POC Conf. Call 5-03-11

POC meeting, Webex Conference Call; Date: Tuesday May 3rd, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell University)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Justin Elsner (OSU)?

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_4-28-11? There were no changes, additions or deletions.

Items arising from previous meetings:

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

Postponed until next meeting.

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.

New terms for Physcomitrella and related taxa (continued)

Plant Tissues

paraphyllium (PO:0030069)

Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."

Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.

Moss Ontology has paraphyllium listed as a plant organ, but they do not arise from the SAM as phyllomes do.

Proposed definition: A portion of epidermal tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.

Comment: Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. Found in pleurocarpous mosses and a few leafy liverworts.

is_a epidermis, part_of gametophore axis

The paraphyllia are the small, dark structures between the leaves.

Remove the word "small" from the definition. Don't need it.

Accepted

paraphysis (PO:0030070)

Moss Ontology definition: Sterile, septate, usually uniseriate hairs intermixed with sex organs. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

From Parihar: sterile, slender filaments accompanying reproductive organs.

From Schofeld: filamentous sterile structures intermixed with the sex organs of most mosses

These are a kind of trichome

Proposed def.: A slender, usually uniseriate multicellular trichome that grows intermixed with the gametangia.

Comment: Found in bryophytes and pteridophytes, especially in mosses.

adjacent_to gametangium, plural: paraphyses; particpates_in gametophytic phase

Should we add the adjacent_to relation? No. Adjacent to means they are in permanent contact, which is not appropriate here.

New proposed def: A slender multicellular trichome that grows between the gametangia.'

Comment: Usually multiseriate. Found in bryophytes and pteridophytes, especially in mosses.

plural: paraphyses; particpates_in gametophytic phase

Accepted

axillary hair (PO:0030060)

Moss Ontology definition: A small filament in an axil consisting of one long terminal cell atop a basal stalk (also called club-hair). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

This is a type of trichome. Axillary trichomes may also be found in angiosperms, but they are different, so suggest we specify that this for hairs in gametophores.

Proposed def., gametophore axillary hair: A multicellular trichome consisting of one long terminal cell atop a basal stalk that grows in the leaf axil of a non-vascular leaf.

Comment: Found in pleurocarpous mosses. Form in the axils of leaf primordia, and may disappear when the gametophore is mature.

synonym: club-hair; part_of gametophore

Make a new general term for axillary hair: A mutlicellular trichome that consists of a long terminal cell atop a basal stalk and grows in a leaf axil.

comment: Found in monocots and mosses. The basal stalk may contain one or more cells.

New proposed def. for gametophore axillary hair: An axillary hair that grows in a leaf axil of a non-vascular leaf.

Will need to double check definitions of the parts of the axillary hair (from last week's agenda) to make sure they are consistent with this.

rhizoid (PO:0030071)

Moss Ontology definition: Filamentous tissue protruding from the gametophore stem with a rooting function.

Rhizoids may also grow from thalli. They arise from an epidermal intial (the rhizoid initial), and so are like trichomes. Like trichomes, they may be uni- or multicellular

Proposed def.: A trichome that is part of a plant in the gametophytic phase and has positive gravitropism.

Comment: Found in bryophytes and pteridophytes growing from the epidermis of the lower surface of a gametophore or thallus. May be multicellular or unicellular. Usually serves to anchor the plant to the substrate.

Should we say: May also arise directly from a protonema or create a separate class for protonemal rhizoids?

develops_from rhizoid initial, participates_in gametophytic phase

There was a discussion of how different rhizoids develop, and whether or not they could be grouped together. As rhizoid is currently defined, can't include protonemal rhizoids, because they don't develop from an epidermal initial. There are rhizoids on monocots (wurztelhalsrhizoid) that are not part of a gametophyte. Also need term for pegged rhizoids in liverworts.

We decided to make a new general class for rhizoids, a child of plant structure, that can include them all. Will put together new definitions and develops_from relations for next meeting.

tmema (PO:0030061)

Moss Ontology definition: An abscission cell at the base of a gemma (vegetative propagule). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

Their definition defines a cell type, but they have tmema as a tissue type. It would be the tissue composed of tmema cells

Proposed def.: A portion of plant tissue that has as parts tmema cells.

Comment: Found in bryophytes at the base of a gemma. Participates in abscission of the gemma.

participates_in gametophytic phase, has_part tmema cell (can't use tmema cell part_of tmema, because they can also occur as single cells in a protonema, next to a brachycyte)

Accepted

antheridium jacket layer (PO:0030053)

Moss Ontology definition: A layer of cells that surrounds the spermatogenous tissue that cannot give rise to sperm.

The term jacket layer is also used for the outer layer of sporangia. Suggest naming this term antheridium wall or antheridium jacket layer

proposed definition: A portion of plant tissue that is a single layer of cells on the outside of an antheridium.

Comment: Cells in the antheridium jacket layer surround the inner spermatogenous cells and do not give rise to sperm cells.

part_of antheridium; synonym: sterile jacket layer, antheridium wall

Accepted. Will use antheridium jacket layer as primary name.

hydrome (PO:0030047)

proposed definition: A portion of plant tissue that has as parts hyrdoids.

Comment: Found in bryophytes, in the center of a non-vascular shoot axis such as a gametophore axis or seta, or in the midrib of a non-vascular leaf. Often surrounded by leptome. May function in conduction of water and minerals and in support, similar to xylem in vascular plants.

disjoint_from xylem, participates_in gametophytic phase

Synonyms: hydrom, leptoxylem (Hebant)

There was some discussion about exact wording of the definition. BS explained that to a logical reasoner, when you say that X has parts Ys, it does not follow that X has as parts all the parts of Y. So, for example, hydrome has_part hydroid cells does not mean that hydrome has_part hydroid cell nucleus.

New proposed def.: A portion of plant tissue that has as parts only hyrdoid cells.

Add to comment: A hydrome is composed of only hydroid cells.

Can't use participates in gametophytic phase, because it can also occur in a seta of mosses.

leptome (PO:0030048)

proposed definition: A portion of plant tissue that has as parts leptoids.

Comment: Found in bryophytes, in non-vascular shoot axes such as a gametophore axis or seta, or in the midrib of a non-vascular leaf. Often surrounding a central hydrome. May function in the conduction of organic substances, similar to phloem in vascular plants.

disjoint_from phloem, participates_in gametophytic phase

Synonyms: leptom, leptophloem (Hebant)

stereome (PO:0030050)

From Hebant: A typical moss stem comprises, from the outside to the inside, an epidermis with a thin cuticle but no stomata, an outer cortex which frequently consists of supporting ells with thickended walls ("stereids"), an inner cortex of thin-walled conducting cells, and, in a number of species, a central strand of hydroids.

proposed definition: A portion of ground tissue that has as parts stereids.

Comment: Found in bryophytes in gametophore axes or non-vascular leaves. May function in support.

participates_in gametophytic phase

central strand (PO:0030051)

From Crum: a group of cells forming a central axis of some stems, usually made of small, elongated cells

From Schofeld: a central strand of smaller cells in the center of stems of many mosses.

proposed definition: A portion of plant tissue that is an axial strand in the center of a gametophore axis and has as part hydrome or leptome.

Comment: Often contains both hydrome and leptome. Found in bryophytes. The term central strand is sometimes used to describe a root protostele in vascular plants, but this term should only be used for non-vascular plants. Should we add: analogous to a vein or vascular bundle in vascular plants?

synonyms: conducting strand, central cylinder

part_of gametophore axis (or can it also be part of a seta?)

costa (PO:0030072)

proposed definition: A portion of plant tissue that is a single or double strand in the center of a non-vascular leaf and has as part hydrome or leptome.

Comment: Found in bryophytes. Often contains both hydrome and leptome. Functions in support and conduction in a phyllid. The term costa is sometimes used for the midrib of monocot leaves, but this term should only be non-vascular leaves.

part_of non-vascular leaf

synonym: phyllid costa, phyllid midvein, phyllid midrib, non-vascular leaf midvein, non-vascular leaf midrib

Parts of sporangium

THIS PART IS STILL UNDER CONSTRUCTION

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