POC Conf. Call 7-2-13

POC meeting, Webex Conference Call; Date: Tuesday July 2nd, 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), Barry Smith

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=76268782&rKey=5e430e96a168fcb9

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=76268782&rKey=7d517838d1c266e7

Items for discussion:

- please see the Items_for_future_meetings page, will be moved here before the meeting

Flower development stage (PO:0021004) and subclasses

Continued from the POC Conf call 6-25-13

Should add as comment to all flower development terms that they should not be used in reference to whole plant development

Link to spreadsheet: gdoc

Added new relationship; developmentally_preceded_by to show the order of the development stages.

Should avoid using developmentally_preceded by, instead we should use preceded_by (developmentally_preceded_by may be too specific, could have stages that are no development)

Current and revised definitions for flower development stages:

• 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).

We should add a vegetative to reproductive transition stage because of its importance in plants. This should include the inflorescence meristem and flower meristem transition (we will need to work on the name for this)

flower formation stage (newPO:0025585)

Proposed that we change the name to floral organ formation stage - proposed synonym flower morphogenesis

Proposed new child of flower development stage

Proposed definition: A flower development stage (PO:0007615) which begins with the floral organ meristem development stage (PO:0007601) and ends with the onset of the flowering stage (PO:0025586).

Proposed children of flower formation stage

• 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.
  • Proposed name and def'n: floral organ meristem development stage (PO:0007601): A flower formation stage (PO:0025585) which begins with the development of the floral organ meristem (PO:0000229) from a portion of meristem tissue (PO:0009013) and ends with the begining of the floral organ primordium development stage (PO:0007602).

• 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]
  • proposed new name and def'n:floral organ primordium development stage (PO:0007602): A flower formation stage (PO:0025585) which begins with the appearance of the floral organ primordium (PO:0025477) and ends with the beginning of the floral organ development stage (PO:0007600).

• • Floral orgran primordium stage should already have taken part in the process of floral organ meristem development stage. In other words you have an organ follows a primordium. We need to figure out a different name for floral organ meristem development stage (PO:0007601)

• may be from existing inflorescence meristem or from a vegetative meristem before meristem visible stage

floral structure primordium (PO:0025477): def'n: A primordium (PO:0025127) that is committed to the development of a plant structure that is part of a flower (PO:0009046), such as a floral organ (PO:0025395), gynoecium (PO:0009062), or anther (PO:0009066) and is part of a reproductive shoot apex (PO:0025222). [source: POC:curators]. Needs to be revised to meet the new floral organ definition.

• See link to images in PlosOne

For DWS - He needs a couple of examples of GO terms related to PO terms

We need to build a parallel hierarchy for the development of conifer cones

flowering stage (PO:0025586)

Proposed new child of flower development stage

proposed definition: A flower development stage (PO:0007615) during which a single flower (PO:0009046) participates in the process of flowering (GO:0010228).

Proposed children of flowering stage:

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

• • proposed new name and 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).

• • 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 name and 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).

The relations make sense, good idea to parallel with fruit morphogenesis

floral organ development stage (PO:0007600):

change name to floral organ differentiation stage'

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

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).

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.

Update on Image analysis: AISO and the Image Annotation DB

From Justin Preece:

• LM has segmented and annotated two dozen images provided by DWS. We will be using these as a test set for linking to and displaying from term detail pages on the PO site.
• Nikhil finished a basic version of an annotated image data import script. We now have versions of DWS' images, annotated w/ whole-image keywords, inserted in our new Annotated Image DB. FYI: Nikhil has left the lab for a summer internship and a subsequent full-time software job in San Francisco. Thanks for your efforts, Nikhil!
• JP has begun expanding AISO to allow access to multiple ontologies, and to make ontology data available offline, when desired.
• Pankaj and JP are collaborating w/ iPlant to integrate AISO features and data structures into iPlant Bisque. We held a conf call on this subject w/ iPlant personnel 2-3 wks ago. Next step: work w/ Kris @ iPlant to run a test insertion of existing plant images and accompanying metadata.

NOTE: All of this work will be dormant for roughly the next four weeks while I attend to another project deadline.

-JP will share the folders with the rest of the group, so we all can look at the segmented images.

Image-Net Site

This is part of the WordNet family of computerized lexica. Image-Net is a computerized lexicon with images.

http://www.image-net.org/synset?wnid=n00017222

Collaboration with New Phytologist

We were contacted by Sarah Lennon from New Phytologist:

"We are undertaking a content enrichment project, which I believe is the first of its kind for a plant science journal. The New Phytologist content enrichment project will involve the creation of a fixed vocabulary to link New Phytologist content to other resources and to provide an enhanced experience for the reader. "

"WE are interested in using PO terms as part of our controlled vocabulary/knowledge model. We aim to build a collection of taxonomies/ontologies/lists which accurately classifies our content and which we will then use to this to make our content even more valuable to readers. The exact delivery method for this is yet to be determined, but we are working with our publisher, Wiley Blackwell, to find the best way that will benefit plant scientists."

-Her colleagues at Wiley Blackwell and requested a copy of the ontology data. I think they just need the data of the ontology itself, and if it could be made available in SKOS format that would be the most helpful, but any other xml/csv type of structure would also be great.

Sent to them: "The latest development version will always be available from this link: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OWL_format/plant_ontology.owl

-"Dr Helen Ougham is a colleague on the project and we have some great ideas for the future. In collaboration with Wiley Blackwell we have been using Plant Ontology terms in some custom software to classify New Phytologist content and the results so far are interesting. Helen is a New Phytologist Co-Editor and has great expertise in both bioinformatics and plant science. Helen is currently assessing the output of the custom software.

We would very much like to discuss the results of Helen's assessment with you and revisit the idea of potential collaboration. Ideally it would be great to meet in person, but a virtual meeting would also be good."

- Should we set up a webex meeting with them? Dennis said he may be able to meet when in London, he knows Matt Pacey.

-PJ will discuss this with DWS

Upcoming meetings and Presentations 2013:

MONOCOTS V Meeting at NYBG, July 7th - 13th, 2013

MONOCOTS V:

5th International Conference on Comparative Biology of Monocotyledons Sunday, July 07, 2013 - Saturday, July 13, 2013

The New York Botanical Garden & Fordham University

ICBO 2013, Concordia University, Montreal, Quebec July 6th - 10th 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)

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 talk on his work: New evidence for the radiation of basal Cupressaceae

- Suggestion that BA, DWS, MAG could present a poster on the PO or a small workshop. BA will follow up with DWS.

Next meeting scheduled for Tuesday, July 23rd, 2013 at 10am Pacific/1pm Eastern

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