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?

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

Exothecium (PO:0030073), endothecium (PO:0030049), and tapetum (PO:0025313) are new general terms. 
The older terms exothecium (PO:0020004, PO:0006059), endothecium (PO:0020002), and tapetum 
(PO:0009071) have been renamed anther wall exothecium, anther wall endothecium, and anther wall tapetum, 
because their definitions clearly said that they were part of an anther wall. However, it would probably 
be better to obsolete the old terms and replace them with the new ones.

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.

Review of rhizoids discussed at the last meeting

Made a new term rhizoid (PO:0030078) is_a plant structure.

Proposed def.: A plant structure that is a uniseriate filament with positive geotropism and without chlorophyll that grows from an epidermis or protonema.

Comment: Serves to anchor the plant to the substrate, and may function in nutrient and water uptake. Includes epidermal rhizoids that grow from the epidermis of bryophytes and pteridophytes in the gametophytic phase or from the stems of some monocots, and protonemal rhizoids that branch from a protonema.

Changed rhizoid (PO:0030071) to epidermal rhizoid

Proposed def.: A rhizoid that develops from an epidermal rhizoid initial.

Comment: Found in bryophytes and pteridophytes growing from the epidermis of a gametophore or the lower surface of a thallus and in some monocots growing from the stem at the cotyledonary node. May be considered a type of trichome.

develops_from epidermal rhizoid initial

Do we want to create a separate child for wurzelhalsrhizoid? Could just be a synonym of this term. 
An alternative name could be cotyldonary node rhizoid.

New term protonemal rhizoid (PO:0030079)

Proposed def.: A rhizoid that develops from a protonemal side branch rhizoid initial.

Comment: A protonemal rhizoid is a branch that arises from a protonema that grows into the substrate and lacks chlorophyll.

Changed the term rhizoid initial (PO:0030068) to epidermal rhizoid initial

Proposed def.: An epidermal initial cell that gives rise to a rhizoid.

Comment: Part of the epidermis of a thallus or gametophore of a bryophyte or pteridophyte in the gametophytic phase or the stem of a monocot in the sporophytic phase.

New term protonemal side branch rhizoid initial

Proposed def.: A protonemal side branch initial that gives rise to a protonemal rhizoid.

is_a protonemal side branch initial (PO:0030067, An initial cell that is produced by division of a sub-apical cell of a protonema.)

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

The problem:

Moss Ontology requested the term apical cell. Apical growth in byrophytes is via division of a single cell at the tip of the shoot apical meristem. They also requested shoot apical cell and phyllid apical cell.

The existing term in the PO, "apical cell (PO:0004000)" referred to "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote". This term was obsoleted and replaced by embryonic apical cell (PO:0025284) for clarity.

A new term apical cell (PO:0030007) was created to be the general class for all apical cell types.

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

meristematic apical cell (PO:0030007): New proposed def'n: A single meristematic cell at the tip of a plant structure where apical growth occurs.

is_a meristematic cell, sibling to initial cell

Proposed revised comment, for clarity: Meristematic apical cells occur only at the tip of a shoot axis apex, leaf apex, root apex, thallus apex or protonema in bryophytes and some pteridophytes. Apical growth in these structures 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). The meristematic apical cell 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) and may be established upon germination of a spore or upon the first cell division of an embryo or later.

Do we need a citation for this comment?

See: Apical cells

The issue:

At the POC_Conf._Call_4-28-11, there was an extensive discussion about whether to modify the definition of the existing 'apical cell' to refer to a general class encompassing the cell at the very tip of an angiosperm leaf or other any other structure.

The problem of adding a generic term for an "apical cell" is that it would cause confusion and it may not be biologically accurate.

The issue was raised that a scientist might isolate such a cell from the tip of a vascular leaf or root and be confused as to where the annotation should go.

Is there actually a single cell at the tip of a vascular leaf or root?

See the ppt below showing SAM and RAM tissues of angiosperms. There are references to stem cells in the central zone of the SAM, initial cells in the quiescent center of the RAM.

File:20-growth and development-02-A.pdf

See P.13: "The root apical meristem (RAM) is subterminal, but like the shoot apical meristem has a layered structure and a center of slowly dividing cells (the Quiescent Center (QC, shown in blue) surrounded by the initials for individual tissue (shown in green). (from Current Opinion in Genetics & Development 2003, 13:551–557)

The solution:

We can use the existing PO terms for cells at the leaf apex (PO:0020137) and leaf tip (PO:0025142),

For more precise work, we have the 'shoot apical meristem'(PO:0020148) and its part_of children (only some shown):

PO:0000224: central zone

PO:0009020: meristem L1

PO:0009021: meristem L2

PO:0009022: meristem L3

PO:0000225: peripheral zone

And the 'root apical meristem' (PO:0020147): and its part_of children (only some shown):

PO:0020149 : quiescent center (and its part_of child: root initial cell (PO:0000059))

PO:0030008 : root apical cell ????

PO:0006307 : root procambium

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

We could also use always_in and never_in taxon relations to help clarify which taxa these are from. (do we have these already?)

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 meristematic apical cell.

See above and 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.

perianth calyptra (PO:0025299)

Proposed def'n: A perianth that is composed of fused perianth parts and located on top of a gynoecium that contains an inferior ovary. (accepted at the POC meeting on 4-28-11)

Comment: May be composed of fused petals, sepals or tepals, but is generally formed from fused petals in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra.

Should we rename calytpra perianth?

is_a perianth

synonyms: floral calyptra (exact) and floral operculum (related)

We already have "angiosperm calyptra" as a narrow synonym of corolla (PO:0009059). Says: In angiosperms, the petals may be fused into a calyptra, which is different than a calytra in mosses.

We may want to remove this synonym, as it is redundant with the new term perianth calyptra PO:0025299.

 to RW: Question: where does it say "In angiosperms, the petals may be fused into a calyptra, which is different than a calytra in mosses."?  Not in the corolla comment.

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