POC Conf. Call 2-28-12

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

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_2-21-12?

Back to POC Meetings Minutes

Streaming recording link:

https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=62730802&rKey=8c69e366cca221f1 Download recording link:

https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=62730802&rKey=38b43dafef2d79ec

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.

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

>>tracheid

>>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).

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

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)

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)

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

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

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).

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)

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.

perforation plate (for GO)

proposed def.: A cell wall part that is the part of a wall of a vessel member 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).

sclerenchyma cells

These edits are done in the obo file.

sclerenchyma cell (PO:0000077)

proposed def.: A ground tissue cell (PO:0025030) with thickened secondary cell walls that are lignified.

comment: May or may not be devoid of protoplast at maturity. Not always easy to distinguish from tracheary elements (PO:0000290) or sclerified parenchyma cells (PO:0000074). Distinguishable from collenchyma cells (PO:0000075) because collenchyma cells are alive at maturity. Collenchyma cells provides flexibility while sclerenchyma cells provide hardness.

sclerid (PO:0025418)

proposed def.: A sclerenchyma cell (PO:0000077) that has thick secondary walls with many pits.

comment: Usually not very elongated.

fiber cells

These edits are done in the obo file.

Need to add exact synonyms to all of these that don't have the word "cell", e.g., fiber for fiber cell.

fiber cell (new term, PO:0025407)

proposed def.: An elongated, tapering schlerenchyma cell (PO:0000077) with a more or less thick secondary cell wall.

comment: May or may not have lignin in the secondary wall or a living protoplast at maturity. It may be difficult to distinguish fiber cells from tracheary elements (PO:0000290).

phloem fiber cell (PO:0004519) (was called phloem fiber)

proposed def.: A fiber cell (PO:0025407) that is part of a portion of phloem (PO:0005417) tissue.

Made part_of phloem, instead of part_of secondary phloem.

xylem fiber cell (PO:0000274) (was called xylem fiber)

proposed def.: A fiber cell (PO:0025407) that is part of a portion of xylem (PO:0005352) tissue.

comment: It may be difficult to distinguish xylem fiber cells from tracheary elements (PO:0000290).

Made part_of xylem, instead of part_of secondary xylem.

libriform fiber cell (PO:0004520)

proposed def.: A xylem fiber cell (PO:0000274) with simple pits.

Comment: Libriform fiber cells have unbordered pits while fiber tracheids (PO:0000355) have bordered pits. Many intermediate forms exists and are generally classified as fiber tracheids. If both libriform fiber cells and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Libriform fiber cells have a slit-like aperture toward the cell lumen, but no pit cavity.

fiber tracheid (PO:0000355)

proposed definition: A xylem fiber cell (PO:0000274) with bordered pits with pit cavities.

comment: Commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures. If both libriform fiber cells (PO:0004520) and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Fiber tracheids have bordered pits with smaller pit cavities than the vessel members (PO:0002003) or tracheids (PO:0000301) of the same wood and a distinct pit cavity leading from the pit cavity to the cell lumen through the thick cell wall.

septate fiber (PO:0004521)

current def.: A fiber with thin transverse walls (septa), which are formed after the cell develops a secondary wall thickening.

Septate fibers can be found in both the xylem and the phloem. PO:0004521 is_a xylem fiber, but both tracheid-type and libriform-type xylem fibers can be septate. There are no annotations on this term, so I suggest we obsolete it, and replace it with two new terms: septate fiber tracheid and septate libriform fiber. Could also add septate phloem fiber, is_a phloem fiber.

proposed definition, septate fiber tracheid: A fiber tracheid (PO:0000355) that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

proposed definition, septate libriform fiber cell: A libriform fiber cell (PO:0004520) that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

proposed definition, septate phloem fiber cell: A phloem fiber cell (PO:0004519) that has as parts one or more thin internal partitions or septa.

comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.

other kinds of fiber cells

gelatinous fiber cell (new term, PO:0025422): A xylem fiber cell (PO:0000274) in which the inner-most layer of the secondary wall contains abundant alpha-cellulose and is poor in lignin.

comment: Commonly found in reaction wood in dicots. The inner layer of the cell wall, or G-layer, can absorb much water and swell and is relatively porous and less compact than the outer layers of the cell wall.

ref: Fahn

synonym: mucilaginous fiber cell

Note: We have a request to add reaction wood, from Wood Ontology meeting.

Open SourceForge Trackers:

coleoptile emergence

This was discussed at the NYBG Meeting, on Sunday_Sept_11th,_2011

From MS (MaizeGDB): It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be: Emergence of coleoptile from the seed. (rather than above ground)

This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.

At the POC meeting on Sunday_Sept_11th,_2011, we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.

current structure:

Shoot emergence (stage) is_a seedling growth (stage). Seedling growth (stage) is_a vegetative growth stage (changes were made at last release).

Imbitition (stage) is_a germination (stage). Will deal with definitions of imbibition and germination later.

current and proposed terms and definitions

All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.

current: shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

proposed: shoot emergence from growth medium development stage (PO:0007030): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the growth medium and ???.

Comment: This terms is used only for seed plants.

proposed: shoot emergence from seed coat development stage (new number): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the seed coat and ???.

Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.

current: coleoptile emergence (PO:0007045): Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]

proposed: coleoptile emergence from growth medium development stage (PO:0007045): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the growth medium and ???

Comment: This terms is used only for seed plants.

proposed: coleoptile emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the seed coat and ???

Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.

current: cotyledon emergence (PO:0007049): Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]

proposed: cotyledon emergence from growth medium development stage (PO:0007049): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the growth medium and ???

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.

proposed: cotyledon emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the seed coat and ???

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination. May occur simultaneously with cotyledon emergence form the growth medium.

current: epicotyl emergence (PO:0007054): Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: epicotyl emergence from growth medium development stage (PO:0007054): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the growth medium and ???

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination.

proposed: epicotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the seed coat and ???

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination. May occur simultaneously with epicotyl emergence form the growth medium.

current: hypocotyl emergence (PO:0007043): Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: hypocotyl emergence from growth medium development stage (PO:0007043): A shoot emergence stage has as a participant a whole plant during the interval between emergence of a hypocotyl from the growth medium and ???

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.

proposed: hypocotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a hypocotyl from the seed coat and ???

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination. May occur simultaneously with hypocotyl emergence form the growth medium.

Could also add terms for feeder emergence for some gymnosperms.

For all of the above terms, need to check existing synonyms and move or copy them as needed.

Updates to the Trait Ontology

Renaming the top level term:

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