POC Conf. Call 3-20-12

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POC meeting, Webex Conference Call; Date: Tuesday Mar 20th, 2012 10am PST/1pm EST

In attendance:

POC members:

Absent:


Collaborators: none


Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_3-13-12?

Back to POC Meetings Minutes

Next PO Release:

Apache update:

JE has managed to port the website code to work with Apache2. Please check http://beta.plantontology.org (no port 8080).

Question: Should we wait until after the release to update? Probably could update with only minor disruption, but there could be unforeseen difficulties. Most of it could be done in parallel to minimize downtime however.

After the switch, all links to :8080 addresses will have to be fixed. There are only about 30, and most of them seem to be links to wiki.plantontology.org.


Timeline:

  • Target date for finishing edits: March 21st
  • Target date for release: Before March 30th


We should aim to have to release out by the end of this month, so we can then focus on the paper to have manuscripts ready by April 15th.

We probably want to have this release out before we submit, so reviewers and editors can look at the web site. If we get feedback from reviewers on manuscripts, we can work those into the next release in two months.

We can get this week's changes, plus the wood development stages and the coleoptile emergence terms in the file by next week, and review them at next week's meeting.

Goals and Priorities:

For more details see: New terms and obsolete terms-March 2012 Release

PO_Release_SOP_Page

After the release in October 2011, LC put together this page to help facilitate the releases

Revisions of PSDS (formerly PGDSO):

Status to 3-19-12

  • ~34 new terms added
  • many existing terms have been modified, eg changed all the 'phase' names to 'stage'
  • all PSDS terms names are now singular. Some still need to have "stage" appended
  • focus has been on the whole plant development stage (PO:0007033) and its children
  • Addition of Wood development stages: (See: SF tracker), started at the NYBG Workshop

New and Revised Terms for the PAE

  • ~125 new terms for this release
  • Complete old user requests/SF tracker items: This is an ongoing process

New association files:

  • Physcomitrella (released Jan 2012)
  • Small set of cotton annotations
  • Updated annotations from SGN received

Glossary of PO terms

See PO Glossary on dev

This was discussed at the RCN meetings 2011, plan is to eventually replace APWeb Glossary. This will be useful for users of APWeb Glossary who need a glossary, but don't want to use AmiGO browser. We could eventually incorporate other terms from APweb into PO if needed.

  • What is the status of this? PJ will follow up with the developers. It should be updated to the version for the release.

Translations

Will need to update translations for PAE terms before release. JE has generated a file that includes all terms and their synonymns so we can determine which ones need Spanish and/or Japanese translations.

icons for new relations

  • We need an icon for the has_participant relation so it can be included in the upcoming release.

According to discussion of POC_Conf._Call_1-31-12 we decided:

It would be good to relate the new icon visually to the reciprocal 'participates_in':

has_participant should be "hP" in a circle, (to distinguish it from has_part: Hp) and that a dark background with white letters is more visible

sent reminder after meeting on 3-13-12

  • derives_by_manipulation_from icon is present but not showing up in dev browser?

Collaborative projects:

  • Mapping of Flora of North America Glossary to PO terms:

For more details see: The FNA collaborators page: Flora_of_North_America-_FNA

Synonyms have been added

Outstanding edits to be finished:

The issues around coleoptile emergence were raised by MaizeGDB and have been open on SF since June 2011.

Discussed on: POC_Conf._Call_3-8-12 and POC_Conf._Call_3-13-12

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.

We had further examination and discussion on POC Conf. Call 3-8-12 and decided we were in favor of eliminating the description of emergence from the ground or growth media, but adding a comment 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 (or does it start sooner?)

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

In reviewing these terms, I went back to our discussions of plant embryo, plant zygote and plant embryo stage on POC_Conf._Call_12-13-11. At that time we agreed to rigorously define the plant embryo stage and define the plant embryo as a whole plant that participates in that stage.

But I found a couple of problems: took out the comments that pteridphytes have cotyledons and clarified the plant embryo stages.

plant embryo stage

these changes have been made in the dev file:

plant embryo stage (PO:0007631):

Revised, annotated def'n:

A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the first cell division of the plant zygote (PO:0000423) and beginning of the next stage of growth, which varies among taxa. In seed plants, the plant embryo stage ends with seed germination stage (PO:0007057). In pteridophytes, the plant embryo stage ends with the formation of the first vascular leaf (PO:0009025). In bryophytes, the (plant) embryo stage ends when the seta meristematic apical cell (PO:0030016) stops dividing and the sporangium (PO:0025094) begins to develop. In cultured plant embryos (PO:0000010), the (plant) embryo stage ends when a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or leaf (PO:0025034) begins to form.

Revised, annotated comment:

Succeeds the plant zygote stage (PO:0001097). The plant embryo stage generally starts after the first division of a plant zygote (PO:0000423), but in the case of an adventitious embryo, somatic embryo (PO:0025302), other embryos that arise through apogamy, or microspore-derived cultured plant embryo (PO:0025305), it is formed after the division of a single cell that is not a zygote.


LC: I am not certain about the end in bryophytes- originally it just said apical cell- changed to 'seta meristematic apical cell (PO:0030016)', but I think the plant embryo stage in bryophytes would end when the seta starts to elongate- maybe we need something like a "seta elongation sporophyte vegetative stage". Raven et al calls it the "young sporophyte".

Sporangium formation should mark the beginning of the sporophyte reproductive stage (PO:0007130).

plant embryo

def'n: A whole plant (PO:0000003) that participates in the (plant) embryo stage (PO:0007631).

modified comment:

A plant embryo is generally formed after the first division of a plant zygote (PO:0000423), but in the case of an adventitious embryo (e.g. nucellar plant embryo (PO:0004537)), somatic embryo (PO:0025302), other embryos that arise through apogamy, or microspore-derived cultured plant embryo (PO:0025305), it is formed after the division of a single cell that is not a zygote.

I don't think we need to repeat all the details of the different taxa here, as it is part of the def'n of the plant embryo stage.

plant zygote stage

Propose revised def'n: A sporophyte vegetative stage (PO:0007134) that occurs during the interval between syngamy and the first cell division. [source: POC:curators]

added relation: plant zygote (PO:0000423) participates_in plant zygote stage

coleoptile emergence

Current def'ns (dev):

PAE terms:

  • coleoptile (PO:0020033): A phyllome that surrounds the plumule of an embryo or the emerging shoot apex of a seedling.

Comment: Found in Poaceae. The coleoptile is the first phyllome formed from the embryonic shoot apical meristem. Protects the emerging shoot system as it grows through the soil.

from Raven et al: The sheath enclosing the apical meristem and leaf primordia of the grass embryo; often interpreted as the first leaf.

>> embryo coleoptile (PO:0025286): A coleoptile that is part of a plant embryo.

>> seedling coleoptile (PO:0025287): A coleoptile that develops from an embryonic coleoptile. Comment: A seedling coleoptile is an elongation of an embryonic coleoptile and is part of a whole plant in the seedling phase.


  • plumule (PO:0020032): A somewhat differentiated terminal bud above the cotyledonary node, in which one or more internodes and leaves or scales can be discerned in a primordial stage.

Comment: Occurs in several embryo types


  • radicle (PO:0020031): An embryonic root that is the basal continuation of a hypocotyl.

Comment: Found in an embryo or a seedling. May develop into the root system of an adult plant. Sometimes abortive.

>> embryo radicle (PO:0025296): A radicle that is part of a plant embryo.

>>seedling radicle (PO:0025297): A radicle that develops from an embryonic radicle. Comment: Part of a whole plant in the seedling phase.

  • coleorhiza (PO:0020034): A plant organ that surrounds a radicle.

>>embryo coleorhiza (PO:0025288)

>>seedling coleorhiza (PO:0025289)

  • cotyledon (PO:0020030): A leaf formed at the first node of a sporophyte.

need new terms: seedling cotyledon (PO:00xxxxx); embryo cotyledon (PO:00xxxxx)

  • hypocotyl (PO:0020100): A stem internode that is the part of a stem below the cotyledonary node and transitional to a root

>> seedling hypocotyl (PO:0025291); >> embryo hypocotyl(PO:0025290)

  • epicotyl (PO:0020035): The first stem internode above a hypocotyl

>>embryo epicotyl (PO:0025292); >>seedling epicotyl (PO:0025293);

PSDS terms:

  • sporophyte development stage (PO:0028002): A whole plant development stage that has as primary participant a whole plant during the interval between fertilization or apogamy and its death
  • sporophyte vegetative stage (PO:0007134): A sporophyte development stage that occurs during the interval between the first division of the zygote and the formation of a sporangium.
  • seedling development stage (PO:0007131): A vegetative growth stage during the interval between germination and development of the first adult leaves.
  • seedling shoot emergence stage (PO:0007030): Shoot or leaf breaks through soil surface.
  • coleoptile emergence (PO:0007045): Emergence of coleoptile above ground
  • cotyledon emergence (PO:0007049): Emergence of cotyledons above ground.
  • epicotyl emergence (PO:0007054): Emergence of the epicotyl above ground.
  • radicle emergence (PO:0007015): The stage at which the radicle or root emerges from seed. (is_a root development stage)


current structure (on dev):

Seedling stages.jpg

Proposed terms and definitions

  • sporophyte development stage (PO:0028002): A whole plant development stage (PO:0007033) that has as primary participant a whole plant during the interval between fertilization (or apogamy) and death.


  • sporophyte vegetative stage (PO:0007134): A sporophyte development stage (PO:0028002) that occurs during the interval between the first division of a plant zygote (PO:0000423) and the formation of a sporangium (PO:0025094).


  • seedling development stage (PO:0007131): A sporophyte vegetative stage (PO:0007134) that succeeds the seed germination stage (PO:0007057) and terminates with the development of the first adult vascular leaf (PO:0006340).

Chronologically:

  • coleorhiza emergence stage (new term): A root development stage (PO:0007520) during which a seedling coleorhiza (PO:0025289) emerges from the seed coat (PO:0009088).
  • radicle emergence stage (PO:0007015): A root development stage (PO:0007520) during which a seedling radicle (PO:0025297) emerges from the seed coat (PO:0009088).

part_of seedling development stage (PO:0007131), part_of germination stage

  • coleoptile emergence stage (PO:0007045): A seedling development stage (PO:0007131) during which the seedling coleoptile (PO:0025287) emerges from the seed coat (PO:0009088).

part_of germination stage, occurs in Poaceae and possibly other monocots

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


  • cotyledon emergence stage (PO:0007049): A seedling development stage (PO:0007131) during which the seedling cotyledon (PO:00xxxxx)emerges from the seed coat (PO:0009088).

Comment: This terms is used only for seed plants, for example bean.

Do we want to keep a corresponding stage for emergence from the growth media? Cannot be used in plants with hypogeal germination.

  • epicotyl emergence stage (PO:0007054): A seedling development stage (PO:0007131) during which the seedling epicotyl (PO:0025293) emerges from the seed coat (PO:0009088).

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.

  • hypocotyl emergence stage (PO:0007043): A seedling development stage (PO:0007131) during which the seedling hypocotyl (PO:0025291) emerges from the surface of the growth medium.

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

Was emergence of the coleoptile/cotyledon/epicotyl above ground.


* seedling shoot emergence stage (PO:0007030): A seedling development stage (PO:0007131) Shoot or leaf breaks through soil surface.

http://www.jki.bund.de/fileadmin/dam_uploads/_veroeff/bbch/BBCH-Skala_englisch.pdf 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.


wood development stages

We came up with these terms at the wood ontology meetings. I have refined the definitions to follow the PO format, but the content of the definitions is based on the group discussion at the meeting.

Keep in mind that these are stages in the development of secondary xylem that are based on developmental processes that are happening in the constituent cell, not cell development stages.

Proposed hierachy

upper level

plant structure development stage

>plant tissue development stage

>>vascular tissue development stage

>>>phloem development stage

>>>xylem development stage

>>>>secondary xylem development stage


All of these terms are defined as, e.g., "A plant structure development stage that has as primary participant a portion of plant tissue."

lower level

secondary xylem development stage

>cell division stage of secondary xylem

>cell differentiation stage of secondary xylem

> >cell expansion stage of secondary xylem

> >secondary cell wall formation stage of secondary xylem

> >cell death stage of secondary xylem

> > >tracheary element death stage of secondary xylem

> > >secondary xylem parenchyma cell death stage of secondary xylem

Proposed terms and definitions

For now I have added POC curators as the definition reference for these terms, but we should credit the wood ontology group participants in some way (Wood Ontology Curators, Wood Curators?)

secondary xylem development stage (PO:0025427)

def.: A xylem development stage (PO:0025425) that has as primary participant a portion of secondary xylem (PO:0005848) tissue (should it be sapwood?) during the interval between the beginning of a cell division stage of secondary xylem (PO:0025463) and the death of the last living cell in the secondary xylem.

comment: During a secondary xylem development stage (also called a wood development stage), the cells of secondary xylem (PO:0005848), including tracheary elements (PO:0000290), xylem fiber cells (PO:0000274), and wood parenchyma cells (PO:0004525) undergo cellular developmental processes (GO:0048869) such as cell division (GO:0051301), cell growth (GO:0016049), cell differentiation (GO:0030154), or cell death (GO:0008219). The transition from sapwood to heartwood marks the end of the secondary xylem development stage.

synonyms: wood development stage, sapwood development stage

has_participant sapwood


>cell division stage of secondary xylem (PO:0025463)

Def.: A secondary xylem development stage (PO:0025427) that occurs during the interval between the first and last cell division in a portion of secondary xylem tissue (PO:0005848), during which cells are produced by divisions of cambial initials (PO:0000295) or xylem mother cells (PO:id).

Comment: This stage includes production of xylem mother cells by cambial initials and production of tracheary elements (PO:0000290) or other cells by xylem mother cells. Precedes a cell differentiation stage of secondary xylem (PO:0025469), although cell differentiation may begin before a cell division stage of secondary xylem ends.


>cell differentiation stage of secondary xylem (PO:0025469)

Def.: A secondary xylem development stage (PO:0025427) that occurs during the interval between the end of a cell division stage of secondary xylem (PO:0025463) and the death of the last living cell in the secondary xylem.

Comment: During a this stage, cells of secondary xylem undergo cell differentiation (GO:0030154), including cell growth (GO:0016049), cell morphogenisis (GO:0000902), or cell death (GO:0008219). Cell death is considered part of differentiation in secondary xylem, because it is an essential part of wood development. This stage succeeds the last cell division in a cell division stage of secondary xylem, even though cell differentiation may begin before all cell division finishes.


> >cell expansion stage of secondary xylem (PO:0025464)

Def.: A cell differentiation stage of secondary xylem (PO:0025469) that occurs during the interval between the end of a cell division stage of secondary xylem (PO:0025463) and the onset of a secondary cell wall formation stage of secondary xylem (PO:0025465), during which the cells undergo cell growth (GO:0016049).

Comment: This stage succeeds a cell division stage of secondary xylem (PO:0025463) and precedes secondary cell wall formation stage of secondary xylem (PO:0025465).


> >secondary cell wall formation stage of secondary xylem (PO:0025465)

Def.: A cell differentiation stage of secondary xylem (PO:id) that occurs during the interval between the onset of secondary wall biogenesis (GO:0009834) of the cells in a portion of secondary xylem and the beginning of a cell death stage of secondary xylem (PO:id).

Comment: During this stage, secondary cell walls (GO:0009531) are being formed in a portion of secondary xylem tissue, preventing further expansion of the cells. This stage succeeds a cell expansion stage of secondary xylem (PO:id) and precedes a cell death stage of secondary xylem (PO:id).


> >cell death stage of secondary xylem (PO:0025466)

Def.: A cell differentiation stage of secondary xylem (PO:0025469) that occurs during the interval between the first cell death of a tracheary element (PO:0000290) or non-septate xylem fiber cell (PO:0000274) and the death of the last secondary xylem parenchyma cell (PO:0004525) or septate fiber cell (PO:0004521) in a portion of secondary xylem (PO:0005848).

Comment: During this stage, the cells of a portion of secondary xylem are undergoing cell death (GO:0008219), sometimes called apoptosis. Death of the tracheary elements and non-spetate xylem fiber cells generally precedes the death of secondary parenchyma cells and septate fiber cells. Once all cells in portion of secondary xylem are dead, it transitions from sapwood (PO:0004513) to heartwood (PO:0004512), and secondary xylem development ends.

synonym: transition to heartwood stage


> > >tracheary element death stage of secondary xylem (PO:0025467)

Def.: A cell death stage of secondary xylem (PO:0025466) that occurs during the interval between the first and last cell death of a tracheary element (PO:0000290) or non-septate xylem fiber cell (PO:0000274).

Comment: During this stage, the tracheary elements and non-septate xylem fiber cells of a portion of secondary xylem (PO:0005848) undergo cell death (GO:0008219), but most of the secondary xylem parenchyma cells (PO:0004525) and septate xylem fiber cells (septate fiber tracheid, PO:0025419, and septate libriform fiber cell, PO:0025420) remain alive. Precedes a secondary xylem parenchyma cell death stage of secondary xylem (PO:0025468).


> > >secondary xylem parenchyma cell death stage of secondary xylem (PO:0025468)

Def.: A cell death stage of secondary xylem (PO:0025466) that occurs during the interval between the last cell death of a tracheary element (PO:0000290) or non-septate xylem fiber cell (PO:0000274) and the last cell death in a portion of secondary xylem (PO:0005848).

Comment: During this stage, the secondary xylem parenchyma cells (PO:0004525) and septate xylem fiber cells (septate fiber tracheid, PO:0025419, and septate libriform fiber cell, PO:0025420) of a portion of secondary xylem (PO:0005848) undergo cell death (GO:0008219). Succeeds a tracheary element death stage of secondary xylem (PO:0025467). Once all cells in portion of secondary xylem are dead, it transitions from sapwood (PO:0004513) to heartwood (PO:0004512), and secondary xylem development ends.

Upcoming meetings and Presentations 2012:

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.

Organizer; Neelima Sinha (Sinha@ucdavis.edu) 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

  • LC is attending and is taking part in the BioCreative workshop

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

For more information see the wiki page: Crop_Ontology_Workshop_at_OSU,_2012

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

  • PO workshop for Sunday, July 8th

The organizer have listed it as a whole day workshop, but it is planned for a half day and will be changed on the schedule. Also need to correct link to abstract (currently goes to wrong abstract).

see: Botany 2012 workshops

Workshop goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

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

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 was submitted for submission for minisymposia consideration.

Joint workshop is planned with PO, Gramene and TAIR

Registration 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

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