POC Conf. Call 2-28-12

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POC meeting, Webex Conference Call; Date: Tuesday Feb 28th, 2012 10am (PST)

In attendance:

POC members: Laurel Cooper (OSU), Justin Elser (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY)

Absent: Dennis Stevenson (NYBG), Justin Preece (OSU), Marie Alejandra Gandolfo (Cornell University), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_2-21-12? none

Back to POC Meetings Minutes

Update from Phenotype RCN meeting, February 23rd-25th, 2012

RW attended.

Talked with Bruce Kirchoff re. images in ontologies. He suggested that images are a crucial part of definitions. Best to include several images that show the range of variation encompassed by the definition - not all variation that everyone includes. Images should be curated to ensure that they are consistent with the definition.

Including line drawings is also appropriate.

Revisit MAG slide collect with a focus on which slides display the range of variation for PO terms, e.g., sieve cells in Arabidopsis, rice, maize, etc., versus trying to scan every slide. Focus on ones that have the annotations on them

There was a general interest in linking images to terms, from many people at the meeting.

PJ: image links should be a web service. Better to keep image collection separate from the ontology, sort of like we keep the annotation data separate.

For the rest of this year, we should prioritize what we want to work on before the next round of funding. We cannot work on everything, so we should focus our efforts on some good biological questions that the PO might help answer. Next grant can be focused on applications of the PO, rather than just ontology development.

Talked with George Gkoutos re. plant quality terms. He is happy to incorporate any terms that we need for plants. We can request terms on their SF tracker. If we have a lot of terms, the RCN could fund a trip for us to work with George for one or two days on a concentrated effort to incorporate terms. His biggest bottleneck for descriptors in the definitions, so if we can supply definitions, it is no problem to incorporate them.

PJ was concerned about using PATO because their framework may be too rigid. They may not think about some of the concepts as qualities as we do. e.g., content versus concentration.

We also had some discussion about things like enzyme activity or photosynthesis rate as quality terms. These are in GO, but never went into PATO. PJ would like to see terms like activity or rate of a function in PATO. Perhaps it would be better to have the activity type in GO (processes), but terms like "activated" and "rate" in PATO.

There is also a need to describe molecular phenotypes. Need to examine how PATO can handle those.

BS suggested that if PO is going to start work on TO, PJ should write a one page statement on how trait, function, character, process, function, etc. relate to one another in his mind.

If we do go ahead and develop our own plant quality terms, we need to make sure that they reference PATO terms. We can work with George on how to link them up and eventually we may want to merge them.

We may want to consider requesting funds in the next round of PO funding to have a half time person work with PATO. S/he can work directly for PATO.

BS: PATO will be divided into modules (e.g., clinical or symptom module, plant module). We will need extra manpower to figure out how to keep those modules in sync with each other.

RW is involved in a potential collaboration with a diverse group of people who were at the meeting. The goal is to use PO and PATO to score phenotypes from several existing data sets (e.g., Lloyd and Meinke 2012) that already link genotype to phenotype, then use those to predict genotype for non-model species for which only phenotype is known.

Project is using PO and PATO rather than TO, so that we don't have to decompose TO. PJ asked if we would use TO if it were already available in a decompose (logical definition) form. CM already ran OBOL to make XPs for TO, so we should look at that and see if it will work.

PJ: This is a contribution toward PO, so it is fine to work on it as a PO activity.

One of the questions from the project is where annotation files would live. PJ: for example, annotations from Lloyd and Meinke would go to both TAIR and PO. For phenotype annotations, annotations could move from PO to other database, as opposed to the other directions (which happens now). PO is trying to serve a leadership role in plant biology community in this way. We can provide the platform that other can enrich or extend to their own needs.

Also talked to people about a population and community ontology RW is working on, outside the scope of the PO.

PJ: It may be outside the knowledge domain of the PO, but PO supports its development, because it will be useful to our users as well.

Continued from last week's discussion: Vascular cells and related cell types

New proposed hierarchy: children of plant cell

plant cell

>sieve element (new term)

>>sieve tube member (syn.: sieve tube element)

>>sieve cell (new term)

>tracheary element


>>vessel member

>ground tissue cell (PO:0025030)

>>sclerenchyma cell (PO:0000077)

>>>sclerid (new term)

>>>fiber cell (new term)

>>>>phloem fiber cell

>>>>xylem fiber cell

axial cell

axial cell (PO:0000081): A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208] Comment: These cells make up the axial system, also known as vertical or longitudinal system.

The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).

We talked about merging axial cell into axial system, but it is not really appropriate to merge a cell type into a tissue type. It could be a broad synonym of tracheary element and xylem fiber.

Suggest that we obsolete this term, replace with new terms for axial system and radial system:

axial system and ray system

axial system (new term, PO:0025410):

proposed definition: A portion of vascular tissue (PO:0009015) that has as parts cells derived from fusiform initials (PO:0000079) and oriented with their longest diameter parallel to a plant axis (PO:0025004).

comment: Includes portions of secondary xylem (PO:0005848) and axial wood parenchyma (PO:0004533).

synonyms: vertical system, longitudinal system

This should be a portion of secondary vascular tissue (existing term; PO:0025409)

Note: There is a typo (word missing) in the definition of portion of vascular tissue.

ray system (new term, PO:0025411):

proposed definition: A portion of vascular tissue (PO:0009015) that has as part ray wood parenchyma (PO:0004534) and extends radially in the secondary xylem (PO:0005848) and secondary phloem (PO:0005848) of a plant axis (PO:0025004).

comment: May include ray tracheids, as in Pinaceae and some Cupressaceae.

synonyms: radial system (exact), horizontal system (exact), ray (broad)

This should be a portion of secondary vascular tissue.

Note: need to add term for ray tracheid

tracheary element and associated cells

These edits are done in the obo file, except as noted:

xylem element (PO:0000273): A cell making up xylem tissue.

Currently, this is parent of tracheary element and xylem fiber. I suggest we obsolete it and make xylem fiber cell a child of fiber cell. Xylem element could be a broad synonym of tracheary element and xylem fiber. (still need to add this)

Okay to obsolete this.

We should add a term for vascular cell: A plant cell that is part of vascular tissue, set up as a cross-product. This still won't include leptoid and hydroid. For now, they should stay separate. In the future, we can set up functional categories as another layer to the PO, like "translocating cell". For now we don't have the means to logically define these types of groupings, but we should keep them in mind for future work.

We could make a term for "wood cell". Any cell that is part of a portion of secondary xylem.

Should we add a term like "substrate (water/sap/photosynthate/mineral) conducting/translocating cell"? To group vascular cells with hydroids and leptoids. Can't be with the vascular cells since they are in non-vascular plants. Problem is that this is a functional category, it should only be created using cross products, may be maintained as a separate layer. BS: Should keep structural anatomy separate from the functional anatomy. May be able to create them using XPs to GO.

tracheary element (PO:0000290)

Currently is part_of primary xylem and part_of secondary xylem. Changed to part_of xylem.

proposed def.: A plant cell (PO:0009002O) that has a lignified cell wall with secondary thickening and bordered pits and is dead at maturity.

comment: More or less elongated and with pits of various types in the cell wall. Tracheary elements function in the conduction of water and dissolved substances such as mineral nutrients from the roots to the shoot system. Tracheary elements can be distinguished from fiber cells (PO:0025407) by the presence of bordered pits, although there are intermediate forms called fiber tracheids (PO:0000355).

participates_in sporophyte stage, part_of xylem, disjoint from hydroid

Should move "dead at maturity" to comment.

Do we want to add separate terms for primary xylem tracheary element, secondary xylem tracheary elements, primary xylem tracheid, etc.? Yes

tracheid (PO:0000301)

proposed def.: A tracheary element (PO:0000290) that has no perforations in its cell wall.

comment: May have any of the kinds of secondary wall thickenings found in tracheary elements. The area of contact between two tracheids has only bordered pits, whereas in vessel members (PO:0002003) it has openings in the cell wall called perforations, organized into perforation plates (term has been requested in GO).

cell wall is s GO term:

vessel member (PO:0002003)

proposed def.: A tracheary element (PO:0000290) that is part of a vessel (PO:0025417) and has as parts perforation plates.

Comment: The cell wall of a vessel member has openings called perforations, which are organized into perforation plates (term has been requested in GO). These are usually on the end walls of a cell, but may also be on the side walls. A perforation plate may be simple, with one perforation, or multiperforate, with more than one perforation.

syn.: vessel element, vessel segment

part_of vessel (new term)

Rename 'xylem vessel member'

vessel (PO:0025417)

proposed def.: A portion of xylem (PO:0005352) tissue that has as parts a tube-like series of vessel members (PO:0002003), the common walls of which have perforations.

Rename 'xylem vessel'

perforation plate (for GO)

proposed def.: A cell wall part that is the part of a wall of a xylem vessel member (PO:id) and bears one or more openings (perforations).

comment: Part of a vessel member (PO:0002003). May be simple, with one perforation, or multiperforate, with more than one perforation. Perforation plates are usually on the end walls of a cell, but may also be on the side walls.

Reference ISBN:0471245194 (Esau's Anatomy of Seed Plants).

Suggest name "xylem vessel member perforation plate".

sclerenchyma cells

Sclerenchyma cells, including fibers, were moved to POC Conf. Call 3-6-12.

Open SourceForge Trackers:

coleoptile emergence

Moved to POC Conf. Call 3-6-12

Updates to the Trait Ontology

Renaming the top level term:

Should rename root term from "plant trait ontology" to "plant trait".

It could also be called "plant phenotype trait". For now, will just start with calling it plant trait.


How to get through more term revisions?

Should PJ join the calls with DWS, MAG, LC and RW? This would not necessarily speed things up, because we still need to work through the anatomy first, then address the definitions from an ontology point of view.

Maybe we will need to set up another 1 hr conference call each week when we just work on definitions, and reserve the Tuesday meetings for definitions plus other PO business. Then JE, JP, and BS would not have to come to the second call.

We could also work through the definitions faster if people commented on them on Source Forge.

Upcoming meetings and Presentations 2012:

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link

LC will present a short talk abstract Friday march 16th, 5:45pm

No PO-Gramene workshop is planned

Katherine Esau Research Symposium

Integrating Plant Structure with Function, Development and Evolution

Hosted by the Katherine Esau Fellowship Program,

Date and location: Thursday, March 29, 2012, 1002 Giedt Hall, UC Davis

Space is limited and registration will close at 5 pm on March 10th.

LC contacted the organizer; Neelima Sinha (Sinha@ucdavis.edu) and she said a short presentation was a possibility and would be pleased if a couple of PO people could attend.

LC may be interested in attending if we can get a slot. Could also combine the visit with a follow up meeting with Jill Wegrzyn and Andrew Groover about the wood terms and data for the PO.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted and has been selected for a poster presentation.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

  • PJ is planning to attend, may do a talk. LC is planning to attend

The early bird registration ends this Friday, February 25.

SPNHC 2012

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Crop Ontology Workshop

We are looking at the tentative dates of either: June 11-13th or Aug 6th to 8th

The focus of the workshop will be on mostly development stages and traits for the crop plants

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

Proposal was submitted, waiting for news.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes.

exhibitor's booth

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

  • Annotation wiki: JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

Bio-Ontologies SIG 2012

Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012

When: Submissions Due: April 13th, 2012 (Fri)

See: Bio-Ontologies SIG 2012

Three types of submissions.

- Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page

Successful papers will be presented at the Bio-Ontologies SIG.

Poster abstracts: time will be allocated during the 2 days for at least one poster session.

Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Link to meeting page: ASPB2012

Abstract submission for minisymposia consideration ends March 2!

Joint workshop is planned with PO, Gramene and TAIR

Registration scheduled is open

Early Bird Registration: by May 11

Advance Discounted: May 12-June 15

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology.

Relevant dates

  • Feb. 28th, 2012: Notification of paper acceptance
  • March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
  • April 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
  • June 30th 2012: Deadline for all camera-ready copies for the proceedings

RW is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts