POC Conf. Call 3-8-11

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

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Dennis Stevenson (NYBG), Justin Elser (OSU), Justin Preece (OSU), Barry Smith (University at Buffalo, NY),

Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo; (Cornell University) Chris Mungall (Lawrence Berkeley National Lab),

Collaborators: none

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

There were no changes, additions, or deletions.

Issues arising from last week's meeting:

anther/sporangium parts

Currently, pollen sac is part_of anther, but this won't work for gymnosperms. Also, anther wall and its parts (such as tapetum) are part_of pollen sac.

We discussed two possible solutions:

1. Create specific terms for both angiosperms and other taxa (for example, have separate terms for microsporangium wall and anther wall).

2. Create general terms, then only create specific terms for angiosperms when there is something structurally different about the part in angiosperms.

These two solutions are not necessarily mutually exclusive.

For this solution we will need to use has_part relations instead of part_of relations in some cases.

Note: 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). Also, the Amigo software will have to be fixed, as we currently have to strip the has_part relations before loading on the browser.

See below figures for possible solutions to dealing with annotations.

Figure 1: the current state

Problems with the current state include inapplicability to non-angiosperms, and incorrect part_of relations for the parietal layers.

Proposed structure, using has_part relations (simplified version):

The sporangium wall is basically the same throughout vascular plants, so this proposal creates a new general term "microsporangium wall". The part_of children are part of microsporangium wall (sort of like the part_of children of leaf). Anther wall has_part sporangium wall, since an anther is composed of multiple sporangia.

This has not yet addressed the issue of the megasporangium, or the sporangium in homosporous plants (which have some of the same parts).

Here is a picture of what it might look like without has_part relations, including only two of the four wall layers, and none of the develops_from relations: Media:sporangium_anther_pollensac7_not_suggested1.jpg

Proposed structure, using has_part relations (complex version):

This image shows all of the develops_from relations. This sort of works for gymnos and angiosperms, will may need some work for other vascular plants.

While external the tapetum and endothecium develop from the parietal layers, the internal tapetum and endothecium (adjacent to the connective in angiosperms) develops from pre-existing ground cells internal to the parietal layers (from the connective in angiosperms).

Furthermore, this developmental pattern of the different wall layers is variable even within the angiosperms, so the pattern here is not general.

Annotations and has_part relations

Annotations should pass through has_part backwards, that is from parent to child (in the opposite direction of the arrow). Furthermore, they should only pass through has_part relations when the instance for which the annotation was created comes from a taxon in which the parent term is part_of the child term.

For example: In anther has_part pollen sac, anther is the child and pollen sac is the parent. Annotation should never go from anther to pollen sac. Annotations should go from pollen sac to anther, but only if they come from an angiosperms.

In order for this to work, the conditions under which annotations should pass through will have to be specified every time a has_part relation is added to the ontology. That means that any class in the PO that has a has_part tag will have to have additional tags specifying the conditions under which annotation should pass through the has_part relation. We would have to create a custom tag for this, perhaps a custom relation, that is conditional. Something along the lines of: if taxon_id=xxxx then treat parent term as part_of child term.

Note: Another problem with this is that we currently have to remove the has_part relations in order to load the ontology on the browser. In order for this to work, the software for Amigo would have to be fixed to accommodate both has_part relations and the conditional tags.

GO has_part relation

There was general agreement that using a combination of part_of and has_part relations is a better way to describe plant structures across all plants, but there was also a lot of concern about the practicality of using has_part relations. There are problems not only with annotations and the Amigo browser, but also, users may be importing the PO into other applications or software (such as Chado) that cannot handle the has-part relations. If we decide to use has_part relations extensively, then we will need to find a solution that works for our user groups as well.'

We might need to change the stable URL for the PO to point to the version without has_part relations.

Dennis suggested an alternative solution which was to have one common upper-level ontology combined with a series of taxon specifc ontologies that cross-reference the upper-level ontology and possibly each other.

Barry suggested that we may want to contact Tod Detwiler, who is the software person for the FMA. Although FMA is a single species ontology, they have many more terms than the PO, and are dealing with many of the same problems.

LC will schedule a special tech meeting to discuss possible software solutions, and to see if it will be feasible to use the has_part relations.

The issue of annotations can also be addressed at the tech meeting we are planning to hold.

Other related terms

• anther lobe should be narrow synonym of pollen sac.

Agreed

• theca (PO:0009069): is_a collective organ part structure, part of anther, has_part pollen sac.

Agreed

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

Agreed that it should be part of microsporangium. Check if "pollen mother cell" is exact synonym, and add it if not. [Pollen mother cell is already a synonym of microsporocyte.]

We should add a new term "sporocyte", parent to megasporocyte and microsporocyte, and also as a class for the sporocytes in homosporous plants like mosses. [We already have the term sporocyte, but the definitions of the sporocyte terms need a little work.]

Restructuring descendants of leaf (PO:0025034) - recap of last week's decisions

vascular and non-vascular leaf

Current definitions are okay. Will add frond and needle-like vascular leaf as narrow synonym of vascular leaf. Agreed to add phyllid and gametophyll as synonyms of non-vascular leaf. Gametophyll may be a little confusing, because it does not parallel sporophyll, but people do use the term. Will also add gametophytic leaf as a synonym.

okay

current is_a children of vascular leaf

• We agreed that juvenile leaf (PO:0006339), transition leaf (PO:0008018), and adult leaf(PO:0006340) 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. See agenda item below on when to obsolete terms.

• We decided to keep simple leaf (PO:0020042) and compound leaf (PO:0020043)for now. May convert them to phenotype terms later (cross-products with PATO), if we go that route.

• We will create a low-priority SF item for rosette leaf and cauline leaf, to check the definitions. Other is_a children of vascular leaf were okay.

okay

Part_of children of 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.

• A new wiki page has been created for software requests at POC_software_requests.

• Leaf aerenchyma, leaf mesophyll, leaf lamina, and leaf margin will be part_of leaf, rather than part_of vascular leaf.

• What about leaf intercalary meristem and leaf sheath (currently part_of vascular leaf). Do they ever occur in non-vascular leaves?

Leaf sheath can occur in mosses, so it should move to leaf. We don't know if there are intercalary meristems in non-vascular plants, so we should keep in general and move it to 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.

Working on new term requests outside the POC meetings

RW and LC suggested that, in order to speed up the addition of new term requests (from the Physco group, Traitnet, and others), Ramona and Dennis could work on those requests outside the meeting, then present suggested definitions to the group at the meetings. Discussion of these new terms at the meetings should be kept brief, unless there is some controversy. All changes will be documented on Source Forge.

Ramona and Dennis went over the items below, so they do not need extensive discussion.

We agreed that this was a good way to move through terms quickly, but we need to check with Alejandra, because she has been traveling for the past 5 days. Ramona and Dennis will consult with Ale on new terms before the conference calls.

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. The moss apical meristem may differ from that of vascular plants, but it is still possible to call it an apical meristem

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.) If we consider that mosses have an apical meristem, then this definition is valid for moss.

Suggest leaving definition as is, adding to comment:

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

The phrase "the epidermis is replaced by periderm" is ambiguous. Need to rewrite the comment to make it clear that a periderm develops and the epidermis goes away.

spore capsule

We need to distinguish a capsule in bryophytes from the caspsule that is part of a fruit in e.g., Eucalyptus. The term capsule is used for the sporangium in all bryophytes, not just mosses.

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.

In fact, the morphology of capsules in the bryophytes is highly diverse, and I cannot think of a unifying characteristic of all of them that distinguishes them from other sporangia. Perhaps it would be better to merge moss capsule (PO:0025232) with sporangium (PO:0025094), making moss capsule an exact synonym. We could also add spore capsule as an exact synonym.

The part of children of capsule in mosses (operculum, peristome, etc.) could still be part_of sporangium.

We agreed that moss capsule (PO:0025232) should be merged into sporangium (PO:0025094).

We still need to add terms for calyptra and operculum in angiosperms such as Eucalyptus. Capsule is also used for angiosperms. Note that capsule is already in the PO as a narrow synonym of fruit. This should be "fruit capsule" or "capsule fruit" instead of just capsule, to distinguish it from a capsule that is a sporangium.

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? -- Don't necessarily need a specialized term.

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.

Actually, it may be the in-growths that are more important. Transfer cells can occur anywhere there is a junction between two individuals, either between sporophyte and gametophyte, or between a parasitic plant and its host. Suggest we leave the definition as is, and add to the comment:

Proposed comment: Appear to be specialized for short-distance transfer of solutes. Transfer cells can occur anywhere there is a junction between two individuals, such as between a sporophyte and a gametophyte, or between a parasitic plant and its host.

New comment is okay.

protonema, chloronema, caulonema

Below are the definitions from the Physcomitrella group:

• 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)

(note from RW: Protonemata may develop from a spore or from a fragment of tissue.)

• 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 Physco group classified protonema as whole plant, in which case it could be considered a life-cycle phase (part of gametophytic phase) in the PO. However, 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.

The MO classified chloronema and caulonema as is_a protonema, therefore is_a whole plant, but instead they could be considered portions of tissue. Suggest that the chloronema and caulonema be part_of protonema.

MO has also requested terms for chloronema cell and caulonema cell. Their definitions:

• chloronema cell: The assimilatory filaments of the protonemal stage of gametophyte development. Compared to caulonemal filaments (q.v.), the cells of P. patens chloronemal filaments contain many well developed chloroplasts. The cross walls of adjacent cells in chloronemal filaments are perpendicular to the filament axis. (Celia Knight,Pierre-François Perroud,David Cove (2009): The moss Physcomitrella patens. The Annual Plant Review 36, Glossary)

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

Suggest we add new terms for protonema, chloronema, and caulonema as portions of plant tissue, chloronema cell and caulonema cell as plant cells, plus add protonema phase as part_of gametophytic phase, and possibly chloronema phase and caulonema phase as is_a or part_of protonema phase.

Proposed definition of protonema: A filamentous portion of chlorenchyma tissue that develops directly from a spore. is_a chlorenchyma, participates_in protonema phase.

Comment: The protonema is the first structure that develops in the gametophytic phase of mosses, some other bryophytes, and leptosporangiate ferns. The term protonema is also used to refer to the phase of development in which protonemal tissue is produced (see PO:xxxxxxx protonema phase). In some species of moss, the protonema is perennial. A protonema may develop from sporophytic tissue during apospory.

(Note: need to request apospory and apogamy, as forms of apomix, as biological processes either in PGDSO or in GO)

Need to rephrase definition as "A portiong of chlorenchyma tissue that develops direction from a spore and ..." where the ... is a definition of what filamentous growth is.

Proposed definition of chloronema: A portion of protonema that has as part chloronema cells.

Comment: Generally, the development of chlornema precedes the development of caulonema. Only the caulonema, and not the chloronema, initiates gametophore buds.

Proposed definition of caulonema:A portion of protonema that has as part caulonema cells and initiates gametophore buds.

Comment: Generally, the development of caulonema follows the development of chlornema. Only the caulonema, and not the chloronema, initiates gametophore buds.

New proposed definitions:

chloronema: A portion of protonema tissue that consists of only chloronema cells.

caulonema: A portion of protonema tissue that consists of only caulonema cells.

Proposed definition of chloronema cell: A plant cell that is part of a chloronema and contains many well-developed chloroplasts and has cross walls of adjacent cells that are perpendicular to the protonema axis. is_a plant cell, part_of chloronema, participates_in protonema phase

Proposed definition of caulonema cell: A plant cell that is part of a caulonema and contains fewer, less well-developed chloroplasts than a chloronema cell and has cross walls of adjacent cells that are oblique to the protonema axis. is_a plant cell, part_of caulonema, participates_in protonema phase

Relative phrases like "fewer, less well-developed chloroplasts" are not ideal in definitions. Better to put in comment.

New proposed definitions:

chloronema cell: A plant cell that is part of a chloronema and has cross walls of adjacent cells that are perpendicular to the protonema axis. Comment: A chloronema cell contains many well-developed chloroplasts.

caulonema cell: A plant cell that is part of a caulonema and has cross walls of adjacent cells that are oblique to the protonema axis. Comment A caulonema cell contains fewer, less well-developed chloroplasts than a chloronema cell.

Proposed definition of protonema phase: A plant life cycle phase that is part of a gametophytic phase in which protonema tissue is produced.

Comment: The protonema phase follows spore germination in mosses, some other bryophytes, and leptosporangiate ferns, and precedes the development of gametophores.

We should not work too much on phases until the PGDSO is sorted out, but it is okay to add protonema phase for now as defined above.

Rather than saying that a protonema phase is part of a gametophytic phase, should say that it is a subphase of the gametophytic phase. Use sub-phase rather than part of in text definition (even though we will use the part of relation) because there can be parts of a phase that are not sub-phases.

Best Practices Guide: 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, ie: "best practises" guide.

See: PO_Developers_Guide

In the examples we talked about (like children of leaf) it is probably okay to leave the existing ID, but we should consult with Chris Mungall about this.

Publications

Paper for ICBO meeting

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

- Could consider doing a paperjust for the workshop: (April 1: Deadline for submission of workshop papers)

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 (Accepted)

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- 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.

Early bird registration deadline - Extended 1 March 2011 Deadline for registration by presenters 1 March 2011

See IBC 2011 Bio-Ontologies Symposium wiki page for more details