POC Conf. Call 2-22-11

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

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Justin Elser (OSU), Justin Preece (OSU)

Absent: Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab),Marie Alejandra Gandolfo; (Cornell University),

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_2-15-11? There were no changes, additions, or deletions.

Phenotype RCN Meeting this week

Feb 25th-27th, National Evolutionary Synthesis Center in Durham, NC,

The Phenotype Ontology RCN

*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 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:

phenotypic descriptors for plants in PATO are lacking (examples?), need bridging/mapping files, need to encourage other groups to send us annotations and use cross refs to the po terms.

5. Vision: where you’d like to go...

Integration of Trait Ontology into PO- phenotype section of PO, PO will provide values and attributes to describe the entities. POC will work on developing a set of precomposed phenotype terms (based on TO), plus improve post-composition scripts. When pre-comps are mature and post-comp scripts are working, community can do their own post-composition.

Phenote annotation tool will allow creation of post composed terms

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?

From 2009 grant: "The overall goals of the PO are 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."

-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, or character descriptions from a systematic study (gymnosperms, monocots?)

Update on Progress of Publications

• Paper for ICBO meeting- suggestion from BS, ICBO call for papers, deadline is March 1st.

Could be expanded for submission to journal later- perhaps for the American Journal of Botany?

We will consider this if there is not too much overlap with the plan phys paper, as we don't want to jepordize getting it published. Could focus more on the ontology aspects. Will talk about it more at next week's meeting.

Target journal for a major, detailed paper: This is the top priority right now:

-Plant Physiology:

RW and LC are working on an outline for a manuscript to submit to Plant Physiology. This will be a more detailed description of the changes made to the PSO in the past year, including restructuring.

Will focus on how PO is now applicable to a wider range of plant species. Note: having the MO terms included will be very helpful to this. Once our draft is prepared, we will work with Nick Provart of BAR to collaborate on the analysis section.

Plant_Physiology_paper-_2011

Possible target journals for a short paper: PO_Paper_Winter_2011

Items arising from last week's agenda:

pollen sac

Current def'n: 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.

This definition and the current part_of relations will be problematic if we want them to include pollen sacs in gymnosperms.

One way around this problem would be define pollen sac directly as part of a sporophyll, then replace the pollen sac part_of anther relation with anther has_part pollen sac:

Alternative suggested definition: A microsporangium that is part of a sporophyll where the pollen grains developed and are contained after they develop.

Comment: A pollen sac is a microsporangium in seed plants. In angiosperms, a single, unfused pollen sac may contain an anther locule or several pollen sacs may fuse so they contain a single anther locule.

Anther locule should remain as part_of anther, not be part_of pollen sac.

Alternative suggested definition seems okay. Will leave open on SF for a week for comment. Need to add term "anther lobe", part_of anther, has_part pollen sac. There was a suggestion to add pollen sac has_part tapetum, but this may not be appropriate for gymnosperms.

Plant cells and embyronic plant cell

Rachael Huntley from EBI/Uniprot is working on annotations that involve plant cells. She would like to be able to import all plant cell types by only using the plant cell branch of the ontology, but this would miss embryonic plant cell (PO:0025028), which is a child of embryonic plant structure. She has requested that we make embyronic plant cell is a plant cell.

Current def'n: An embryonic plant structure that is a plant cell that is found only in an embryo.

Her point that an embryonic plant cell is still a plant cell is correct (based on the definition), but have tried to avoid dual parentage.

Embryonic plant cell has three is_a children: apical cell (PO:0004000), basal cell (PO:0002002), and hypophysis (PO:0020109)

We can either:

Make embryonic cell a child of both plant cell and embryonic plant structure

or

Make embryonic cell a child of plant cell, and add intersection of relations:

embryonic plant cell [intersection_of] plant cell and part_of embryo,

plus embryonic plant structure [intersection_of] plant structure and part_of embryo.

Then the reasoner would figure out that embryonic plant cell is an embryonic plant structure, with the relation being asserted.

It is was decided that we should probably make embryonic cell a child of both plant cell and embryonic plant structure, but we need to revisit this whole branch of the ontology

For example, a coleoptile can be present in both embryo and in a seedling. Solution may be to have "embryonic coleoptile" and "seedling coleoptile" with develops from relation between them. Generic term coleoptile is a plant structure (phyllome?), embryonic coleoptile is an embryonic plant structure.

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.

prophyll and scale leaf

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

• prophyll (PO:0009042)

Def'n: The first leaf or two leaves formed at the base of an axillary shoot, often smaller and/or in a distinctively different position from those formed subsequently;

is_a phyllome

• scale leaf (PO:0006003) is_a phyllome

Current def'n: A reduced and more or less non-photosynthetic leaf, often associated with a vegetatively propagating organ such as a rhizome or perennating bud. Comment: Sometimes referring specifically to such leaves on a seedling.

Proposed def'n: 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.

new proposed def'n:: A phyllome that is reduced in size (relative to vascular leaves on the same plant) and is often associated with a perennating or dormant bud or a vegetatively propagating organ such as a rhizome.

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.

we will add 'or dormant' to the def'n

To make the comment clearer: "Annotations for scale-like leaves should go under vascular leaf (PO:0009025), not scale leaf"

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

Current def'n: A reduced leaf surrounding a dormant bud.

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

new proposed def'n:: A scale leaf that surrounds a dormant or perennating bud.

Primary name should be "bud scale leaf", with bud scale as exact synonym.

Should add new term for rhizome scale leaf: A scale leaf that grows from a rhizome.

Will add scale-like leaf as a narrow synonym of vascular leaf. See: http://oregonstate.edu/trees/conifer_genera/false_cedars.html

vascular and non-vascular leaf

These items were postponed until next week

*non-vascular leaf: (PO:0025075)

Def'n: A leaf in a non-vascular plant. [source: POC:curators] Comment: Include moss and liverwort leaves. Occurs in the gametophytic phase of a plant life cycle.

Synonyms: exact: gametophyte leaf

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

*vascular leaf: (PO:0009025) Def'n: A leaf in a vascular plant. [source: POC:curators]

Synonyms: related: foliage leaf

Comment:In angiosperms, commonly thought of as one of the three basic parts of the seed plant body, a structure usually of determinate growth, without secondary thickening, and of superficial origin, often flattened and photosynthetic in part, and in the axil of which is found a bud (APweb Glossary). Occurs in the sporophytic phase of a plant life cycle.

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

Ramona sent a response to Sharon Lewis, telling her that we are adding "leaf, vascular" as a synonym

postponed until next week

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 (PO:0006339)

Def'n: Distinct from adult leaves, being characterized by particular anatomical traits namely, wax and trichome distribution, presence or absence of epidermal cell types, cell wall shape and biochemistry.

• transition leaf (PO:0008018),

Def'n: A leaf that is part of an heteroblastic series, and is characterized by anatomical features that are intermediate between juvenile and adult leaves.

• adult leaf (PO:0006340)

Def'n: Adult leaves are characterized by particular anatomical traits namely, wax and trichome distribution, presence or absence of epidermal cell types, cell wall shape and biochemistry.

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 normally 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 (PO:0020042) Def'n: A leaf in which the lamina is undivided.

• compound leaf (PO:0020043) Def'n: A leaf having two or more distinct leaflets that are evident as such from early in development.

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'n: 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

(see part_of children of leaf)

Terms that 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?

• 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.

From MAG: I did a search and I could not find any references on the presence or absence of aerenchyma in non-vascular leaves. It seems that they all should have some type of "mesophyll", since they have at least one layer of parenchyma and they photosynthesizes (for example Amblystegium and Funaria). Although they do not developed "vascular bundles" they can have some sort of midrib composed of conductive elements.

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

These items were postponed until next week

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.

Collective plant structures:

gametophore

Def'n supplied by MO: The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia).

Ref: Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.

Suggest is_a shoot system.

Proposed def'n.: 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.

gametophore bud

The term "bud" has been requested: Def'n 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.

Ref: 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'n: A bud on a protonema that develops into a gametophore. participates_in gametophytic phase

Comment: Occurs in mosses.

cauloid

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

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

Proposed def'n: 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.

Ref: 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 def'n: 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.

Additional moss terms:

These items were postponed until next week

These were not requested by the Physcomitrella group, but are commonly used to describe mosses, so we may as well add them now.

perichaetal bract

Proposed def'n: 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.

gametophytic perianth

Proposed def'n: A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on an axis that are fused laterally and surround the calyptra.

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.

Suggested def'n: A plant axis that that holds up a spore capsule. participates_in sporophytic phase

Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

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

*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.

Abstract deadlines: Your abstract must be submitted by March 11 if you want it to be considered for a minisymposium talk.

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 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