POC Conf. Call 3-8-11

POC meeting, Webex Conference Call; Date: Tuesday Mar 8th, 2011 10am (PST)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_3-1-11?

Issues arising from last week's meeting:

anther/sporangium parts

• 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.

Last week, we agreed to make new term anther lobe: a pollen sac that is part of an anther. After more discussion we decided to try out a new arrangement for the parts of an anther. (see below)

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

Last week, we agreed that this should be is_a collective organ part instead of is_a pollen sac.

• Microsporocyte (PO:0020047) is part_of pollen sac. Not appropriate for all plants (including gymnos). Should probably be part_of microsporangium, so it is more general.

• Anther wall (PO:0000002) is part_of pollen sac. Suggest making part_of anther

Definition (A multicellular layer with outer epidermis and an inner endothecium.) is a bit vague.

Suggested definition: A cardinal organ part that is the outer tissue layers of an anther and has as parts an outer epidermis and an inner endothecium.

The issue with anther wall is also a problem for tapetum and other structures that are part_of anther. We discussed two possible solutions. One is to create specific terms for both angiosperms and other taxa (for example, have separate terms for microsporangium wall and anther wall). The other is just to create general terms, then only create specific terms for angiosperms when there is something structurally different about the part in angiosperms (for example, replace anther wall with synangium wall). These two solutions are not necessarily mutually exclusive. If we only use general terms, we may need to use has_part relations instead of part_of relations in some cases. If we do that, then it is crucial that we get the software properly developed so that annotations will accumulate properly through has_part relations. This is also an issue for develops_from relations.

RW: I still need to make a figure of possible solutions for dealing with the different parts of anthers. Will insert on Monday.

When to obsolete terms

If the definition of a term stays more or less the same, but the is_a parent changes, should the term ID remain, or should it be obsoleted and replaced by a new term with the same name.

Many people say that "if in doubt, obsolete," but this creates a lot of work and often confusion for our users.

We should establish a policy on when to obsolete in cases like this.

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.

Terms requested that are already in PO but need some work

epidermis (PO:0005679)

Current def: A portion of plant tissue composed of epidermal cells that develops from the protoderm and covers the surface of a plant structure. [source: POC:curators].

Comment: The epidermis can be composed of one or more layers of cells. In some species, the epidermis is replaced by periderm. Epidermis can also include trichomes and stomatal pores.

Growth in mosses (and other bryophytes?) results from divisions of a single apical cell. Branches or leaves form from division and differentiation of sub-apical cells. Mosses do not have an apical meristem in the same sense as vascular plants.

Is there a protoderm in non-vascular plants? (def of protoderm: A portion of meristem tissue that develops from the outer layer of an apical meristem and gives rise to a portion of epidermis.) Maybe we need to move the phrase 'develops from protoderm' to the comment, and add new comment about bryophyte epidermal development.

Also suggest adding comment that epidermis can include root hairs and rhizoids too (in addition to trichomes and stomatal pores).

Proposed definition: A portion of plant tissue composed of epidermial cell that covers the surface of a plant structure.

Comment: In vascular plant, the epidermis develops from the protoderm. In non-vascular plants, the epidermis develops form sub-apical cells. The epidermis can be composed of one or more layers of cells. In some species of vascular plant, the epidermis is replaced by periderm. The epidermis can also include trichomes, stomatal pores, root hairs, and rhizoids.

phyllid base and phyllid apex

We already have the terms leaf base (PO:0020040) and leaf apex (PO:0020137). The choice is to make phyllid base (=non-vascular leaf base) and phyllid apex (=non-vascular leaf apex) synonyms of these terms, or to make them is_a children (see discussion of part_of children of leaf, above).

The same issue also applies for phyllid trichome/leaf trichome.

spore capsule

We have the term moss capsule (PO:0025232), but having a taxon name in the term name is not desirable, nor is having it defined based on its taxa. Suggest renaming it spore capsule and defining it based on its unique characteristics.

Current definition: A sporangium in mosses.

Proposed def.: A sporangium...

Comment: Found in mosses.

transfer cell

We have the term transfer cell (PO:0000078). Def: A cell with wall ingrowths (or invaginations) that increase the surface of the plasmalemma. [source: ISBN:0471245208] Comment: Appears to be specialized for short-distance transfer of solutes.

MO suggested definition: Specialized cell at the junction of the gametophyte and sporophyte that function in nourishing the sporophyte. [source: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition]

Are transfer cells always at the junction between the sporophyte and gametophyte? Do we want to include that in the definition or in a comment?

Do we want to add a specialized term for transfer cells in mosses? Are they different from other transfer cells?

Basal endosperm transfer cell (PO:0009018) is currently the only is_a child of transfer cell.

Comment from Barry via email: My instincts tell me that the reference to 'at the junction' is more central to the definition of 'transfer cell' then is the reference to 'ingrowths'. But in any case the definition would be overloaded to have both sets of information. One or other should be in a comment.

Whole plant structures

protonema - The filamentous stage of gametophyte development. Protonemal tissue is produced following spore germination or the regeneration of most tissues (whether gametophytic or sporophytic). In most moss species, protonemal filaments comprise two cell types, caulonema (q.v.) and chloronema (q.v.). Both types of filament extend by the serial division of their apical cells. Sub-apical cells may branch. (MO definition, from Celia Knight,Pierre-François Perroud,David Cove (2009): The moss Physcomitrella patens. The Annual Plant Review 36, Glossary)

Protonemata may develop from a spore or from a fragment of gametophytic tissue.

The Physco group classified protonema as whole plant, but could be considered a life-cycle phase (part of gametophytic phase). Need to decide how to handle it. After the leafy part of the gametophyte develops from the protonema, the protonema still persists, so there is some part of the life cycle in which the protonema is not the whole plant.

Proposed definition of protonema:

chloronema - The assimilitory filaments of the protonemal stage of gametophyte development. Compared to caulonmeal filaments, the cells of P. patens chloronemal filaments contain many well developed chloroplasts. The cross walls of adjacent cells in chloronemal filaments are perpenicular to the filament axis. (MO definition, from Celia Knight,Pierre-François Perroud,David Cove (2009): The moss Physcomitrella patens. The Annual Plant Review 36, Glossary)

caulonema - The adventitious filaments of the protonemal stage of gemtophyte development. Compared to chloronemal filaments, the cells of P. Patnes caulonemal filaments contain only fewer, less well developed chloroplasts. The cross walls of adjacent cells in caulonemal filaments are oblique to the filament axis. (MO definition, from Celia Knight,Pierre-François Perroud,David Cove (2009): The moss Physcomitrella patens. The Annual Plant Review 36, Glossary)

The MO classified chloronema and caulonema as is_a protonema, therefore is_a whole plant, but maybe they could be considered portions of tissue. They also have terms for chloronema cell and caulonema cell, but those are pretty straight-forward.

Proposed definition of chloronema:

Proposed definition of caulonema:

MO has also requested terms fro chloronema cell and caulonema cell, which I have on a future agenda.

Upcoming meetings 2011:

* 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.

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