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 (=exothecium), and endothecium.

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

Summary and suggestions from previous meetings:

• 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. Suggest we flag this to work on during next round of revisions.

-Suggest adding sporocyte develops_from archesporial cell. We already have megasporocyte develops_from female archesporial cell and microsporocyte develops from primary sporogenous cell (which develops_from male archesporial cell).

Agreed

• At the POC_Conf._Call_4-28-11 we agree to rename theca (PO:0009069) 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.

Now that sporangium is_a plant organ (and therefore pollen sac is_a plant organ), anther theca should be is_a collective plant structure, because it has two pollen sacs as parts.

Anther should also be a collective plant structure, for the same reason.

Problem with this is that anther and anther theca are part_of stamen, which is a plant organ. This makes them cardinal organ parts.

Does this cause a circularity? Not now, because of how has_part is treated, but maybe it will be a problem.

Barry felt this was not a problem, logically, even though it is unusual. Are there other cases of this in animals or in plants? We will leave anther and anther theca as collective plant structures, part of stamen, because that best reflects the biology.

See Media:antherCPS1.jpg and Media:pollen sac sporophyll.jpg

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

-Anther theca, as it is now defined, is a collective organ part structure, because it consists of two fused sporagia (two pollen sacs). This is different than the theca of a single sporangium.

Will not make anther theca a child of sporangium theca, but leave it as collective plant structure.

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 wall part of nucellus (megasporangium in angiosperms).

Current ontology structure:

The problem is that classes like exothecium, endothecium, 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.

Proposed solution:

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

Also suggest making pollen sac part_of microsporophyll, instead of part_of anther, and adding anther has_part pollen sac.

Proposed ontology structure:

Here is how the PO would look using the above suggestion, showing just the exothecium

Here it is showing the megasporangium:

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

Check which subsets this should go under. (bryophytes, pteridophytes, and gymnosperms)

"inside the sporangium wall" is ambiguous. Instead, say "bounded by sporangium wall".

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 and may include other layers such as endothecium, tapetum and parietal layers.

is_a cardinal organ part, part_of sporangium

New proposed definition: A cardinal organ part that is composed of the outer layers of a sporangium and bounds the archesporium or spores.

Add to comment: Early in development, the sporangium wall bounds the archesporium. Later, after spores develop from the archesporium, it bounds the spore or spores.

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

Should say "outermost layer of a sporangium wall".

Add epithecium as a synonym.

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

Change comment: The outermost layer of a sporangium internal to the exothecium (since we don't have a term for parietal layer).

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

Say that it can have "one or more layers of cells". Instead of saying "other layers", say "the inner-most layer of the sporangium wall.

PJ suggested having two types of tapetum, one that develops from parietal cell layers, one that develops from other layers of sporangium. We sort of have this, because we have a specific term for anther wall tapetum that develops from parietal layer (see below). We can add others as we need them.

Maybe we should have a general term for parietal layer? See more discussion below about parietal cell layers.

Say that it may provide nutrition to developing sporocytes or pollen, instead of just to sporocytes.'

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 might 
be better to obsolete the old terms and replace them with new ones.

We agreed that it would be better to rename the terms, rather than obsolete them, because the
definitions and relations did not change

NOTE: each of the pairs of terms below represents two new PO terms.

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): A tapetum that is part of a micro/megasporangium wall.

The above terms were accepted.

New definitions for existing terms:

NOTE: the use of parentheses below denotes a change in the term name. The parentheses will not be part of the obo file.

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 endothecium and may have additional layers.

Agreed

(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.

Agreed

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.

Agreed to add the intersection_of terms. Change names to stamen epidermal stomatal complex, etc. (RW: Maybe stamen epidermis stomatal complex is better, b/c it is part of stamen epidermis?). This analogous to using "anther wall entothecium" as a name, rather than "anther endothecium". Need to be consistent in naming.

(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.

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)

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. OFten developz from an anther wall secondary parietal cell layer, but in the reduced type of anther wall development, it develops from the anther wall primary parietal cell layer.

Add comment: there can be more than one layer in an anther endothecium

(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.

Add to comment: Innermost part of the anther wall, involved in the nutrition of the pollen.

(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.

proposed def.: A portion of ground tissue directly internal to an anther endothecium that develops from an anther wall secondary parietal cell 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 ground tissue, part_of anther wall, develops_from anther wall secondary parietal cell layer, adjacent_to endothecium

say "is adjacent to anther wall endothecium", not just endothecium.

At this point, there does not appear to be a need for the term middle layer outside angiosperm anthers, so we can just use this term. However, if the need arises for a middle layer in other taxa, we could add general classes for sporangium middle layer, microsporangium middle layer, and megasporangium middle layer. PO:0004700 would then be a descendent of microsporangium middle layer. --Agreed

anther wall parietal cell layers and develops from relations

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

For now, suggest renaming all parietal cell layers, since they are all part_of anther wall:

(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)

Should change them from is_a portion of plant tissue to is_a portion of ground tissue. Already have part_of relations to anther wall.

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.

Agreed to the above changes.

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.

Agreed

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.

-Should add "pegged rhizoid" to list of terms to add in the future.

Will create cotyledonary node rhizoid as a child of epidermal 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.)

Agreed to the above changes.

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? (RW: Yes! Will add definition dbxrefs that cover this)

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 ???? Should this be part_of RAM or part of root tip? Might be confusing if we make it part of RAM.

PO:0006307 : root procambium

We could also use always_in and never_in taxon relations to help clarify which taxa these are from. (once those relations are added)

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.

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.

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). In the synonym dbxref comment, it says: In angiosperms, the petals may be fused into a calyptra, which is different than a calytra in mosses. Note: this text does not show up on the Amigo browser, but it is in the obo file.

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

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