Report from the Phenotype Ontology RCN Summit

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

Laurel and Pankaj attended

pollen sac/anther lobe

At least week's meeting we had a new definition for pollen sac: 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.

Replace the pollen sac part_of anther relation with anther has_part pollen sac

The old term for pollen sac (PO:0009070) was obsoleted and replaced it with a new term pollen sac (PO:0025277), because it has gone through a name change and several definition changes, and may no longer be the same as the original term.

There was also a suggestion to add a new term anther lobe which has_part pollen sac. This would be consistent with the PGDSO term "C four anther lobes formed" (PO:0001025). However, anther lobe is already a related synonym of pollen sac.

Are they the same thing in angiosperms? Can't use the name anther lobe for gymnosperms.

Should we create a new term anther lobe for angiosperms (is_a pollen sac?) or make it a narrow synonym?

Other issues:

We also have the term theca (PO:0009069): A part of the anther consisting of paired sporangia that dehisce down a common slit.

Theca currently is_a pollen sac, but it is really two pollen sacs. Should be is_a collective organ part structure.

Anther wall (PO:0000002) is part_of pollen sac. Won't work for gymnosperms.

Microsporocyte (PO:0020047) is part_of pollen sac. Should probably be part_of sporangium.

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.

vascular and non-vascular leaf

*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.

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

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:

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.

Bryphyte/moss terms should have their own subset?

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.

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 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 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)

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?

From 2-22: We will consider this if there is not too much overlap with the plan phys paper, as we don't want to jeopardize getting it published. Could focus more on the ontology aspects.

Special paper for American Journal of Botany

DWS contacted the editor of AJB, who felt that a special invited paper on the Plant Ontology would be a good idea. She asked for a target date.

Possible topics for the paper:

-What the PO is and why it is important to the readers of AJB (botanists and other plant scientists)

-How the PO unifies the study of plant sciences - cross-disciplinary studies

-Ontologies for systematics

-Examples/case studies: reproductive axes across land plant or seed plants, others?

Plant Physiology

LC and RW have been working on a draft 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

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

Next meeting scheduled for Tues, Mar. 8th, 2011 at 10am PST

POC Conf. Call 3-1-11

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