POC Conf. Call 3-8-12

POC meeting, Webex Conference Call; Date: Thursday Mar 8th, 2012 9am PST/12pm EST

In attendance:

POC members:Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Marie Alejandra Gandolfo (Cornell Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY).

Absent: Dennis Stevenson (NYBG), Justin Elser (OSU), Chris Mungall (Lawrence Berkeley National Lab)

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=63005082&rKey=52f2cd21379cf029

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=63005082&rKey=d8d6f53054b0d2da

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 to vascular tissues and cell types:

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 secondary phloem sieve tube element

We were all in agreement that we should add these terms

companion cell (PO:0000071)

background info on these is still on: Items_for_future_meetings page.

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)

These definitions and new terms have been discussed already and all are in agreement that they are acceptable. MAG will send them to Bob Turgeon at Cornell to get his opinion. The definitions will have the Turgeon reference and PMID as dbxrefs.

Need to be consistent with the hyphenation of "sieve-tube element".

Revisions to Wood terms:

sclerenchyma cells

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.

leave off "thickened", avoid mentioning that they are dead in the def'n, revised comment: may be dead at maturity

Revised def'n: A ground tissue cell (PO:0025030) with a lignified secondary cell wall.

check GO for "protoplast", compare with PO: 0000000 cultured protoplast

protoplast is a synonym for the GO term: cell part (GO:0044464): Any constituent part of a cell, the basic structural and functional unit of all organisms.

sclerid (PO:0025418)

revised name: sclerid cell (PO:0025418)

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

comment: Usually not very elongated.

Revised def'n: A sclerenchyma cell (PO:0000077) with many pits in the secondary cell wall.

check GO for "pit" and request 'secondary cell wall pit', 'simple pit'

add to comment:'lumen is occluded by the secondary cell wall', add synonym 'sclerid' and check for other spellings

GO term: GO:0009531 secondary cell wall: "A plant cell wall that is no longer able to expand and so does not permit growth. Secondary cell walls contain less pectin that primary cell walls. The secondary cell is mostly composed of cellulose and is strengthened with lignin."

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

get rid of 'more or less thick', secondary cell wall is a GO term, GO: "plant-type cell wall"

Comment: avoid 'living protoplast'

Revised def'n: A sclerenchyma cell (PO:0000077) that is elongated and tapering, unlike a sclerid cell.

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

Move some comments from the specific fiber cell types to the parent term to explain how to differentiate the xylem fiber cells from tracheary elements.

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 exist 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

simple pit = unbordered pits, need to be consistent, request from GO, also pit cavity

Should avoid mixing the plural and singular in the comments.

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.

Avoid "thick-walled", hard to explain unless they are both present

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 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 def.: 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 def.: 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 def.: 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

We decided that we should keep septate fiber cell (PO:0004521) as a generic type of plant cell and add the others with dual parentage in this case.

Avoid referring to 'living protoplast'

Need to define the septum (pl. septa); mitosis occurs after the secondary cell wall has formed, so the septum is actually a primary cell wall of two internal cells that are dead at maturity. Differentiate from the septum (PO:0000030) in the PO.

Need to request from GO: Septate fiber cell septum

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 cell 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

We had quite a bit of speculative discussion about the nature of alpha-cellulose: is pure or primary cellulose. The term comes from the chemical industry

Pectin is generally found in the primary cell wall and also between the cells

Good reference for the gelatinous fiber cell and the G layer: Roach et al (2011) Development of Cellulosic Secondary Walls in Flax Fibers Requires β-Galactosidase. Plant Physiology 156: 1351 –1363

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

Wood parenchyma cells and tissues

From the Items_for_future_meetings#Wood_parenchyma_cells_and_tissues page:

We decided that the primary term names should use "secondary xylem" and use "wood" as a synonym. Add exact synonyms "portion of SXP tissue". We will do this for all tissues and cell types below.

wood parenchyma (PO:0004532):

Current def.: Parenchymatous tissue occurring in the wood.

Currently is_a secondary xylem. Should be is_a parenchyma.

Proposed def.: A portion of parenchyma (PO:0005421) tissue that is part of a portion of secondary xylem (PO:0005848) and has as parts wood parenchyma cells (PO:0004525).

part_of secondary xylem

OK

axial wood parenchyma (PO:0004533):

Current def.: Parenchyma tissue in the axial system of secondary xylem.

Proposed def.: A portion of wood parenchyma (PO:0004532) that is part of an axial system (PO:0025410) and has as parts axial wood parenchyma cells (PO:0004526).

part_of axial system

OK

ray wood parenchyma (PO:0004534):

Current def.: Radially oriented parenchyma tissue in secondary xylem.

Proposed def.: A portion of wood parenchyma (PO:0004532) that is part of a ray system (PO:0025411) and has as parts ray wood parenchyma cells (PO:0004527).

comment: Occurs in bands or rays of variable width and height that extend radially in the secondary xylem (PO:0005848) and secondary phloem (PO:0005043) of a plant axis (PO:0025004).

part_of ray system

synonym: ray (broad)

OK

wood parenchyma cell (PO:0004525):

Current def.: Parenchyma cell occurring within secondary xylem.

Proposed def.: A parenchyma cell (PO:0000074) that is part of a portion of wood parenchyma (PO:0004532).

comment: Found in secondary xylem (PO:0005848) or secondary phloem (PO:0005043).

part_of wood parenchyma

Problem with the comment: how can it be part of secondary phloem (PO:0005043)??

Otherwise, OK

ray wood parenchyma cell (PO:0004527):

Current def.: Parenchyma cell of a ray in secondary xylem.

Proposed def.: A parenchyma cell (PO:0000074) that develops from a ray initial (PO:0000082) and is part of a portion of ray wood parenchyma (PO:0004534).

part_of ray wood parenchyma, develops_from ray initial

OK

upright wood ray parenchyma cell (PO:0004528)

Current def.: Ray cell in secondary xylem oriented axially (vertically in the axis) with its longest dimension.

Proposed def.: A ray wood parenchyma cell (PO:0004527) that is oriented with its longest dimension parallel to the plant axis (PO:0025004) in which it is found.

new name: upright ray secondary xylem parenchyma cell, add broad synonym 'upright cell'

OK

procumbent wood ray parenchyma cell (PO:0004529)

Suggest naming it "procumbent ray wood parenchyma cell".

Current def.: Ray cell within secondary xylem having its longest axis in radial direction.

Proposed def.: A ray wood parenchyma cell (PO:0004527) that is oriented with its longest dimension radial to the plant axis (PO:0025004) in which it is found.

new name: procumbent ray secondary xylem parenchyma cell, add broad synonym 'procumbent cell

OK

axial wood parenchyma cell (PO:0004526)

Current def.: Parenchyma cell in the axial system of secondary xylem.

Proposed def.: A wood parenchyma cell (PO:0004525) that is part of a portion of axial wood parenchyma (PO:0004533).

part of axial wood parenchyma, develops from fusiform initial.

Also see tile cell (PO:0004530) and sheath cell (PO:0004531)- need to look at these a bit more, make the names more specific

Items_for_future_meetings#wood_types

Open SourceForge Trackers:

coleoptile emergence

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

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.

Suggestion from MS (MaizeGDB):

coleoptile emergence PO:0007045: Emergence of coleoptile from the seed. (rather than above ground)

Compare to radicle emergence (PO:0007015): The stage at which the radicle or root emerges from seed.

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.

We all agreed that this is an issue. Also there are about 25,000 annotations on this stage, may have to keep both

Can eliminate the description of emergence from the ground or growth media and add a note that you might not observe it if the seed is underground. Additional issue is how to define this as a stage. It is actually a stage of elongation, which starts with emergence from the seed coat

Note about image annotations:

These cell types (above) are good candidates to tag with the photos- start putting them in the directory, go by priorities. KN will visit NYBG on 3-19, will discuss linking NYBG and PS.org. Annotation software will be ready around the end of March, so will be able to add labels and sections on the images. Will discuss on 3-12 Monday meeting, developing the links, KN may be able to take part.

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. The PO will not take part this year, because the timing is too short. We will look at attending next year.

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 is now closed.

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