roadblock in your work 5. Vision: where you’d like to go... 6. Collaborators? Type of person or resource who could help?

• We also have an opportunity to do a demonstration of our resource on Saturday, so LC will bring a short demo presentation.

Some questions for us to consider (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.

Items arising from last week's agenda

pollen sac

Current definition: A microsporangium in an angiosperm that is a cavity in an anther that contains pollen grains.

The anther locule is actually the cavity.

Proposed def'n: A microsporangium that encloses an anther locule where the pollen grains develop.

Comment: Two or more pollen sacs may fuse to form a single anther locule.

Restructuring descendants of leaf (PO:0025034)

-Some of the part_of children of vascular leaf can also be part of non-vascular leaf. This needs to be done before we can add terms for bryophytes.

-Need to double check the is_a children of leaf.

current is_a children of leaf

• prophyll (PO:0009042) is_a phyllome and scale leaf (PO:0006003) is_a phyllome (see prophyll and scale leaf).

We decided it was best to leave prophyll and scale leaf as phyllomes, but definition of scale needs work.

Proposed definition of scale leaf: A phyllome that is reduced in size relative to vascular leaves on the same plant and is often associated with a vegetatively propagating organ such as a rhizome or perennating bud.

Comment: May be photosynthetic or non-photosynthetic. Some species have vascular leaves that are scale-like (such as Juniperus, Calocedrus, Thuja, and Chamaecyparis). Annotations for these should go under vascular leaf (PO:0009025), not scale leaf.

Suggest adding scale-like leaf as a narrow synonym to vascular leaf. See: http://oregonstate.edu/trees/conifer_genera/false_cedars.html

Also need to fix definition of bud scale (PO:0020054)

Current definition: A reduced leaf surrounding a dormant bud.

Proposed def: A scale leaf that surrounds a dormant bud.

vascular and non-vascular leaf

• non-vascular leaf - ok as is - Physco group has asked us to add phyllid as exact synonym. Can also add gametophyll as exact synonym.

• vascular leaf - ok as is - Suggest adding frond and needle as exact synonyms of vascular leaf.

current part_of children of leaf

• leaf apex - ok as is - applies to both vascular and non-vascular leaf

• leaf base - ok as is - applies to both vascular and non-vascular leaf

• leaf epidermis - ok as is - The term may be used for non-vascular leaves, even though many are only one cell thick.

Will need to consider if the definition of epidermis works bryophytes (see section on Physco terms on next week's agenda).

• leaf endodermis -- Does not occur in non-vascular leaves. This should probably be part_of vascular leaf, not leaf.

current is_a children of vascular leaf

Is there heteroblasty in non-vascular leaves? do these terms apply?

• juvenile leaf

• transition leaf

• adult leaf

Physco group has included these terms in their ontology, but said they are not sure if they are necessary. Said there are differences among phyllids based on their position on the stem (more basal versus more terminal), but the terms juvenile and adult are not normaly used to describe them. If we want to use them for non-vascular leaves, we either need to make them children of leaf instead of vascular leaf, or add separate terms for vascular and non-vascular juvenile, transition and adult leaves.

Do we want to keep the terms below (as phenotype terms)? At one point we discussed getting rid of them.

• simple leaf

• compound leaf

Terms that are probably okay as children of vascular leaf:

• cotyledon - ok

• leaf spine - ok

• cigar leaf - ok

• rosette leaf - probably ok as child of vascular leaf - Are there ever rosette's in gametophytes?

• cauline leaf - definition is a bit weird, actually applies to leaves that are part of an inflorescence (which we define as bracts)

Current def: Leaf or pairs/whorls of leaves borne on the stem. [source: TAIR:ki]. Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.

Suggest we flag this definition for later, but not deal with it for now, and leave it as is_a vascular leaf.

current part_of children of vascular leaf

Terms that are probably okay (only occur in vascular leaves):

• auricle - ok

• bundle sheath - ok

• leaf abscission zone - ok

• leaf collar - ok

• leaf vascular system - ok

• ligule - ok

• petiole - ok

• stipule - ok

• leaf intercalary meristem - probably ok - does it ever occur in non-vascular leaves? Normal growth in non-vascular leaves if from the tip.

• leaf sheath - probably ok - does it ever occur in non-vascular leaves?

(see part_of children of leaf)

• leaf aerenchyma- is there ever aerenchyma in non-vascular leaves?

• leaf mesophyll - should probably be part of leaf. Is there a mesophyll in non-vascular leaves?

I (RW) haven't found any examples of the use of leaf aerenchyma or leaf mesophyll in leaves of bryophytes. Probably okay to leave them as children of vascular leaf.

Terms that are part of vascular leaf but should be part of leaf:

• leaf lamina - should be part_of leaf

• leaf margin - should be part_of leaf

• leaf base and leaf apex are already part of leaf (rather than vascular leaf)

Do we keep these terms for vascular leaf and rename them, move them to non-vascular leaf, or obsolete them and create new children of leaf?

Physcomitrella terms

See Terms requested by Physco group for a list of terms.

-This was identified as a priority, since if we can get their terms in by the next release, they will use PO instead of continuing to develop their own ontology.

The Moss Ontology (MO) has about 65 PSO terms. About 20 of those already exist or are trival to add to the PO (e.g. non-vascular leaf base, non-vascular leaf apex). Many of the terms will be fairly straight-forward to add, but some will require discussion.

They have requested about about 35 PGDSO terms. About 10 of those already exist. The others should be fairly easy to add once the PGDSO is restructured.

• Do we want to give MO/Physco terms their own number space? Maybe a subset of the NYBG number space.

New items for Physco

Collective plant structures

gametophore - definition supplied by MO: The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia). Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.

Suggest is_a shoot system.

Proposed def.: A shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase. participates_in gametophytic phase

Comment: A gametophore is the leafy part of a moss gametophyte, without the protonema. Antheridia and archegonia arise on the gametophore.

bud - definition supplied by MO: A structure produced by a caulonema and able to develop into a gametophore or a stem that includes an apical cell able to develop into a gametophore. The earliest recognizable stage of gametophore development. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered by David Cove

Suggest a new term gametophore bud. This could be a child of bud (PO:0000055: An undeveloped shoot system).

Proposed def.: A bud on a protonema that develops into a gametophore. participates_in gametophytic phase

Comment: Occurs in mosses.

Plant organs

cauloid - This is the term used for the gametophore stem or axis.

Suggest using gametophore axis as primary name, cauloid as synonym.

Proposed definition: A plant axis that is part of a gametophore. is_a plant axis, part_of gametophore, participates_in gametophytic phase

Synonyms: cauloid, gametophyte axis

Also suggest adding terms for gametophore stem and gametophore branch (similar to stem and branch).

perigonial bract - The specialized phyllids surrounding the antheridia. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

A bract (PO:0009055) is defined as: A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure. [source: POC:curators] Comment: Often used to refer to what is called here floral bract.

Proposed definition: A bract that subtends an antheridium. part_of gametophore, participates in gametophytic phase

Comment: When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts.

perichaetal bract - MO did not request this term, but it is commonly used in mosses, so suggest adding it at the same time.

Proposed definition: A bract that subtends and archegonium. part_of gametophore, participates_in gametophytic phase.

Comment: When an archegonium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually parichaetal bracts. If an archegonium occurs on a main axis of the gametophore, only the terminal phyllomes are usually parichaetal bracts. The two or three terminal-most perichaetal bracts may fuse to form a gametophytic perianth.

Suggest adding the term gametophytic perianth as well.

Proposed definition of gametophytic perianth: A collective phyllome structure that consists of two or more of the most distal parachaetal bracts that are fused laterally and surround the calyptra (or should it be surrounds the capsule, in case no calyptra is present). has_part parachaetal bract, part_of gametophore, participates_in gametophytic phase, disjoint from perianth (PO:0009058)

Comment: The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.

seta- The stalk of a moss sporophyte. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

Suggested definition: A plant axis that is a stalk that hold up a spore capsule. participates_in sporophytic phase

Cardinal organ parts

Terms requested by MO:

calyptra

base

peristome

theca

lid

foot

neck canal

Other terms, not from MO

epiphram

spore capsule mouth

pseudopodium

venter

Upcoming meetings 2011:

• 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.

See comments on today's agenda

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

ICBO

LC contributed to the workshop proposal "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" Authors: Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland and Laurel Cooper

Submitted: February 15th, 2011

- LC will attend and represent the PO. Invite other plant people? Will talk with Elizabeth Arnaud at the upcoming meeting.

-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