POC Conf. Call 3-8-12

POC meeting, Webex Conference Call; Date: Thursday Mar 68th, 2012 9am PST/12pm EST

This meeting was rescheduled from the regular time.

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_2-28-12?

Back to POC Meetings Minutes

Revisions of existing PO terms

Continued from previous week's discussion

sieve elements (PO:0025406)

Do we want to add the following terms:

primary phloem sieve element

secondary phloem sieve element

primary phloem sieve cell

primary phloem sieve tube element

secondary phloem sieve cell

secondary phloem sieve tube member

companion cell (PO:0000071)

proposed terms and definitions:

companion cell (PO:0000400): A parenchyma cell (PO:0000074) that is adjacent to a sieve-tube element (PO:0000289) and arises from the same phloem mother cell (PO:0000400) as the sieve tube element.

comment: Companion cells are connected to sieve tube elements through plasmodesmata and function in phloem loading of small molecules, including photosynthate (either sucrose or raffinose-family oligosaccharides). May participate in phloem sucrose loading (GO:0009915). Molecules can be loaded into the companion cells from surrounding cells through either symplastic (via plasmodesmata) or apoplastic (transmembrane) transport. Unlike sieve tube elements, companion cells retain their nuclei and other organelles at maturity. A sieve tube element may have one or more or no companion cells associated with it. This term should not be used for other types of parenchyma cells (PO:0000074) that do not arise from the same phloem mother cell as a sieve tube element. Companion cells are found in angiosperms, as compared to albuminous cells (PO:0025412), which are found in non-angiosperm vascular plants. Companion cells may be specialized as transfer companion cells (PO:id), intermediary companion cells (PO:id), or ordinary companion cells (PO:id). Multiple types of companion cells may be found in the same plant. adjacent_to sieve tube element, part_of phloem

synonym: minor vein companion cell

transfer companion cell (new term): A companion cell (PO:0000400) that is a transfer cell (PO:0000078) with many cell wall invaginations.

Comment: Plasmodesmata between a transfer companion cell and adjacent mesophyll cells may be few in number. Transfer companion cells are found in plants that use apoplastic phloem loading. Unlike sieve tube elements (PO:0000289), transfer companion cells retain their nuclei and other organelles at maturity.

syn: transfer cell (broad)

is_a companion cell and is_a transfer cell. No way to set up transfer cell as a cross-product, so must have dual parentage for now.

ordinary companion cell (new term): A companion cell (PO:0000400) that lacks cell wall invaginations and has few or no plasmodesmata connecting it to adjacent mesophyll cells.

Comment: Found in plants that use apoplastic phloem loading. Unlike sieve tube elements (PO:0000289), ordinary companion cells retain their nuclei and other organelles at maturity.

syn.: regular companion cell, standard companion cell

intermediary companion cell (new term): A companion cell (PO:0000400) that has dense cytoplasm, a small vacuole, proplastids rather than chloroplasts, and abundant and highly branched plasmodesmata linking it to mesophyll cells.

Comment: Intermediary companion cells translocate high concentrations of raffinose-family oligosaccharides and are found in plants that use symplastic phloem loading. Unlike sieve tube elements (PO:0000289), intermediary companion cells retain their nuclei and other organelles at maturity.

syn.: intermediary cell

References:

PMID:21669666 (Turgeon et al. 2001, AJB)

PO_REF:00011 (Turgeon 2006, BioScience)

Wood terms

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

plant 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).

synonyms: fiber, plant fiber

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.

synonym: phloem fiber

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.

synonym: xylem fiber

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.

synonym: libriform fiber

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.

synonym: septate libriform fiber

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.

synonym: septate phloem fiber

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.

Other terms for wood

Still on the items for future meetings page:

Items_for_future_meetings#Wood_parenchyma_cells_and_tissues

Items_for_future_meetings#wood_types

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.

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. This paper was accepted and is being revised. Wiki page for notes on Plant Disease Ontology.

Relevant dates

• Feb. 28th, 2012: Notification of paper acceptance
• April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• May 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