POC Conf. Call 2-08-11
POC meeting, Webex Conference Call; Date: Tuesday Feb 8th, 2011 10am (PST)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_2-01-11?
Wrapping up the TAIR requests on SF:
Note: new terms requested by TAIR get ID's from the TAIR number space (0000000-0005000)
stomatal meristemoid cell
Changed meristematic cell part_of meristem to meristem has_part meristematic cell.
Merged meristermoid into initial cell. 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: 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.
ovary septum vs carpel septum
- septum
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.
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.
- 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 false ovary septum (PO:xxxxxxx) is from early contact of placental tissue from opposite sides of the ovary.
- false ovary septum
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 that divides an ovary into two chambers or more chambers and is formed by contact of placental tissue from opposite sides of the ovary early in gynoecium development.
Comment: A false septum develops along with the ovary has not 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?
- Ovary
Right now, ovary 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.
- Anther septum
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
- 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, and ovary, plus pseudostem. Will probably find others.
dispersed meristematic cell
Decided to add three new terms:
-procambial cell: A meristematic cell that is part of a portion of procambium. part_of procambium
-leaf procambrium: A portion of shoot procambrium tissue that is part of a leaf. part_of leaf
-leaf procambial cell: A procambial cell that is part of a leaf procambium. part_of leaf procabium syn: DMC, dispersed meristematic cell
suggest adding comment: Leaf procambial cells may be derived from the shoot apical meristem or can arise throughout the mesophyll of a developing leaf. (wording?)
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 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 a developing phyllome.
It is okay to say that root procambium and shoot axis procambium are part of an apical meristem. 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: 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 is_a root apical meristem. Changed it to is_a initial cell, part_of root apical meristem.
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
Restructuring descendants of leaf (PO:0025034)
-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 endodermis -- Is there ever an endodermis in non-vascular leaves? If not, this should be part_of vascular leaf. Physco group requested the term leaf endodermis. Wrote to them to ask if they really want this term.
- leaf epidermis - 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).
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, so they want to use them. In that case, 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.
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:
-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
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. Suggest renaming it spore capsule.
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
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
- 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?
Target journal for a major, more detailed paper:
-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 PO in the past year, including restructuring of PSO and PGDSO. Will focus on how PO is now applicable to a wider range of plant species. Plant_Physiology_paper-_2011
Upcoming meetings 2011:
- Phenotype Ontology RCN Summit
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
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 togehter 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
* International Botanical Congress (IBC2011)
July 23rd-30th 2011, Melbourne, Australia
Registration is open Important dates
Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.
Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.
See IBC 2011 Bio-Ontologies Symposium wiki page
Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology. Abstracts have been submitted.
No additional abstracts were submitted for our proposal, and Angelica does not think she will be able to attend because of lack of funds.
Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Still waiting for abstract from Rudi Appels, who will speak on crop genomics and phenomics.
We received permission to use the 6th time slot for a discussion session. PJ will lead the discussion.
