Difference between revisions of "POC Conf. Call 7-2-13"
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- Should we set up a webex meeting with them? Dennis said he may be able to meet when in London, he knows Matt Pacey. | - Should we set up a webex meeting with them? Dennis said he may be able to meet when in London, he knows Matt Pacey. | ||
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| + | =Upcoming meetings and Presentations 2013:= | ||
==MONOCOTS V Meeting at NYBG, July 7th - 13th, 2013== | ==MONOCOTS V Meeting at NYBG, July 7th - 13th, 2013== | ||
Revision as of 21:11, 1 July 2013
POC meeting, Webex Conference Call; Date: Tuesday July 2nd, 2013 10am PST/1pm EST
In attendance: Absent:
Items for discussion:
- please see the Items_for_future_meetings page, will be moved here before the meeting
Update on Image analysis: AISO and the Image Annotation DB
From Justin Preece:
- 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.
Upcoming meetings and Presentations 2013:
MONOCOTS V Meeting at NYBG, July 7th - 13th, 2013
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
- 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
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
