POC Conf. Call 2-19-13

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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.


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.

File:shoot sytem development stages.jpg

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

Phenotype Ontology RCN

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.


  1. To educate members of the PRO, PO and GO communities concerning developments in each of the three ontologies, with a view to enhanced coordination
  2. To identify potentially fruitful applications which such enhanced coordination might bring
  3. To enhance the Protein Ontology treatment of plant-related proteins
  4. To address coordination issues between the GO and PO, for example as concerns treatment of development stages
  5. 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


  • 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.


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

BSA 2013

- MAG is planning to present the work she has been doing with the images and slides, will circulate the abstract

Next meeting scheduled for Tuesday, Feb 26th, 2013 at 10am Pacific/1pm Eastern

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