POC Conf. Call 6-25-13

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

In attendance: Absent:

Update on Image analysis: AISO and the Image Annotation DB

• Laura Moore 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!
• I have begun expanding AISO to allow access to multiple ontologies, and to make ontology data available offline, when desired.
• Pankaj and I 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.

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.

Flower development stage (PO:0021004) and subclasses

Put in links to trackers, if they exist and open new ones if needed. gdoc

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).

• • 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).

• • 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.

• • 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.

• • 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 new is_a and part_of relationships for floral organ development stage (PO:0007600):

is_a - plant organ development stage (PO:0025339)

part_of - flower development stage (PO:0021004)

Current and revised definition of floral organ development stage (PO:0007600):

3 floral organ development stage (PO:0007600): Stages of development of floral organs defined by characteristic morphological, structural, histological or other visible features.

Revised 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)

• is_a collective phyllome structure development stage (newPO:0025578): A collective plant organ stucture development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023)

• part_of floral organ development stage

• • 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).

• is_a phyllome development stage (newPO:0025579): A plant organ development stage (PO:0025339) that has aprimary 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).

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