POC Conf. Call 3-1-11

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

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Justin Elser (OSU), Justin Preece (OSU), Marie Alejandra Gandolfo; (Cornell University),

Absent: Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab), Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_2-22-11? There were no changes, additions, or deletions.

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 attended

Minutes are now posted on the site and the slide presentations will be up soon

pollen sac/anther lobe

From last week:

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.

Issues:

• 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?

agreed to make new term anther lobe: a pollen sac that is part of an anther But, see comments below.

• 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.

agreed that this should be is_a collective organ part.

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

Having annatations accumulate properly through different relation types is a high priority. RW and LC should contact Chris and find out if he can do this, and if he needs someone from PJ's lab to work on it.

Will put together a proposal for next week (in graphical form) of possible solutions for dealing with the different parts of anthers.

• 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.

Will include this term in the proposal for next week

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.

agreed to add phyllid and gametophyll as synonyms. Gametophyll may be a little confusing, because it does not parallel sporophyll, but people do use the term. Can also add gametophytic leaf as a 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 narrow synonyms of vascular leaf. Already added scale-like leaf as a narrow synonym of vascular leaf.

Will add frond as narrow synonym. Use 'needle-like vascular leaf' instead of needle as synonym. Will still show up in search for needle.

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 below).

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

We agreed that in general, it is better to have the part_of children only be part of the general term leaf, and not create new terms for vascular parts of and non-vascular parts of. Terms that only occur in one or the other (like leaf endodermis) will only be the child of the appropriate term.

If someone put an annotation on leaf epidermis for rice, it will be collected by leaf, but not by vascular leaf, even though it should also be on vascular leaf. We will suggest to users that in cases like this, they annotate to both leaf epidermis and vascular leaf. Also, we will write an algorithm that automatically adds the annotations to vascular leaf, in case the curators miss it. It will search for annotations for parts of leaf, then check the taxon ID, and then add the appropriate annotation to either vascular leaf or non-vascular leaf. This will assure that annotations end up on the correct terms, but reduce term inflation.

We need to create a wiki page for software requests, and put this request on there. Should provide examples with any requests.

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.

We agreed that these terms should be children of leaf (PO:0025034), rather than vascular leaf (PO:0009025).

The definitions are okay, but the parentage will change. We did not know if they should just be moved, or if they should be obsoleted and recreated. This is an issue in which we need to develop a consistent policy. We will ask Barry for more input on this next week, since it is an issue that is likely to come up repeatedly as we work on new terms.

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.

We agreed to keep these terms for now. May convert them to phenotype terms later, if we go that route.

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.

Will create a low-priority SF item for these terms.

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?

need to double check with Dennis and Alejandra about leaf intercalary meristem and leaf sheath.

• 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.

Dennis pointed out example of aerenchyma in bryophytes (in Sphagnum). Will move leaf aerenchyma and leaf mesophyll to be children of leaf (PO:0025034).

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?

See comments above. Will keep all part of children that can be in either vascular or non-vascular leaves as part_of leaf (PO:0025034).

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.

• Bryphyte/moss terms should have their own subset?

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 (add root hairs and rhizoids too).

Is there a protoderm in non-vascular plants? (def: A portion of meristem tissue that develops from the outer layer of an apical meristem and gives rise to a portion of epidermis.)

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.

Other items

Alejandra has finished the list of Spanish translations for the PSO terms. Ramona tried putting two terms with accents (embryo and plant cell) in the file, to see how they load onto the dev browser. We will prepare a list of new terms for translation before each release, so that Ale is not working on it constantly.

Publications

Paper for ICBO meeting

-suggestion from BS, ICBO call for papers, (deadline is ~March 11th)

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

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

Proposal has been accepted, workshop date:

-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

*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