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 of existing PO terms:
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".
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 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.
Note about image annotations:
These cell types 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.
Note about image annotations:
These cell types 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.
Other terms for wood
From the Items_for_future_meetings#Wood_parenchyma_cells_and_tissues page:
Wood parenchyma cells and tissues
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
Should this be part_of secondary vascular tissue instead, if it can be found in secondary phloem as well.?
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
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)
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
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
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.
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.
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).
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
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)
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
