POC Conf. Call 2-01-11

POC meeting, Webex Conference Call; Date: Tuesday Feb 1st, 2011 10am (PST)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Maire Alejandra Gandolfo; (Cornell University), Barry Smith (University at Buffalo, NY), Dennis Stevenson (NYBG).

Absent: Pankaj Jaiswal (OSU), Justin Elser (OSU), Justin Preece (OSU), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators:

Acceptance of the minutes from the POC Conf. Call 1-25-11? No changes, additions, or deletions.

Publications

- An abstract/proposal was submitted to Trends in Plant Science on Dec 31st, 2010. Unfortunately, it was declined. The goal is still to put together a short write up for rapid publication and then a longer, more comprehensive one for later this year.

Possible target journals:

-See this page for more details of the different journals:PO_Paper_Winter_2011

• 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

-Current Opinions in Plant Biology, We had talked about this as a possibility, but it is too late for this year, they have very focused issues. Next year it might be an option

-Nucleic Acids Research- We should aim for inclusion in the 2012 Database issue (deadline July 2011,for Jan 2012 publication)

-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

- Others?

• 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?

• Paper for ICBO meeting- suggestion from BS, ICBO call for papers, deadline is March 1st

Action items:

LC is working on a draft manuscript to send around to the group.

Barry suggested preparing some images that show how the upper level of the ontology has changed/improved. RW will work on this.

User requests: for PSO

- Deal with and complete the list of user requests on SourceForge- top priority is TAIR and Physco terms

- Begin with terms for mosses, requested by Physcomitrella group. If we can get their terms in by the next release, they will use PO instead of creating their own ontology.

TAIR requests on SF: stomatal meristemoid cell ovary septum vs carpel septum dispersed meristematic cell xylem pole pericycle cell

TAIR requests on SF

dispersed meristematic cell

-This term is probably best incorporated as a synonym of leaf procambial cell (new term). See SF tracker item for details of discussion.

Suggest using the following hierarchy:

meristematic cell (PO:0004010)

-[is_a] procambial cell (new)

- -[is_a] leaf procambial cell (new); synonym: dispersed meristematic cell

procambium (PO:0006074)

-[is_a] leaf procambium (new)

- -[part_of] leaf procambial cell (new)

Proposed definitions:

-procambial cell: A meristematic cell that is part of a portion of procambium. part_of procambium

-leaf procambium: A portion of procambium 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 procambium syn: DMC, dispersed meristematic cell

These new terms and definitions were accepted as is. Root procambium and shoot procambium already exist. Will add terms for shoot axis procambium and change existing definitions to genus-differentia form.

We had some discussion about how this term 'dispersed meristematic cell' is misleading, as it sounds like it is a cell which is mobile in the plant, but it actually refers to meristematic cells that are dispersed in the leaf or other organ. Thus it is better to put the requested term in as a synonym of 'leaf procambial cell' as RW has proposed.

ovary septum vs. carpel septum

There was a request for a new term 'ovary septum.' but after a long discussion on SF, the conclusion seems to be that ovary septum should be a synonym of carpel septum.

Current definition of carpel septum (PO:0005009): A thin partition or membrane that divides multilocular ovary. Often found in species with syncarpous (multiple carpels fused) pistil. [source: GR:cwt, GR:pj]

Suggest placing the second sentence in a comment and removing the word often.

Suggested definition: septum that divides a multilocular ovary. Comment: Found in species with syncarpous gynoecia (fused carpels). Synonym: ovary septum

Current def'n: septum (PO:0000030): A thin partition or membrane that divides a cavity or a mass of tissue, e.g., in anther, ovary or fruit. [source: APWeb:Glossary], is_a portion of plant tissue.

Suggest that septum should be a cardinal organ part, rather than a portion of plant tissue.

Proposed def'n: A cardinal organ part that forms a partition that divides a cavity formed by the fusion several plant structures such as anthers or ovaries.

New proposed def'n:

A plant structure composed of two or more layers of various tissues that form a partition that divides a cavity formed by the fusion of two or more organs.

-add comments: like an orange in cross-section, white part= "albedo",

-Look for an image to illustrate this, look on plantsystematic.org, add link to image

Comment: A septum is formed by the fusion of the walls of two adjacent organ parts (ovary walls or anther walls).

Question: can a septum also be formed internally as part of an organ, that is, not by the fusion of two adjacent organs?

Yes, it can. This occurs in Brassicaceae, and also in some legumes. This may be what is called a false septum. It is a cardinal organ part, and not a plant structure, so it will need to be named and defined separately. RW and DWS will look into this for next week.

The term "carpel septum" should be used to describe the false septum that separates a single carpel into mutilple locules, while "ovary septum" should be used to describe the septum that divides a multi-locular ovary that is part of fused gynoecium. Will change primary name of carpel septum (PO:0005009) to ovary septum.

stomatal meristemoid cell and meristemoid/initial cell

TAIR has requested the term "stomatal meristemoid cell". guard mother cell develops_from stomatal meristemoid cell.

Right now, guard mother cell (PO:0000351) develops_from meristemoid cell (PO:0000070) and also develops_from epidermal initial (PO:0000349).

Current def'ns:

- meristemoid: A cell or a group of cells constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells.

- epidermal initial: A relatively unspecialized cell that will give rise to specialized cell types of the epidermis. is_a intial cell

- initial cell: Cell in a meristem that by division gives rise to two cells one of which remains in the meristem, the other is added to the plant body. is_a meristematic cell

- meristematic cell: A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall.

- guard mother cell: Epidermal cell that divides to produce the guard cells.

Perhaps a better arrangement would be:

- meristemoid is_a meristematic cell - change meristematic cell (part_of meristem) to meristem has_part meristematic cell (because a meristemoid is a meristematic cell that is not part of a meristem)

Is the current definition of initial cell correct?

The two children of initial cell (cambial initial and epidermal initial) are, in fact, not part of a meristem.

Suggestion: -define initial cell as 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.

Would it be better to have initial cell be a child of meristemoid, rather than a child of meristematic cell?

Suggestion: -Propose new definition for epidermal initial (see below). The new 'term stomatal initial'/'stomatal meristemoid cell' could be a child of epidermal initial.

Possible new structure:

Suggested new def'ns:

- meristematic cell: okay as is, but change from part_of meristem to meristem has_part meristematic cell (since not all meristematic cells are part of a meristem -- we can discuss this)

- meristemoid: A meristematic cell that is part of a portion of tissue that is composed mostly of somewhat older, differentiating cells.

- initial cell: A meristemoid that by (uneven?) division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body.

- epidermal initial: An initial cell that is part of an epidermis and gives rise to specialized cell types of the epidermis. Synonym: epidermal initial cell

New term:

stomatal initial/stomatal meristemoid: 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.

stomatal initial will be primary name, stomatal initial cell and stomatal meristemoid will be synonyms.

>>It might also be better to merge meristemoid and initial cell, rather than keeping them as separate classes. Meristemoid has no other children besides initial cell. Are they the same thing?

We will merge initial cell and meristemoid, keeping initial cell as primary name.

Proposed def.: 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 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.

BS suggested that terms like "epidermal initial" should have exact synonyms with the word cell in the name (e.g., epidermal initial cell).

>>Question: This is how stomatal initials develop in Arabidopsis. Is it the same across all species?

RW and MAG will look into this for next week.

xylem pole pericycle cell

TAIR has asked us whether or not the term xylem pole pericycle cell should be added to the PSO?.

A quick Google search reveals a bunch of papers that refer to xylem pole pericycle cells or to the pericycle cells at the xylem poles, so the term seems to be in common usage. The use of the term "xylem pole" also seems to go way back. There is also a phloem pole.

For example: The publication De Rybel et al, 2010 describes the identification of "A novel aux/IAA28 signaling cascade (that) activates GATA23-dependent specification of lateral root founder cell identity."

In this paper, they state: "GATA23 is expressed specifically in xylem pole pericycle cells before the first asymmetric division and is correlated with oscillating auxin signaling maxima in the basal meristem. Also, functional studies revealed that GATA23 controls lateral root founder cell identity. Finally, we show that an Aux/IAA28-dependent auxin signaling mechanism in the basal meristem controls GATA23 expression."

-This paper also use the term basal meristem, to refer to the basal part of the root apical meristerm: http://www.cell.com/current-biology/abstract/S0960-9822(10)01088-2?script=true

The name "basal meristem" is too vague, and could refer to a meristem anywhere on the plant. Better to name the term "basal part of root apical meristem". However, since no one has requested this term yet, we won't add it yet.

-The term 'xylem pole' refers to a column of xylem running through the root stele and xylem pole pericycle cells are pericycle cells adjacent to the xylem cells

Additional example: From Parizot,2008 :

"The Arabidopsis (Arabidopsis thaliana) root displays two different levels of tissue organization: a concentric organization formed by the ground layers (endodermis/cortex) and the epidermis, and a bilateral symmetry of the diarch vascular bundle consisting of two poles of xylem elements and two poles of phloem elements (Dolan et al., 1993)."

"Up to now, the outermost layer of the stele, the pericycle, has always been regarded, in accordance with the outer tissue layers, as one uniform concentric layer. However, considering its lateral root-forming competence, the pericycle is composed of two different cell types, with one subset of cells being associated with the xylem, showing strong competence to initiate cell division, whereas another group of cells, associated with the phloem, appears to remain quiescent."

Suggested def'n:

- xylem pole pericycle cell: 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

Suggest new term:

- pericycle cell: A ground tissue cell that is part of a pericycle.

Suggested def'n:

- phloem pole pericycle cell: 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

These terms and definitions were accepted as suggested.

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 creating their own ontology.

They have requested about 65 PSO terms. About 15 of those already exist or are trival to add (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. RW is working on a spread-sheet with definitions and parents.

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

Ran out of time to talk about these, tabled for next meeting.

Restructuring descendants of leaf (PO:0025034)

-many 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 if some of the is_a children of leaf should be there.

-See descendants of leaf for summary.

Ran out of time to talk about these, tabled for next meeting.

NYBG outreach activities

• Jan Stevenson from NYBG took part in discussion at NYBG on 11-6-2010. She is available to help with preparing text for a public audience, or producing AV materials.

An online audio-video exhibit will cost about $6000. A double display case with audio-video in the NYBG gallery will cost at least $12,000.

-Possibly use flowering time examples from rice and brassicas

• Look at mirroring NYBG AV material from the Plants and Fungi Exhibit on the POC web site. DWS will confirm the copyright issues etc.

• Create modified version of the tree of life from NYBG exhibit for online exhibit. Can add different images to tips to tell different stories, such as different types of fruits or flowers in angiosperms.

-DWS will provide the tree diagrams and text and images of the sequenced genome plant examples.

-Ran out of time to talk about this, tabled for next meeting. PJ was not present. Ramona will follow up with Dennis at NYBG.

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 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.