POC Conf. Call 2-19-13
POC meeting, Webex Conference Call; Date: Tuesday Feb 19th, 2013 10am PST/1pm EST
In attendance: Laurel Cooper (OSU), Dennis W Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU).
Absent: Pankaj Jaiswal (OSU)
Defining the plant structure development stages
On last week's conf call Barry said we should not be defining the plant structure development stages as a stage that has as a primary participant a plant structure and also adding the has_participant (or participates_in) relation as well. That makes sense as it does seem to be somewhat circular,and if the definitions are ever formalized, then it would be redundant. The problem is that we already have a whole bunch of them defined this way, besides the new ones added for the shoot system.
Examples already in the Plant Ontology:
- collective plant organ structure development stage (PO:0025338)
- whole plant development stage (PO:0007033)
- fruit development stage (PO:0001002) (currently no has_participant relation to fruit)
- plant organ development stage (PO:0025339)
- plant tissue development stage (PO:0025423)
- seed development stage (PO:0001170)
- trichome development stage (PO:0025368)
- gametophyte development stage (PO:0028003)
- sporophyte development stage (PO:0028002)
For the terms I have recently added, I think the best solution is to change the definitions. These include most children of the shoot system development stage (new PO:0025527). I think I will to have to go back and revise the others at some point so that they are consistent.
shoot system development stage
- Current def'n: shoot system development stage (new PO:0025527): A plant structure development stage (PO:0009012) that has as primary participant a shoot system (PO:0009006).
Current relation: shoot system (PO:0009006) participates_in shoot system development stage
Revised relation: shoot system (PO:0009006): shoot system development stage has_participant shoot system
This should be shoot system development stage has_participant shoot system since the shoot system can exist outside of the shoot system development stage
What about the development of vegetative shoots?? Also we decided that the shoot system development stage begins with the development of the plant organs and ends when the plant undergoes senescence and or death.
Proposed Revised def'n:
- shoot system development stage (new PO:0025527): A plant structure development stage (PO:0009012) that begins with the plant organ development stage (PO:0025339) and ends with either gametophyte senescent stage (PO:0025343) or sporophyte senescent stage (sporophyte senescent stage) or death.
Revised relation: shoot system (PO:0009006): shoot system development stage has_participant shoot system.
Notes:
Need to revise the definition of the shoot system to include all meristems in the shoot system, not just the the shoot apical meristems (axial and lateral as well).
current def'n:
- shoot system (PO:0009006): A collective plant organ structure (PO:0025007) that produces shoot apical meristems (PO:0020148) and the plant structures that arise from them.
The rest of the terms in this hierarchy have been moved back to the Items_for_future_meetings page
Image Annotations
Upcoming meetings and Presentations 2013:
Phenotype Ontology RCN Annual Summit Meeting, Feb. 25th - 27th, 2013, Durham, NC
The workshop and meeting will be held at the National Evolutionary Synthesis Center in Durham, NC, from Monday morning, February 25 through Wednesday noon, February 27th (you would arrive Sunday evening).
Overall goals: To introduce and establish communication and collaboration among scientists from different research backgrounds. The two primary themes: The use of text mining phenotypes and representing behavior in ontologies.
For more information: please contact Paula Mabee (pmabee@usd.edu)
Biocuration 2013 conference, Cambridge, 7-10th April 2013
submission deadline for abstracts for posters is Jan 31st.
website and registration are now open: Biocuration 2013
PRO-PO-GO meeting, May 15-16th 2013
Please see this page for more information: PRO-PO-GO_Meeting
Location: Buffalo, NY
Dates: May 15-16th, 2013.
Goals:
- To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
- To identify potentially fruitful applications which such enhanced coordination might bring
- To enhance the Protein Ontology treatment of plant-related proteins
- To address coordination issues between the GO and PO, for example as concerns treatment of development stages
- To further those aspects of CROP which relate to PRO and GO [this is assuming that PRO is included as one of the external ontologies in CROP]
Tentative participant list:
PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?
GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?
PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)
BS would like a list of who we would like to include in the meeting and whose costs can be covered by PO
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 dates: May 26-27, 2013
IMPORTANT DATES:
- Pre-submission inquiry deadline: February 24, 2013 (Abstract up to 500 words)
- Submission Deadline: March 4, 2013 (may be a little flexible)
- Notification: April 1, 2013
- Camera ready: April 15, 2013.
TOPICS:
Scientific themes of interest (include but are not limited to):
- sustainable agriculture
- plant
- health and habitat
- relationship between plant-pests/pathogens
- usages of plants by community
- biodiversity conservation
- ecosystems services
- quality of biodiversity data
Informatics technologies of interest (include but are not limited to):
- ontology applications
- knowledge engineering
- linked biodiversity data
- remote sensors
- mobile devices
- vizualization tools
- data mining
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)
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
