POC Conf. Call 2-08-11

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

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Maire Alejandra Gandolfo; (Cornell University), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG).

Absent: Barry Smith (University at Buffalo, NY), Justin Elser (OSU), Justin Preece (OSU), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_2-01-11? There were no changes, additions, or deletions.

Wrapping up the TAIR requests on SF:

Note: new terms requested by TAIR get ID's from the TAIR number space (0000000-0005000)

this is okay for these terms, but we may want to take a look at the numberspace distribution at some point

stomatal meristemoid cell

Changed meristematic cell part_of meristem to meristem has_part meristematic cell.

Merged meristermoid (PO:0000070) into initial cell (PO:0004011). New definition: A meristematic cell that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body.

Comment: Initial cells are often part of a portion of tissue that is composed mostly of somewhat older, differentiating cells. The division of an initial cell is often uneven, with the smaller daughter cell remaining meristematic.

Added new term stomatal initial (PO:0000062): An epidermal initial that undergoes several rounds of uneven division, each time giving rise to a larger daughter cell that differentiates into an epidermal ground cell and a smaller daughter cell that remains meristematic, until the meristematic cell differentiates into a guard mother cell. Synonyms: stomatal initial cell, stomatal meristermoid.

Guard mother cell now develops from stomatal initial, instead of epidermal initial and meristemoid.

We couldn't find examples of other patterns of stomatal development. If users come to us in the future with different developmental patterns in other species, we can modify accordingly.

xylem pole pericycle cell

Added the following terms:

- pericycle cell (PO:0025261): A ground tissue cell that is part of a pericycle.

- xylem pole pericycle cell (PO:0000064): A pericycle cell that is adjacent to a xylem cell.

Comment: Xylem pole pericycle cells may retain some meristematic activity and are the site of lateral root initiation. ref: PMID: 17993548

- phloem pole pericycle cell (PO:0000065): A pericycle cell that is adjacent to a phloem cell.

Comment: Phloem pole pericycle cells are distinct from xylem pole pericycle cells in that they display cytoplasmic characteristics of a more differentiated status. ref: PMID: 17993548

We has some discussion as to whether or not the xylem pole pericycle cell should be defined as a pericycle cell that is next to a xylem pole cell, instead of next to a xylem cell. Also discussed whether or not we should add a term for xylem pole and phloem pole. Generally, we agreed that the xylem pole and phloem pole are not structures per se, but more of a way of describing the orientation of the vascular bundle.

DWS pointed out that there are pericycle cells that are adjacent to xylem cells that are not adjacent to the xylem pole, so we will need a more specific description of the location of xylem pole pericycle cell. The xylem pole adjacent to where lateral roots develop are the first tracheary elements to develop in the xylem (protoxylem), but there might also be a metaxylem pole (?- check this).

RW and DWS will work on terms for next week to put on dev browser.

ovary septum vs carpel septum

septum (PO:0000030)

Wrote new definition for parent term septum: A plant structure composed of two or more layers of various tissues that is a partition that divides locules formed by the fusion of two or more organs.

Comment: A septum is formed by the fusion of the walls of two adjacent organ parts (ovary walls or anther walls), for example, the partition between two sections of an orange, seen in cross-section.

Images to illustrate septum are on plantsystematic.org, but they are not linked to the key word septum (to locule instead). Will wait to add link until we can properly annotate the image.

Septum had to be is_a plant structure, rather than cardinal organ part, because it is composed of parts of two adjacent organs.

Definition is okay.

DWS can add correct key words to images, so we can put in links to Plantsystematics.org

locule

This would probably be a good time to address the open term request for locule. Locule can refer to the cavity in a carpel or in an anther. In the PGDSO, we have the term PO:0001026 locules established, which is an anther development stage. For clarity, suggest adding three terms: locule, anther locule and carpel locule.

locule: A plant anatomical space that is a cavity within a sporophyll or within several fused sporophylls. Synonym: loculus

carpel locule: A locule that is a cavity in a carpel. Comment: A carpel locule generally contains at least one ovule. A syncarpous gynoecium may have multiple locules, or the locules of multiple carpels may be fused to form a single space.

anther locule: A locule that is a cavity in an anther formed by a single pollen sac.

See original term request at [1].

Since the above proposed definitions only deal with sporophylls, we should create a more specific term for sporophyll locule. We could not think of an example of the term locule being used in vegetative structures, so for now we will only deal with locules in reproductive structures.

New terms and definitions:

locule: A plant anatomical space that is a cavity a reproductive structure. Comment: May be a cavitiy in a sporophyll, within several fused sporophylls, or within a sporangium. Synonym: loculus

sporophyll locule: A locule that is a cavity within a sporophyll or within several fused sporophylls.

ovary locule: A sporophyll locule that is a cavity in an ovary. Comment: Generally contains at least one ovule, buy ovules may be absent in sterile fruits. An ovary locule may be part of a single carpel, in the case of unicarpellate flowers. An ovary that is part of a syncarpous gynoecium may have multiple locules, or the locules of multiple carpels may be fused to form a single space. part_of ovary

anther locule: A locule that is a cavity in an anther formed by a single pollen sac. part_of anther (or part of pollen sac?)

sporangium locule: A locule that is a cavity in a sporangium. part_of sporangium.

Will may want to add term for synangium locule as well, or perhaps sporangium locule will work, since the synangium is composed of fused sporangia.

carpel/ovary septum

PO:0005009 is currently named carpel septum, which suggests that it is within a carpel, rather than between carpels, as we would define septum. There are annotation to this term from Arabidopsis, but the Arabidopsis gynoecium has a false septum (see below), rather than a true septum.

To avoid ambiguity, I suggest that we obsolete PO:0005009, and add two new terms: ovary septum and false ovary septum (with consider relations from the obsolete term to the new terms).

Suggested def of ovary septum: A septum that divides a multilocular ovary. part_of ovary

Comment: Found in species with syncarpous gynoecia (fused carpels). An ovary septum is derived from the fused walls of two adjacent carpels, while a replum (PO:xxxxxxx) develops from early contact of placental tissue from opposite sides of the ovary.

Definition is okay, but make it part of gynoecium, instead of part of ovary. develops_from ovary wall

Add to comment: Annotations for Arabidopsis should go under replum, not here.

false ovary septum/replum

In many species with unilocular, fused gynoecia, placenta tissues from opposite sides of the ovary come in contact early in gynoecium development, and thus grow to form a bridge through the center of the gynoecium, known as a false septum. Unlike a true septum, there is no suture in the middle of the false septum This is common in Brassicaceae. For example, Arabidopsis has two fused carpels. The ovary would be unilocular, except a false septum divides it into two chambers, each of which is formed out of half of each carpel locule. This also occurs in tomatoes, which also has true septa.

Proposed new term false ovary septum: A plant structure/portion of plant tissue that divides an ovary into two more chambers and develops from contact of placental tissue from opposite sides of the ovary early in gynoecium development.

Comment: A false septum develops along with the ovary and has no suture line in its center, while a true ovary septum (PO:xxxxxxx) is derived from the fusion two adjacent carpel walls.

Is it a portion of plant tissue, or does it have multiple tissue types?

Just discovered that we already have the term replum (thanks Dennis!).

replum (PO:0005016): A false septum formed by the ingrowth from the placenta of an ovary rather than from the carpel walls. This is formed post fertilization. is_a portion of plant tissue, part_of fruit, develops_from placenta.

Could keep the existing term, add false ovary septum as a synonym.

Current TAIR annotations to carpel septum (PO:0005009) should move to replum.

Will keep existing term replum (PO:0005016), but update definition:

New definition: A portion of placenta tissue that divides an ovary into two or more chambers and develops from contact of placental tissue from opposite sides of the ovary early in gynoecium development. develops_from placenta, part_of ovary; synonyms: false ovary septum, placental septum

Comment: A replum develops along with the ovary and has no suture line in its center, while a true ovary septum (PO:xxxxxxx) is derived from the fusion two adjacent carpel walls. Common in Brassicaceae. Annotations for Arabidopsis should go here, and not under ovary septum.

be sure replum is part of the Arabidopsis subset, but ovary septum is not.

Ovary

Right now, ovary (PO:0009072) is part of carpel, but should be part_of gynoecium, since it can be part of multiple carpels. Should be is_a plant structure, like septum.

Current def. of ovary: The basal portion of a carpel or group of fused carpels, that encloses the ovule(s). [source: APWeb:Glossary, TAIR:lr]

Change to part_of gynoecium. Should be is_a plant structure (not is_a cardinal organ part)

New comment: may not contain ovules in the case of sterile fruit.

DWS commented on the term 'pseudomonomery' which refers to the "selective abortion of carpels during development to leave only one fertile carpel by anthesis" (Rudell and Bateman, 2004). Not sure if we need to add a comment about it here or not

I looked up a couple of references on this: *Rudall, P. J., and Bateman, R. M. (2004). Evolution of zygomorphy in monocot flowers: iterative patterns and developmental constraints. New Phytologist 162, 25-44.

*Rudall, P. J., Stuppy, W., Cunniff, J., Kellogg, E. A., and Briggs, B. G. (2005). Evolution of reproductive structures in grasses (Poaceae) inferred by sister-group comparison with their putative closest living relatives, Ecdeiocoleaceae. Am. J. Bot. 92, 1432-1443.

Anther septum (PO:0005010)

Current definition of anther septum: A thin partition or stretch of cells that are present in the anther dehiscence zone. [source: GR:cwt, GR:pj] part_of anther dehiscence zone, which is part_of anther.

This does not really fit our definition of septum. Should be part of androecium, if it really composed of the walls of two adjacent anthers (just like ovary septum was part of ovary, not part of carpel)

Proposed def.: A septum that divides two anther locules. part_of androecium

proposed definition is okay

collective organ part structure?

We may want to add a new upper level term for structures that are composed of parts of multiple organs (collective organ part structure). Children would be septum, false septum, plus pseudostem. Will probably find others. Ovary is problematic, because it can be part of a single carpel or multiple fused carpels, so it probably has to stay under plant structure.

Proposed structure:

plant structure

> collective plant structure

> > collective plant organ structure

> > > collective phyllome structure

> > > shoot system

> > > etc.

> > collective organ part structure

> > > septum

> > > pseudostem

Proposed new definition for collective plant structure (PO:0025007): A plant structure that is a proper part of a plant and is composed of two or more adjacent plant structures and any associated portions of plant tissue.

Proposed new term collective organ part structure: A collective plant structure composed of two or more of the same cardinal organ parts from adjacent organs and any associated portions of plant tissue. Comment: Includes plant structures like a septum that consists of the walls of two fused carpels or a pseudostem that consist of multiple, overlapping leaf sheaths.

We liked the proposed structure, but felt it was not good to change upper level term names or definitions. Will add collective organ part structure as sibling of collective plant structure (child of plant structure). Will add 'collective plant organ structure' as synonym of collective plant structure (PO:0025007).

dispersed meristematic cell

postponed until next week

Decided to add three new terms:

-procambial cell (PO:0025258): A meristematic cell that is part of a portion of procambium. part_of procambium

-leaf procambium (PO:0025259): A portion of shoot procambium tissue that is part of a leaf. part_of leaf

-leaf procambial cell (PO:0000063): A procambial cell that is part of a leaf procambium. part_of leaf procabium syn: DMC, dispersed meristematic cell

Comment: Leaf procambial cells may differentiate in the mesophyll tissue layer and divide to form and extend the vascular tissue network of the leaf.

Problem that arose during editing:

* procambium (PO:0006074) is defined as "A portion of primary cambium that undergoes differentiation to form the primary vascular tissue. is_a cambium, part_of apical meristem," but cambium is defined as a lateral meristem (which procambium isn't), and procambium is defined as part_of apical meristem (which it isn't always -- think of leaves).

Suggest making procambium is_a meristem, similar to protoderm.

Suggested definition for procambium: A portion of meristem tissue that undergoes differentiation to form primary vascular tissue. Comment: May occur in an apical meristem or in the mesphyll of a developing phyllome.

Perhaps it is okay to say that root procambium and shoot axis procambium are part of an apical meristem, but not leaf procambium. Right now, root procambium is part_of root meristem, should be part_of root apical meristem.

Current term: shoot procambium (PO:0006306) is vague, because it does not specify shoot system or shoot axis. Changed definition to make it clear it is for a shoot system (any above ground part of plant), then made leaf procambium a child of shoot procambium, and also added new term for shoot axis procambium.

Proposed def. shoot procambium (PO:0006306): A portion of procambium tissue that is part of a shoot system.

Proposed def. shoot axis procambium: A portion of shoot procambium that is part of a shoot apical meristem and gives rise to the primary vascular tissue of a shoot axis.

Also found that root initial cell (PO:0000059) is_a root apical meristem. Changed it to is_a initial cell, part_of root apical meristem.

Restructuring descendants of leaf (PO:0025034)

postponed until next week

-Some of the part_of children of vascular leaf can also be part of non-vascular leaf. This needs to be done before we can add terms for bryophytes.

-Need to double check the is_a children of leaf.

current is_a children of leaf

• non-vascular leaf - ok as is

• vascular leaf - ok as is

• prophyll (PO:0009042) is_a phyllome and scale leaf (PO:0006003) is_a phyllome (see prophyll and scale leaf).

Suggest making prophyll a child of vascular leaf.

Suggest making scale leaf is_a leaf (because the term could be used to refer to non-vascular leaves, even though it is usually used for vascular leaves.

• Suggest adding frond and needle as exact synonyms of vascular leaf

current part_of children of leaf

• leaf apex - ok as is - applies to both vascular and non-vascular leaf

• leaf base - ok as is - applies to both vascular and non-vascular leaf

• leaf epidermis - ok as is - The term may be used for non-vascular leaves, even though many are only one cell thick.

Need to consider if the definition of epidermis works bryophytes (see section below on Physco terms).

• leaf endodermis -- Is there ever an endodermis in non-vascular leaves? If not, this should be part_of vascular leaf.

current is_a children of vascular leaf

Is there heteroblasty in non-vascular leaves? do these terms apply?

• juvenile leaf

• transition leaf

• adult leaf

Physco group has included these terms in their ontology, but said they are not sure if they are necessary. Said there are differences among phyllids based on their position on the stem (more basal versus more terminal), but the terms juvenile and adult are not necessarily used to describe them. If we want to use them for non-vascular leaves, we either need to make them children of leaf instead of vascular leaf, or add separate terms for vascular and non-vascular juvenile, transition and adult leaves.

Do we want to keep these (as phenotype terms)? At one point we discussed getting rid of them.

• simple leaf

• compound leaf

Terms that are probably okay:

• cotyledon - ok

• leaf spine - ok

• cigar leaf - ok

• rosette leaf - probably ok as child of vascular leaf - Are there ever rosette's in gametophytes?

• cauline leaf - definition is a bit weird, actually applies to leaves that are part of an inflorescence (which we call bracts)

Current def: Leaf or pairs/whorls of leaves borne on the stem. [source: TAIR:ki]. Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.

Proposed def: A leaf that is borne on a stem.

Comment:

current part_of children of vascular leaf

Terms that are probably okay (only occur in vascular leaves):

• auricle - ok

• bundle sheath - ok

• leaf abscission zone - ok

• leaf collar - ok

• leaf vascular system - ok

• ligule - ok

• petiole - ok

• stipule - ok

• leaf intercalary meristem - probably ok - does it ever occur in non-vascular leaves?

• leaf sheath - probably ok - does it ever occur in non-vascular leaves?

(see part_of children of leaf)

Terms I'm not sure about:

• leaf aerenchyma- is there ever aerenchyma in non-vascular leaves?

• leaf mesophyll - should probably be part of leaf. Is there a mesophyll in non-vascular leaves?

Terms that should be part of leaf:

• leaf lamina - should be part_of leaf

• leaf margin - should be part_of leaf

• leaf base and leaf apex are already part of leaf (rather than vascular leaf)

Physcomitrella terms:

postponed until next week

-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.

See Terms requested by Physco group for a list of terms.

• Do we want to give MO/Physco terms their own number space? Maybe a subset of the NYBG number space.

Term requested by MO 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 (add root hairs and rhizoids too).

Is there a protoderm in non-vascular plants? (def: A portion of meristem tissue that develops from the outer layer of an apical meristem and gives rise to a portion of epidermis.)

phyllid base and phyllid apex

We already have the terms leaf base and leaf apex. The choice is to make phyllid base (=non-vascular leaf base) and phyllid apex (=non-vascular leaf apex) synonyms of these terms, or to make them is_a children (see discussion of part_of children of leaf, above).

The same issue also applies for phyllid trichome/leaf trichome.

spore capsule

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.

Proposed def.:

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?

Basal endosperm transfer cell (PO:0009018) is currently the only is_a child of transfer cell.

Update on Progress of Publications

Target journal for a major, more detailed paper: This is the top priority right now:

-Plant Physiology:

RW and LC are working on an outline 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

Possible target journals for a short paper: PO_Paper_Winter_2011

• Paper for ICBO meeting- suggestion from BS, ICBO call for papers, deadline is March 1st. could be expanded for submission to journal later

• Bioinformatics see: Author info, possibly an 'Application Notes' (up to 2 pages; this is approx. 1300 words or 1000 words plus one figure)?

• Briefings in Bioinformatics: This one seems particularly relevant for a short article informing people about the PO

• Database: We aren't strictly a database, but still think this journal could be a decent fit

• BMC Bioinformatics

• Short topics paper for American Journal of Botany?

While we were at PAG, DWS mentioned the editor of AJB wants him to put together a short paper for them- maybe can focus on PO?

Upcoming meetings 2011:

• Phenotype Ontology RCN Summit

The Phenotype Ontology RCN

February 25-27, 2010 at the National Evolutionary Synthesis Center in Durham, NC,

Laurel and Pankaj will be attending.

From RW: -What is official PO strategy for dealing with phenotypes?

-Should it differ between description of mutant phenotypes and descriptions needed for systematic studies?

-Should PO develop a list of terms to be submitted to PATO (rather than our current piecemeal suggestions)?

-Possible case study: description of inflorescence types.

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

ICBO

CALL FOR WORKSHOP AND TUTORIAL PROPOSALS: The deadline for workshop and tutorial proposals for the ICBO conference is February 1, 2011

- We decided we are too shorthanded to put together a PO workshop, but Melissa, Alan and Chris are organizing an anatomy ontology workshop.

- 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

* 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.

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