POC Conf. Call 5-06-11

POC meeting, Webex Conference Call; Date: Tuesday May 10th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_5-03-11?

Issues arising from previous meetings:

Review of apical cell (PO:0030007) and its descendents

At the POC meeting on 4/28/11, we decided to name this term meristematic apical cell

Proposed def.: A single meristematic cell at the tip of a shoot axis apex, leaf apex, root apex or thallus apex, in a plant structure where apical growth occurs.

Comment: Occurs in bryophytes and some pteridophytes, where apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. May be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge shaped with two cutting faces (in non-vascular leaves or thalli). An apical cell may be established upon germination of a spore or upon the first cell division of an embryo or later.

is_a meristematic cell, sibling to initial cell

See: http://www.anbg.gov.au/bryophyte/case-studies/apical-cells.html

There was an extensive discussion last week and the week before about whether we should keep the term 'apical cell' to refer to the very tip or apical cell in an angiosperm leaf or other structure. The problem of adding a generic term for an apical cell is that it would cause confusion. Additionally is there really a single cell at the tip of a vascular leaf? For cells at the leaf apex (PO:0020137) and leaf tip (PO:0025142), we can use the existing PO terms. We decided to go with the proposed changes below and perhaps reconsider the issue of general term 'apical cell' in the future.

To ensure clarity, we should append the names of the child terms with 'meristematic' in their names, except for embryonic apical cell.

We could use always_in and never_in taxon relations to help clarify which taxa these are from

New proposed definition: A single meristematic cell at the tip of a plant structure where apical growth occurs.

Comment: Occurs in only bryophytes and some pteridophytes, at the tip of a shoot axis apex, leaf apex, root apex, thallus apex, or protonema. This term is only used when apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an apical meristem. May be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge shaped with two cutting faces (in non-vascular leaves or thalli). An apical cell may be established upon germination of a spore or upon the first cell division of an embryo or later.

New terms and definitions for apical cells

The definitions for the descendents of apical cell (listed below) were approved, pending approval of final definition of apical cell. See POC_Conf._Call_4-26-11#apical_cell for more details.

gametophytic apical cell (PO:0030014) > gametophytic meristematic apical cell

sporophytic apical cell (PO:0030015) > sporophytic meristematic apcial cell

thallus apical cell (PO:0030025) > thallus meristematic apical cell

root apical cell (PO:0030008) > root meristematic apical cell

shoot apical cell (PO:0030009) > etc.

gametophore apical cell (PO:0030019)

leaf apical cell (PO:0030011)

non-vascular leaf apical cell (PO:0030013)

vascular leaf apical cell (PO:0030012)

shoot axis apical cell (PO:0030010)

gametophore axis apical cell (PO:0030023)

vascular shoot axis apical cell (PO:0030024)

seta apical cell (PO:0030016)

embryonic apical cell (PO:0025284, replaces PO:0004000)

Also need to add a term for protonema meristematic apical cell.

Parts of sporangium

This is continued from our discussion at the POC_Conf._Call_3-8-11

Moss Ontology has requested the terms archesporium, amphithecium, and endothecium.

For background, see Summary of sporangium development in various non-angiosperm taxa.

Summary from previous meetings:

• At the POC_Conf._Call_3-8-11, we agree that anther lobe should be narrow synonym of pollen sac.

• At the POC_Conf._Call_4-28-11 we agree to rename theca anther theca.

• At the POC_Conf._Call_3-8-11, we agree that anther theca (PO:0009069) should be is_a collective organ part structure, part of anther, has_part pollen sac.

• At the POC_Conf._Call_4-28-11 we discussed making anther theca a child of sporangium theca.

However, anther theca, as it is now defined, is a collective organ part structure, because it consists of two fused sporagia theca (two pollen sacs)

• At the POC_Conf._Call_3-8-11, we agree that microsporocyte (PO:0020047) should be part_of microsporangium instead of part_of pollen sac, so it is more general.

• Also agreed to add a new term "sporocyte", parent to megasporocyte and microsporocyte, and also as a class for the sporocytes in homosporous plants like mosses. Actually, we already have the term sporocyte, but definition needs a little work.

anther wall and problems with current ontology

In the current set up, sporangium wall parts are only listed as part_of an anther wall. Nucellar epidermis is the only part of nucellus (megasporangium in angiosperms).

Current ontology structure:

The problem is that classes like exothecium, endothecium, primary parietal cell layer and tapetum are part of anther wall (PO:0000002), but these layers and their constituent cell types can be part of any sporangium, not just a pollen sac.

Propose making general class sporangium wall, with general terms for the part of the sporangium wall.

Will have children microsporangium wall and megasporangium wall, with requisite parts.

Another problem is that the anther wall is part_of pollen sac, but pollen sac should not be part_of anther (b/c pollen sacs occur in gymnos). Also, an anther is not a microsporangium, but rather a part of the stamen and a collection of microsporangia. Therefore, an anther wall is not technically a microsporangium wall.

Two alternative suggestions:

1. Merge anther wall into a new term pollen sac wall and keep anther wall as a narrow synonym. Pollen sac wall will be child of microsporangium wall (see separate tracker for sporangium wall). The existing parts of the anther wall would be obsoleted and replaced by "pollen sac exothecium", "pollen sac endothecium", etc.. These terms have multiple annotations for Arabidopsis and maize, but if we use replaced_by, they should transfer easily.

This is biologically correct, but still leaves the problem that annotations from pollen sac wall will not carry up to anther, because pollen sac is not part_of anther.

2. Leave existing terms for anther wall (but make them part of anther, not part_of pollen sac), which would be a child of microsporangium wall. Then all annotations for angiosperms would go on anther wall, and annotations for gymnosperms and other heterosporous plants would go on microsporangium wall.

Suggest making pollen sac part_of microsporophyll, instead of part_of anther, and add anther has_part pollen sac.

Proposed ontology structure:

Here is how the PO would look using option 2, showing just the endothecium and exothecium

New terms for parts of sporangium

Proposed defintions

archesporium (PO:0030074): A portion of plant tissue that is the internal part of a sporangium, inside the sporangium wall, and has as parts archesporial cells.

Comment: Gives rise to sporocytes and may give rise to other sterile cells such as elators.

synonym: sporogenous tissue. part_of sporangium, has_part archesporial cell

sporangium wall (PO:0025306): A cardinal organ part that is composed of the outer layers of a sporangium, external to the sporogenous tissue or spores.

Comment: Includes an exothecium (sporangium epidermis) and may include other layers such as endothecium, tapetum and parietal layers.

is_a cardinal organ part, part_of sporangium

endothecium (PO:0030049): A portion of ground tissue that is the sub-epidermal layer of a sporangium wall.

Comment: The outermost of the parietal layers of a sporangium, internal to the exothecium.

is_a portion of ground tissue, part_of sporangium wall, adjacent to exothecium

exothecium (PO:0030073): A portion of epidermis that is the outermost layer of a sporangium. [Crum]

is_a epidermis, part_of sporangium wall

synonyms: sporangium epidermis, ampithecium

tapetum (PO:0025313): A portion of ground tissue that is the inner-most layer of a sporangium wall.

comment: May function in providing nutrition to developing sporocytes. May have one or two layers of cells. May break down as spores mature. A tapetum does not develop in some plants, such as Psilotum. In angiosperms, the tapetum develops from one of the parietal layers. In non-seed plants, the tapetum may develop from the outer cells of archesporium or from other layers of the sporangium wall.

part_of sporangium wall

microsporangium wall (PO:0025307): A sporangium wall that is part of a microsporangium.

megasporangium wall (PO:0025308): A sporangium wall that is part of a megasporangium.

microsporangium/megasporangium exothecium (PO:0025311, PO:0025312): An exothecium that is part of a micro/megasporangium wall.

microsporangium/megasporangium endothecium (PO:0025309/PO:0025310): An endothecium that is part of a micro/megasporangium wall.

microsporangium/megasporangium tapetum (PO:0025314, PO:0025315): An tapetum that is part of a micro/megasporangium wall.

New definitions for existing terms:

anther wall (PO:0000002)

current def.: A multicellular layer with outer epidermis and an inner endothecium.

proposed def.: A microsporangium wall that is part of an anther.

comment: Has an outer epidermis (exothecium) and an inner endothecium and may have additional layers.

(anther wall) exothecium (PO:0020004, PO:0006059)

current def.: A portion of stamen epidermis that is part of a pollen sac, sometimes with distinctively thickened walls and involved in its dehiscence, usually only when this is poricidal.

proposed def.: A microsporangium exothecium that is part of an anther wall.

Comment: Often with thickened cell walls. Involved in anther dehiscence.

We should define stamen epidermis using cross products (intersection_of is_a epidermis and intersection_of part_of stamen), then anther exothecium would be inferred to be a portion of stamen epidermis. First, we need to redefine the part of relations of all of the descendents of stomatal complex.

(anther wall) endothecium (PO:0020002)

current def.: A portion of hypodermis of an anther sac with distinctively thickened walls and involved in its dehiscence, especially when this is by slits.

Can't say it is a hypodermis, b/c hypodermis is defined as portion of ground tissue between vascular tissue and epidermis, and there is no vascular tissue in anther wall.

proposed def.: A microsporangium endothecium that part of an anther wall.

Comment: May have secondary thickening of the walls of cells that are involved in anther dehiscence.

Also, can't say it develops from the secondary parietal cell layer, b/c that is not always the case (see Davis 1966, reduced type of anther wall development)

(anther wall) tapetum (PO:0009071)

current def.: Innermost part of the anther wall, involved in the nutrition of the pollen.

proposed def.: A microsporangium tapetum that is part of an anther wall.

Comment: develops from a primary or secondary parietal cell layer

part_of anther wall; need to remove develops_from inner secondary parietal cell layer relation, because this is not true for all angiosperms.

(anther wall) middle layer (PO:0004700)

current def.: Usually a single cell layer between tapetum and endothecium which almost invariably degenerates early during angiosperm anther development and is eventually absorbed by adjacent cells.

Is the term middle layer used outside angiosperms? Do we need a general class for sporangium middle layer or microsporangium middle layer? For now, will only add this term for anther wall, since I haven't found any references to a middle layer outside angiosperms. We can always add the other terms later as needed or as time allows.

proposed def.: A portion of plant tissue directly internal to an anther endothecium that develops from an anther wall secondary parietal layer.

Comment: May be a single or double layer. Usually crushed by the endothecium and therefore almost invariably degenerates early during anther development.

is_a portion of plant tissue, part_of anther wall

Parietal layers and develops from relations

Do we need to add parietal cell layers for non-angiosperms? Parietal layer just means wall layer, and is sometimes used as a general term for the layers of the anther wall (e.g., Esau 1965)

Okay to keep secondary parietal cell layer develops_from primary parietal cell layer.

Still need to look into some of the develops_from relations (like what develops from male archesporial cell in angiosperms versus other plants). Suggest working on this for next release. For now, have renamed parietal cell layers as anther wall parietal layers:

(anther wall) primary parietal cell layer (PO:0006006)

(anther wall) secondary parietal cell layer (PO:0006007)

(anther wall) inner secondary parietal cell layer (PO:0006008)

(anther wall) outer secondary parietal cell layer (PO:0006009)

Can change them from is_a portion of plant tissue to is_a portion of ground tissue.

Other Issues

*Review for OBO Foundry Acceptance

BS brought up the topic of review for OBO Foundry acceptance at the POC_Conf._Call_4-19-11. He suggested that the PO can be submitted for OBO Foundry membership within the next weeks

List of Foundry Principles:[Accepted] with a brief summary of each:

• FP 001 open:

The ontology must be open and available to be used by all without any constraint other than (a) its origin must be acknowledged and (b) it is not to be altered and subsequently redistributed under the original name or with the same identifiers.

• FP 002 format:

The ontology is in, or can be expressed in, a common shared syntax. This may be either the OBO syntax, extensions of this syntax, or OWL.

• FP 003 URIs:

The ontology possesses a unique identifier space within the OBO Foundry. The identifier uniquely and persistently identifies a definition, which itself unambiguous identifies some type of biological entity. The identifier is for the definition: it is NOT the name and it is NOT an identifier for the name.

• FP 004 versioning:

The ontology provider has procedures for identifying distinct successive versions.

• FP 005 delineated content:

The ontology has a clearly specified and clearly delineated content. The ontology must be orthogonal to other ontologies already lodged within OBO.

• FP 006 textual definitions:

The ontologies include textual definitions for all terms.

• FP 007 relations:

The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.

• FP 008 documented:

The ontology is well documented.

• FP 009 users:

The ontology has a plurality of independent users.

• FP 010 collaboration:

The ontology will be developed collaboratively with other OBO Foundry members.

• FP 011 locus of authority:

single locus of authority, tracker (SOP), responsive help desk

• FP 012 naming conventions:

See naming conventions

• FP 016 maintenance

OBO is an open community and, by joining the initiative, the authors of an ontology commit to its maintenance in light of scientific advance and to working with other members to ensure the improvement of these principles over time

Upcoming meetings 2011:

Phenotype RCN Meeting: June 1-3rd, Boulder CO

PJ will attend

More details TBA

2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.

Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.

-JE and JP will be attending

-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.

For more Workshop details: Semantic web.

* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

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?

*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.

TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.

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 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

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