POC Conf. Call 6-4-13

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POC meeting, Webex Conference Call; Date: Tuesday June 4th, 2013 10am PST/1pm EST

In attendance: Laurel Cooper (OSU), Justin Preece (OSU), Justin Elser (OSU), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY).

Absent: Dennis W Stevenson (NYBG)

Contents

Plans for Upcoming Release #20

Need to discuss the timing of the Release. Scheduled for "June".

See details on the Release_20 page.

LC will be out June 19-23rd and 28th.

We will plan to do the next release around the end of July, will aim to include the update to AmiGO 1.8 and can introduce and announce the mirrored site at iPLant

Continuation of discussion about fused collective tepal from 5-28-13

See the discussion on 5-28-13 for full details: fused collective tepal structure

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:

perianth

  • perianth (PO:0009058): A collective phyllome structure composed of two or more petals, sepals, or tepals. additional tracker
    • REVISED:A collective phyllome structure (PO:0025023) that includes as parts the corolla (PO:0009059) and/or the calyx (PO:0009060); or one or more tepals (PO:0009033).

A collective tepal structure is_a perianth. Make it explicit by listing the options "It could include both the corolla and calyx, one of them alone, or the tepals by themselves.

Discussion about whether or not the perianth should be defined on the basis of a perfect flower. We could write the description based on a "perfect or complete perianth", but no one uses those terms. Consensus was that it was not necessary in this case, since perianth is a widely used botanical term.

corolla and petal

  • corolla (PO:0009059):A collective phyllome structure composed of two or more petals.
    • A collective phyllome structure (PO:0025023) composed of one or more petals (PO:0009032), which comprises the inner whorl of non-fertile organs and surrounds the androecium (PO:0009061) and/or gynoecium (PO:0009062).

what if there is no calyx?, Is it still the inner whorl?- look at example form Betulaceae or Fagaceae. In some cases, they are distinguished on the basis of different color.

Don't need the parentheses, it is grammatically correct to say "one or more petals"

In other cases such as the e.g. Weinmannia from the Cunoniaceae, there are only sepals, forming the calyx.

  • 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).

What makes a petal: position, color, many exceptions

Revised def'n: A phyllome (PO:0006001) that is part of the corolla (PO:0009059), that is usually colored (not green).

Add comment that these definitions are based on the complete flower, which has all four whorls. In many species, and in mutants one or more of the whorls are missing. Functions in attraction to pollinators. A "perfect" flower has both stamens and carpels, and may be described as "bisexual" or "hermaphroditic".

Do we need to add a terms: for the

  • complete flower: A flower having all four floral parts: sepals, petals, stamens, and carpels. (Raven 5th edition)
  • perfect flower: A flower having both stamens and carpels, and may be described as "bisexual" or "hermaphroditic".

calyx and sepal

  • 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 sepals (PO:0009031), and comprises the outer whorl of non-fertile floral organs (PO:0025395).

Add comment that these definitions are based on the perfect flower, which has all four whorls. In many species, and in mutants one or more of the whorls are missing

  • 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].
    • A phyllome (PO:0006001) that is usually green, and is part of the calyx (PO:0009060).

collective tepal structure, tepal and fused CTS

  • collective tepal structure (PO:0025021): A perianth (PO:0009058) consisting of two or more tepals (PO:0009033).
    • REVISED: A perianth (PO:0009058) consisting of one or more tepals (PO:0009033). Comment: This structure is analogous to the whorls like corolla

Could it be only 1?

Yes, we decided that it was ok to define it as having one or more- and it is consistent with the other 2 collective structure, the corolla and calyx.


  • 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]
    • REVISED: 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).

Cannot say all parts as that include molecules etc, maybe should say "cardinal parts';

Revised def'n: A phyllome (PO:0006001) that is part of a perianth (PO:0009058) where it is not possible to distinguish between the petals (PO:0009032) and sepals (PO:0009031). Explain in comments: There is no differentiation between the petals and the sepals. (Is this true?)

fused collective tepal structure

  • 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. In subset Musa
  • REVISED: fused collective tepal structure (PO:0025138): A collective tepal structure (PO:0025021) in which at least two tepals (PO:0025137) are fused (PATO:0000642).
    • Comment:The fused collective tepal structure (PO:0025138) includes as parts two or more fused tepals (PO:0025137) and may also include one or more free tepal(s) (PO:0025136), which are unfused.
      • Moved comment about Musa to XXXX term, made free tepal part of collective tepal structure; added DBXref to PATO

Note: in this case there has to be more than 1, but there was an objection to saying that it can also include free tepals. So, we will make the free petal or free tepal be part of the collective tepal structure (does this work?, maybe we have to call it a fused perianth.)

We will need to introduce a new relation which will specify that the free tepal/sepal have to occur connected to the FCTS.

BS: Important question: Is the free petal actually fused at the bottom or is it a separate structure? If it was then it could be part of the FCTS.

We will need to add a new relation to convey a relationship that the free petal and the FCTS are connected. One problem is that we cannot make a free petal part of the CTS, as it is defined now.

We will look in the FMA for an appropriate relation that we could include.

Also: Ontobee Relations, includes FMA. Could we use: connected_to?

Need to have a relation that confers the relationship between the fused CTS and the free petal.


  • fused tepal (PO:0025137): A tepal (PO:0009033) that is fused to another tepal (PO:0009033).
    • REVISED:A tepal (PO:0009033) that is part of a fused collective tepal structure (PO:0025138) and is fused (PATO:0000642) to at least one other tepal.
      • added DBXref to PATO
  • free tepal (PO:0025136): A tepal that is separate from all other tepals
    • Revised:A tepal (PO:0009033) that is part of a collective tepal structure (PO:0025021), along with a fused collective tepal structure (PO:0025138), but is separate from (PATO:0001505) the other tepals.

File:Perianth parts.png

New terms needed:

  • fused perianth:
  • fused corolla: - parent to calyptra corolla (PO:0025330): A corolla (PO:0009059) that is composed of fused petals (PO:0009032).
  • fused calyx: - parent to calyptra calyx (PO:0025329):
  • fused petal-

part of the corolla spur (PO:0025512): A collective organ part structure (PO:0025269) that is a slender, hollow extension of a corolla and has as parts segments of two more fused petals.


  • fused sepal
  • free petal: A petal (PO:0009032) that is part of a perianth (PO:xxxxx) where some of the parts(xxx) are fused. [source: POC:cooperl]

rather than 'fused' use "connate": two or more of the same whorl are fused

adnate: two or more structures of the different whorls are fused

Question about epicalyx

  • epicalyx (PO:00090630): A collective phyllome structure (PO:0025023) composed of two or more phyllomes immediately outside the calyx (PO:0009060). [source: POC:curators]

Do we need a new term for epicalyx bract? - What are the individual members of the epicalyx; they are bracts.

Existing term: flower bract (PO:0009034): A bract that subtends a perianth that is part of a flower. [source: POC:curators]

Add epicalyx bract as an exact synonym?, or make a new child of flower bract . Not every flower bract is part of an epicalyx

Example from MAG: In the Trocodondraceae, the perianth is completely lacking, but they have little bracts subtending the reproductive structure.

Decided that we needed to add a new term:

epicalyx bract (new PO:0025577): A flower bract (PO:0009034) that is part of the epicalyx (PO:0009063). It will be sibling to the existing terms lemma and palea.

collective tepal structure, tepal and fused CTS

Continued from POC_Conf._Call_6-4-13:

Comment: This structure is a perianth (PO:0009058) where there is no differentiation between calyx (PO:0009060) and corolla (PO:0009059).

  • tepal (PO:0009033): A phyllome (PO:0006001) that is part of a perianth (PO:0009058) where it is not possible to distinguish between the petals (PO:0009032) and sepals (PO:0009031).
    • Comment: There is no differentiation between the petals (PO:0009032) and the sepals (PO:0009031) in color, placement, and size (e.g. some species of Magnolia).

fused collective tepal structure

Comment: none

  • fused tepal (PO:0025137): REVISED: A tepal (PO:0009033) that is part of a fused collective tepal structure (PO:0025138) in which it is fused to at least one other tepal.

Comment: none

  • free tepal (PO:0025136): A tepal (PO:0009033) that is part of a collective tepal structure (PO:0025021), along with a fused collective tepal structure (PO:0025138), but is separate from (PATO:0001505) the other tepals.


    • There currently is no special relation here to indicate that the free tepal must occur along with the fused structure, so for now, we added an explanatory comment
    • revised comment: A free tepal (PO:0025136) only occurs in a perianth (PO:0009058) that contains a fused collective tepal structure (PO:0025138). If you are describing a tepal (PO:0025137) that is part of a perianth (PO:0009058) where none of the tepals (PO:0009033) are fused, you should use tepal.


File: Tepal structures.png

Upcoming meetings and Presentations 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

Next meeting scheduled for Tuesday, June 11th, 2013 at 10am Pacific/1pm Eastern

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