POC Conf. Call 2-12-13

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POC meeting, Webex Conference Call; Date: Tuesday Feb 12th, 2013 10am PST/1pm EST

In attendance: Laurel Cooper (OSU), Justin Elser (OSU), Dennis W Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Preece (OSU).

Absent: , Pankaj Jaiswal (OSU)


Contents

Update from Cornell

MAG: We have added 6 more slides and 200 photos, I am also working on the editing of the slides

Total: 512 slides in database, 8573 images in database at CUPAC site

LC will send Ale the list of new terms we need the Spanish translations for, from the last release

PO paper

Final version is available online: PAE Paper 2013

NYBG Advertisement for hire

-Sent out on Po-announce, on BSA site and NYBG site

Will also send to the The International Society for Biocuration

Open trackers: To be addressed: PSDS Terms

shoot system development stage

Revisions and new terms needed for grape data set:

We were deficient in terms to describe the stages of development of the shoot system (PO:0009006).

We currently have collective plant organ structure development stage (PO:0025338) with two direct child terms: flower development stage (PO:0007615) and inflorescence development stage (PO:0001083).

New terms added:

  • shoot system development stage (new PO:0025527): A plant structure development stage (PO:0009012) that has as primary participant a shoot system (PO:0009006).

added relations: shoot system (PO:0009006) participates_in shoot system development stage (or should this be shoot system development stage has_participant shoot system).

Comment from BS: You do not need to have the has_participant (or participates_in) relations in both the comment and the definition.

BS: For each of these cases (on today's agenda), you need to add an axiom (relation) that asserts what the thing is from which the developing thing has developed from, for example the shoot system participates_in bud development.

Question: is this not encompassed by the parent term? for example we assert that shoot system development stage (PO:0025527) has_participant shoot system (PO:0009006). Bud is_a shoot system and bud development stage is a shoot system development stage.

Note: we have numerous cases of this: see trichome development stage, whole plant development stage, plant tissue development stage, collective plant organ structure development stage, etc. Do all of these need to be fixed?

---> Might be best to revise the definitions to avoid repeating the relation later if and when these are formalized.


  • bud burst stage (new PO:0025532):

A shoot system development stage (PO:0025527) during which a shoot system (PO:0009006) emerges from the bud (PO:0009006). Synonyms: exact: E-L 4

Agreement that the bud burst stage is_a shoot system development stage, even though it is much shorter than the two stages. In fact, it could almost be considered as a landmark of the transition from bud to shoot, but we have gene expression data annotated to it, so we will keep it as a separate stage.

The covering of the bud is the bud scale leaf (PO:0020054).


  • bud development stage (new PO:0025528): A shoot system development stage (PO:0025527) that has as primary participant a bud (PO:0009006).

added relations: bud (PO:0009006) participates_in bud development stage (PO:0025528).

Comment from BS: You do not need to have the has_participant bud in both the definition and as a separate relation, since when the definition is formalized, the has_participates relation will fall out trivially. You do need to add a relation to what the bud develops from, for example the stem or the shoot system.

  • shoot system (PO:0009006) A collective plant organ structure (PO:0025007) that produces shoot apical meristems (PO:0020148) and the plant structures that arise from them.

see comments and revisions to shoot system on tracker


  • bud dormancy stage (new PO:0025529):

proposed def'n: A bud development stage (PO:0025528) during which a bud (PO:0009006) participates in a bud dormancy process (GO:0097207)

bud dormancy process GO:0097207

Definition: A dormancy process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a bud. Bud dormancy is a suspension of most physiological activity and growth that can be reactivated. It may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. The exit from bud dormancy is marked by the resumed growth of the bud.

Source: GOC:PO_curators, PO_REF:00009 Comment: Bud dormancy may precede dormancy of the whole plant.

Then we added:

  • bud swell stage (new PO:0025531)

Definition: A bud development stage (PO:0025528) during which a bud (PO:0009006) enlarges due to growth of the shoot system (PO:0009006).

Synonyms: exact: E-L 2


reproductive shoot system development stage (new PO:0025530)

Proposed def'n: A shoot system development stage (PO:0025527) that has as primary participant a reproductive shoot system (PO:0025082).

add relation: reproductive shoot system (PO:0025082) participates_in reproductive shoot system development stage (PO:0025530).

and revise the two existing child terms:

Old def'n: flower development stage (PO:0007615): A collective plant organ structure development stage (PO:0025338) that has as primary participant a flower (PO:0009046).

New def'n:flower development stage (PO:0007615): A reproductive shoot system development stage (PO:0025530) that has as primary participant a flower (PO:0009046).

already has a cross product flower is participant, needs to be revised for the new parent term.


inflorescence development stage (PO:0001083)

current def'n: Stages of development of an inflorescence defined by characteristic morphological, structural, histological or other visible features.

Revised: A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).

added relation: inflorescence (PO:0009049) participates_in reproductive shoot system development stage (PO:0025530)

All have DbxRef to OBO_SF_PO: 3595703


File:shoot sytem development stages.jpg


References for grape terms:

Coombe (1995) Growth Stages of the Grapevine: Adoption of a system for identifying grapevine growth stages. Australian Journal of Grape and Wine Research 1: 104–110 link

Lorenz et al (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale†. Australian Journal of Grape and Wine Research 1: 100–103 link

Open trackers: To be addressed: PAE terms

basal axillary shoot system (tiller) (PO:0005001)

Currently: An axillary shoot shoot system (PO:0006343) that develops from an axillary vegetative bud (PO:0004712) that is part of a stem base (PO:0008039).

Comment: Called a tiller in the Poaceae. Are there basal axillary shoot system in other monocots; no one thought there was

This should be revised to develop from an axillary bud rather than an axillary vegetative bud (PO:0004712), since tillers often become reproductive.

Proposed def'n: An axillary shoot system (PO:0006343) that develops from an axillary bud (PO:0004709) that is part of a stem base (PO:0008039).

-added SF DBXref


Revised def'n: An axillary shoot system (PO:0006343) that is part of a stem base (PO:0008039). We do not need to specify "that develops from an axillary bud (PO:0004709)" in the def'n as it is implied since it now is_a axillary shoot system, but it could be included in the comment.


File:tiller.jpg

prothallial cell

On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.

prothallial cell (PO:0025533):

proposed def'n: A vegetative plant cell (PO:0009002) that develops from the division of the microspore (PO:0020048) and is part of the microgametophyte of vascular plants other than angiosperms.

should add the PO id for microgametophyte (PO:0025280) to the definition


For reference about prothallial cells in gmnosperms see:

Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.

Available online: Coulter + Chamberlain, 1910

Put in "A plant cell (PO:0009002), which is vegetative...

Comments from SF:

  • 'prothallium (new term): A whole plant (PO:0000003) in the gametophyte development stage (PO:0028003)

- is a gametophyte, early stage in gametophyte development


Date: 2013-02-15 11:17:46 PST Sender: cooperl09

prothallial cell (new term): A plant cell (PO:ID) that is part of a prothallium (need to add)

rename existing term: child of prothallial cell

microspore prothallial cell (PO:0025533): A plant cell (PO:0009002) that develops from a division of the microspore (PO:0020048) and is part of the microgametophyte (PO:0025280).

Comment: Commonly used in gymnosperms, is vegetative, does not develop into a sperm cell.

seta

seta (PO:0030032):

Currently: A plant axis that holds up a spore capsule. [source: ISBN:0962073342, POC:curators]

proposed def'n : A stalk (PO:0025066) that supports a spore capsule, the sporangium (PO:0025094). [source: ISBN:9780473067304]

Comment: Found in some bryophytes, especially mosses and liverworts.

Malcolm B, Malcolm N (2000) Mosses and other bryophytes: an illustrated glossary. Micro-Optics Press


Comments from SF: "A stalk is a cardinal organ part, and should be part of the same organ as the thing it is holding up (e.g., a petiole is part of a leaf and holds up the lamina that is part of the same leaf). The seta and the capsule are not part of the same organ. The seta is like the stem of a moss sporophyte and is thus a plant axis. It could more specifically be a shoot axis." (RW)


stalk (PO:0025066): A cardinal organ part that is elongated and sub-cylindrical to cylindrical and supports another cardinal organ part. Comment: Some stalks may be ridged or grooved.

note: It does not say it has to be part of the same organ as the thing it is holding up.


  • plant axis: An axial plant organ, narrow synonym= stalk

Other examples of stalks: filament of stamen, antheridium stalk (PO:0030035), archegonium stalk (PO:0030036), funicle (PO:0020006), petiolule (PO:0020050), petiole (PO:0020038), leaf rachis (PO:0020055)

antheridiophore (PO:0030033)

Def'n: A stalk (PO:0025066) that supports an antheridium head (PO:0030075). [source: ISBN:0962073342] Comment: Found in mosses and other bryophytes such as the liverwort Marchantiales.

archegoniophore (PO:0030034): Def'n: A stalk (PO:0025066) that supports an archegonium head (PO:0030034). [source: ISBN:0962073342]

Comment: Found in Marchantiales.


The seta is part of the sporophyte (not a PO term) and supports the moss capsule (synonym of sporangium)

Upcoming meetings and Presentations 2013:

Phenotype Ontology RCN Annual Summit Meeting, Feb. 25th - 27th, 2013, Durham, NC

Phenotype Ontology RCN

The workshop and meeting will be held at the National Evolutionary Synthesis Center in Durham, NC, from Monday morning, February 25 through Wednesday noon, February 27th (you would arrive Sunday evening).

Overall goals: To introduce and establish communication and collaboration among scientists from different research backgrounds. The two primary themes: The use of text mining phenotypes and representing behavior in ontologies.

For more information: please contact Paula Mabee (pmabee@usd.edu)

Biocuration 2013 conference, Cambridge, 7-10th April 2013

submission deadline for abstracts for posters is Jan 31st.


website and registration are now open: Biocuration 2013

PRO-PO-GO meeting, May 15-16th 2013

Please see this page for more information: PRO-PO-GO_Meeting

Location: Buffalo, NY

Dates: May 15-16th, 2013.

Goals:

  1. To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
  2. To identify potentially fruitful applications which such enhanced coordination might bring
  3. To enhance the Protein Ontology treatment of plant-related proteins
  4. To address coordination issues between the GO and PO, for example as concerns treatment of development stages
  5. To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP]


Tentative participant list:

PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?

GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?

PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)

BS would like a list of who we would like to include in the meeting and whose costs can be covered by PO


10th Extended Semantic Web Conference (ESWC) Montpellier, 26-30 May 2013

Extended Semantic Web Conference Montpellier

Location: Montpellier, 26-30 May 2013.

Semantics for Biodiversity (S4BIODIV)

Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.


Paraphrased from email exchange with EA (Bioversity):

Ontologies will be part of the workshop discussion. The latest development sent by Justin on AISO also raised interest of the organizing committee. So, we would you like that the Plant Ontology team be represented in the scientific committee of our workshop.

This is a very first draft of course but will provide you with the context, scientific objectives, and expected outputs. Would you accept in principle (if the workshop is accepted and funds raised) to join our committee and submit a a paper for a presentation and/or poster? Deadline will be March and April.

MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013

MONOCOTS V:

5th International Conference on Comparative Biology of Monocotyledons Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)

The New York Botanical Garden & Fordham University

Botanical Society Meeting July 27-31st New Orleans

BSA 2013

- MAG is planning to present the work she has been doing with the images and slides, will circulate the abstract

Next meeting scheduled for Tuesday, Feb 19th, 2013 at 10am Pacific/1pm Eastern

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