POC Conf. Call 6-25-13

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POC meeting, Webex Conference Call; Date: Tuesday June 25th, 2013 10am PST/1pm EST

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

Absent:Justin Preece (OSU)

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=76067222&rKey=14a3342a493b5b36

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=76067222&rKey=ae02e0a9148c9c81


Translations for next Release

We have prepared a Google doc. Ale has added all the new Spanish translations. We will continue to add to this list as we go along.


Flower development stage (PO:0021004) and subclasses

Link to spreadsheet: gdoc

Current and revised definitions for flower development stages: Propose to remove the numbers in front of all the child terms

  • Flower development stage (PO:0021004): A reproductive shoot system development stage (PO:0025530) that has as primary participant a flower (PO:0009046). [source: POC:curators]

Revised def'n: Flower development stage (PO:0021004): A reproductive shoot system development stage (PO:0025530) which begins with the onset of the flower meristem visible stage (PO:0007601) and ends after the post anthesis stage (PO:0007617).

    • 1 flower meristem visible stage (PO:0007601): Stage of flower development marked by the emergence of the floral meristem on the flank of the inflorescence meristem.

Revised def'n: 1-flower meristem visible stage (PO:0007601): A flower development stage (PO:0007615) marked by the emergence of the flower meristem (PO:0000229) on the flank of the apical meristem (PO:0020144).

  • proposed def'n: flower meristem visible stage (PO:0007601): A flower development stage (PO:0007615) marked by the emergence of the flower meristem (PO:0000229) from a portion of meristem tissue (PO:0009013).

Proposed that we add the flank statement to the comment.

    • 2 flower meristem notched stage (PO:0007602):Stage of floral development that begins when the floral meristem becomes demarcated from the inflorescence meristem by a slight indentation. [source: POC:curators]

Revised def'n: 2-flower meristem notched stage (PO:0007602): A flower development stage (PO:0007615) that begins when the flower meristem (PO:0000229) becomes separated from the apical meristem (PO:0020144) by a slight indentation.

  • proposed def'n 1: flower meristem notched stage (PO:0007602): A flower development stage (PO:0007615) that begins when the flower meristem (PO:0000229) transitions into a floral structure primordium (PO:0025477).
  • proposed def'n 2: flower meristem notched stage (PO:0007602): A flower development stage (PO:0007615) that begins when the flower meristem (PO:0000229) becomes separated from a portion of meristem tissue (PO:0009013) by a slight indentation.

proposed that we rename the term to get rid of the notched term. One way to do this would be to add a comment that states that the initiation of this stage is indicated by a slight indentation.

    • 4 anthesis stage (PO:0007616): The phase of a flower when pollen is presented and/or the stigma is receptive. [source: APweb:Glossary]

Revised def'n: 3-anthesis stage (PO:0007616): A flower development stage (PO:0007615) when pollen (PO:0025281) is presented and/or the stigma (PO:0009073) is receptive.

  • proposed def'n: anthesis stage (PO:0007616): A flower development stage (PO:0007615) that begins when pollen (PO:0025281) is presented and/or the stigma (PO:0009073) is receptive and ends with pollination (GO:0009856).

Should think about the use of the word presented. May add comment stating that this usually occurs when the flower is open.

    • 5 post anthesis stage (PO:0007617): The phase of a flower after the pollen is presented and/or the stigma is receptive. [source: POC:curators]

Revised def'n: 4-post anthesis stage (PO:0007617): A flower development stage (PO:0007615) that occurs after the anthesis stage (PO:0007616).

proposed def'n: post anthesis stage (PO:0007617): A flower development stage (PO:0007615) that occurs after the anthesis stage (PO:0007616) and lasts until flower morphogenesis is complete (GO:0048439).

Flowers snap shot.jpg


floral organ development stage (PO:0007600):

is_a plant organ development stage (PO:0025339); part_of flower development stage (PO:0021004)

Proposed to not use the part_of relationship and use 2 is_a relationships for the time being. The thought process behind this is that by using part_of it infers that floral organ development is a sub stage of flower development meaning that flower development is not a "whole" stage because it is made up of floral organ development.

Current Name and def'n: 3 flower organ development stage (PO:0007600): Stages of development of floral organs defined by characteristic morphological, structural, histological or other visible features.

Revised name and def'n: floral organ development stage (PO:0007600): A plant organ development stage (PO:0025339) that has as primary participant a floral organ (PO:0025395).

new relations, current definitions and revised definitions for subclasses of floral organ development stage (PO:0007600): these were all children of flower organ development stage (PO:0007600).


Made new parent term: collective phyllome structure development stage (new PO:0025578): A collective plant organ structure development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023).

* Made these part_of floral organ development stage, need to work on the definitions....

    • androecium development stage (PO:0007605): Stages of development of the androecium defined by characteristic morphological, structural, histological or other visible features.

Revised def'n: A collective phyllome structure development stage (PO:0025578) that has as a primary participant an androecium (PO:0009061).


    • calyx development stage (PO:0007603):Stages of development of the calyx defined by characteristic morphological, structural, histological or other visible features.

Revised def'n: A collective phyllome structure development stage (PO:0025578) that has as a primary participant a calyx (PO:0009060).


    • corolla development stage (PO:0007604): Stages of development of the corolla defined by characteristic morphological, structural, histological or other visible features.

Revised def'n: A collective phyllome structure development stage (PO:0025578) that has as a primary participant a corolla (PO:0009059).


    • gynoecium development stage (PO:0007606): Stages of development of the gynoecium defined by characteristic morphological, structural, histological or other visible features.

Revised def'n: A collective phyllome structure development stage (PO:0025578) that has a primary participant a gynoecium (PO:0009062).

Collective phyllome snap shot.jpg

New parent term for the phyllome development (new PO:0025579) terms:

phyllome development stage (new PO:0025579): A plant organ development stage (PO:0025339) that has a primary participant a phyllome (PO:0025023)

  • part_of floral organ development stage
    • lemma development stage (PO:0001047):Stages of development of the lemma defined by characteristic morphological, structural, histological or other visible features.

Revised def'n: A phyllome development stage (PO:0025579) that has as a primary participant a lemma (PO:0009037).

    • lodicule development stage (PO:0001049):Stages of development of the lodicule defined by characteristic morphological, structural, histological or other visible features.

Revised def'n: A phyllome development stage (PO:0025579) that has as a primary participant a lodicule (PO:0009036).

    • palea development stage (PO:0001048): Stages of development of the palea defined by characteristic morphological, structural, histological or other visible features.

Revised def'n: A phyllome development stage (PO:0025579) that has as a primary participant a palea (PO:0009038).

  • moved leaf development (PO:0001050) to be subclass of new term, will be adding flower bract development (PO:000XXXX)

Phyllome snap shot.jpg


GO flower development terms and definitions:

flower development (GO:0009908): The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem.


Part_of Children:

floral meristem growth (GO:0010451): The increase in size or mass of a floral meristem, a population of undifferentiated cells in a plant that gives rise to a flower.

floral meristem determinacy (GO:0010582): The process in which a floral meristem becomes determinate (i.e. ceases to produce lateral organs and may or may not terminally differentiate).

floral organ development (GO:0048437): The process whose specific outcome is the progression of the floral organ over time, from its formation to the mature structure.

floral whorl development (GO:0048438): The process whose specific outcome is the progression of a floral whorl over time, from its formation to the mature structure. A floral whorl is a circular arrangement of parts of a flower arising from a stem of a plant.

flower morphogenesis (GO:0048439): The process in which the anatomical structures of the flower are generated and organized.

nectary development (GO:0010254): The process whose specific outcome is the progression of the floral nectaries over time, from its formation to the mature structure.

perianth development (GO:0090428): The process whose specific outcome is the progression of the perianth over time, from its formation to the mature structure. The perianth is a collective phyllome structure composed of two or more petals, sepals, or tepals.

specification of floral organ number (GO:0048833): Any process that modulates the number of floral organs formed in a floral whorl.


Is_a Children:

regulation of flower development (GO:0009909): Any process that modulates the frequency, rate or extent of flower development.

negative regulation of flower development (GO:0009910): Any process that stops, prevents, or reduces the frequency, rate or extent of flower development.

positive regulation of flower development (GO:0009911): Any process that activates or increases the frequency, rate or extent of flower development.

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

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

Botanical Society Meeting July 27-31st New Orleans

BSA 2013

- MAG will present the work she has been doing with the images and slides CUPAC- The Cornell University Plant Anatomy Collection: a web-based tool for the Plant Sciences teachers and researchers

- BA will present a poster on his work: New evidence for the radiation of basal Cupressaceae

Next meeting scheduled for Tuesday, July 2nd, 2013 at 10am Pacific/1pm Eastern

BS probably will absent July 2nd, July 9th MAG, DWS, BS will away

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