Difference between revisions of "POC Conf. Call 5-28-13"
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POC meeting, Webex Conference Call; Date: Tuesday May 28th, 2013 10am PST/1pm EST | POC meeting, Webex Conference Call; Date: Tuesday May 28th, 2013 10am PST/1pm EST | ||
| − | In attendance: | + | In attendance:''Laurel Cooper (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell)'' |
| − | Absent: | + | |
| + | Absent: ''Barry Smith (University at Buffalo, NY)'' | ||
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*fused collective tepal structure (PO:0025138): A collective tepal structure that has as parts at least two fused tepals. | *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. | + | ** 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.'' | ||
| − | The | + | 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. '' | |
| − | + | [http://www.cropontology.org/terms/CO_325:0000520/ 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: [https://sourceforge.net/tracker/index.php?func=detail&aid=3614109&group_id=76834&atid=835555 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 [http://www.uq.edu.au/_School_Science_Lessons/51.7.3.GIF 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 | |
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| − | + | 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'. '' | |
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| − | + | ''Suggestion to add 'perianth phyllome' to classify the petals, sepals and tepals. But it was decided that would be redundant.'' | |
=Upcoming meetings and Presentations 2013:= | =Upcoming meetings and Presentations 2013:= | ||
Latest revision as of 18:18, 11 June 2013
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.
* 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.
Upcoming meetings and Presentations 2013:
1st International Workshop on Semantics for Biodiversity (S4BIODIV), Montpellier, 26-30 May 2013
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
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
- MAG is planning to present the work she has been doing with the images and slides, will circulate the abstract
