POC Conf. Call 5-28-13

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POC meeting, Webex Conference Call; Date: Tuesday May 28th, 2013 10am PST/1pm EST

In attendance:Laurel Cooper (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell)

Absent: Barry Smith (University at Buffalo, NY)


fused collective tepal structure

An issue has been raised about using the term fused collective tepal structure from the Musa vocabulary:

From Chelsea Specht:" ... in Zingiberales there are sepals and petals, not tepals. and its a free petal, not a free tepal. and you can use the same terminology for the 'fused collective tepal structure' -- and technically, developmentally, its not fused: it just never separates. if we're talking about developmental genetics, that sort of thing matters."

See photo: Musa ornata

Originally added as part of this set: Musa Plant Structure terms in response to their request for a term "compound tepal"

  • fused collective tepal structure (PO:0025138): A collective tepal structure that has as parts at least two fused tepals.
    • Comment: This is a phenotype that is a cross-product of PO:0025021 (collective tepal structure) and PATO:0000642 (fused with). In Musa, there are there are 5 fused tepals which form 3 major lobes and 2 minor lobes. This is not actually a cross-product.

We will keep this term, but modify and revise it. There are numerous plants with fused tepals, but it does not actually apply in the Musa.

Proposed new term name and def'n: fused perianth (PO:new): A collective phyllome structure composed of two or more fused petals and/or sepals or two or more fused tepals.

comment: The perianth maybe composed of more than one type of perianth structure, ie: petals and sepals or tepals.

  • free tepal (PO:0025136): A tepal that is separate from all other tepals.

All tepals are free, unless they are fused. Should get rid of this term. Merge into an existing term- into tepal and redirect the users to use free petal. Or maybe we should leave it for now to parallel the new 'free petal' term. With a comment to redirect users.

free tepal on Crop Ontology

* This is actually a free petal, not a tepal. It is actually not fused to the rest of the fused perianth. So this is actually just a petal, so we may not need to specify that it is free. But we decided that it warranted making a specific term to describe it, as the flower

Based on the revised def'n

Proposed new term and def'n: free petal (new PO:0025569): A petal (PO:0009032) that is part of a collective phyllome structure (PO:0025023) where some of the petals are fused.


Diagram of banana flower

The term "compound tepal" and "free tepal" are widely used in the literature and floras: e.g. http://www.fruitipedia.com/leaf_banana%20Musa%20balbisiana.htm

http://www.botany.hawaii.edu/faculty/carr/mus.htm

http://www.efloras.org/florataxon.aspx?flora_id=2&taxon_id=240001486

http://ejournal.sinica.edu.tw/bbas/content/2002/1/bot431-09.html

In Magnolia, the tepals are arranged in a spiral, rather than in whorls, so the petals and sepals are indistinguishable. In the monocots there are 2 whorls of three petals or sepals. In Alliaceae or Yucca, they are obviously different. Could also talk about the inner whorl tepal and an outer whorl tepal. In monocots you always have the whorls, so we should not use tepals. We agreed that we do not want to use "compound'.

Suggestion to add 'perianth phyllome' to classify the petals, sepals and tepals. But it was decided that would be redundant.

tepal, petal and sepal and the collective floral structures: perianth, corolla and calyx

Need to also revise the definition of petals and sepals, open trackers

Existing def'ns and revised ones:

    • REVISED:A collective phyllome structure (PO:0025023) that includes as parts the corolla (PO:0009059) and/or the calyx (PO:0009060).
  • corolla (PO:0009059):A collective phyllome structure composed of two or more petals.
    • A collective phyllome structure (PO:0025023) composed of one or more petal(s) (PO:0009032), which comprises the inner whorl of non-fertile organs and surrounds the androecium (PO:0009061) and/or gynoecium (PO:0009062). Comment: Only occurs in dicots?
  • calyx (PO:0009060): A collective phyllome structure composed of two or more sepals.
    • A collective phyllome structure (PO:0025023) that is composed of one or more sepal(s) (PO:0009031), and comprises the outer whorl of non-fertile floral organs (PO:0025395).
  • petal (PO:0009032): A member of the corolla, the inner whorl of non-fertile parts surrounding the fertile organs of a flower, usually soft and colored conspicuously. [source: APweb:Glossary]
    • A phyllome (PO:0006001) that is usually soft and conspicuously colored, and is part of the corolla (PO:0009059).
  • sepal (PO:0009031): A member of the (usually green) outer whorl of non-fertile parts surrounding the fertile organs of a flower. [source: APweb:Glossary]

Only occurs in dicots?

    • A phyllome (PO:0006001) that is usually green, and is part of the calyx (PO:0009060).
  • tepal (PO:0009033): A phyllome that is part of a perianth in which all parts are similar in appearance and are neither petals nor sepals. [source: POC:curators]




Suggested revised def'n: tepal (PO:0009033): A phyllome (PO:0006001) that is part of a perianth (PO:0009058) in which all parts are similar in appearance and it is not possible to distinguish between the petals (PO:0009032) or sepals (PO:0009031).

Upcoming meetings and Presentations 2013:

1st International Workshop on Semantics for Biodiversity (S4BIODIV), Montpellier, 26-30 May 2013

S4BIODIV

Registration Information ESWC 2013

Early Registration deadline March 17th

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.

Held in parallel with the 10th Extended Semantic Web Conference (ESWC 2013)

Workshop date: May 27, 2013

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


ICBO 2013, Concordia University, Montreal, Quebec July 7th - 9th 2013

4th International Conference on Biomedical Ontologies 2013 (ICBO2013)

Concordia University, Montreal, Quebec, July 7th - 9th 2013 call for papers

The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience.

The event is part of the Semantic Trilogy 2013 featuring:

  • International Conference on Biomedical Ontologies (ICBO 2013)
  • Canadian Semantic Web Symposium (CSWS 2013)
  • Data Integration in the Life Sciences (DILS 2013)

Workshop on Semantic Systems Biology 2013 (SSB2013) will be held as part of the International Conference on Biomedical Ontologies (ICBO2013) at Concordia University, Montreal, Quebec, on July 7th, 2013. The event is part of the Semantic Trilogy 2013 (above)

Topics of interest include, but are not limited to:

  • ontologies & terminologies for modeling computational biology
  • ontologies & terminologies for simulation (and result data) in computational biology/medicine/neuroscience
  • semantic web technologies for description, integration, query and discovery of models, simulations and result data
  • semantic web technologies for biological data and analysis
  • semantic annotations of bio-models
  • applications of ontologies in computational systems biology/medicine/neuroscience
  • semantic platforms for undertaking and visualizing simulation results

We welcome four types of submissions:

  • short papers, up to 4 pages.
  • long papers, up to 7 pages.
  • position papers, up to 1 page.
  • late breaking reports, up to 1 page.

See the ICBO website for further information on the submission types.

All submission are due on Monday, April 15 2013. Notification of acceptance: May 6th, 2013

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

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