SONet 2nd Community Meeting: Agenda, June 7-9, 2009

Overall arrangement

Time: June 7 - June 9, 2010 9:00am - 5:00/5:30pm (depending on the progress)
      People are encouraged to assemble at the lounge@NCEAS at 8:45am.
Lunch time: generally 1 hour lunch time starting from 12:00pm
Break time: generally there is a 15-minute break in morning session and another one in afternoon session. The break time in the schedule is tentative.

Main themes

1. Review and update SONET's vision: framework and inter-operability challenges
2. Review and update the core conceptual OBOE model
3. Discuss the practical ways to incorporate domain knowledge
4. Report and discuss the current project progress
5. Discuss the future direction.

Outputs

1. Workable plans for the demo project
   (1) Define tasks (e.g., demo for O&M and OBOE exchange)
   (2) Define timelines  
   (3) Two concrete use-cases (e.g., with benchmark datasets and query sets)
2. SONET direction
   (1) Workable tasks for the period before next workgroup meeting
   (2) Plan for the next community meeting
   (3) Plan (refinement) for finishing NSF annual report
   (4) Plan for the Cornell Data Conservancy meeting
3. Decide the core model and the data annotation language
4. Design patterns (or practices) to incorporate domain knowledge to SONET core model

 Agenda

June 7, 2010, Monday

Focus: the big picture, the core conceptual model, and domain ontology.

1. SONET vision in combining different models, ontologies and data and updates
   Mark + Shawn, about 1hr

2. Introduction to the plant ontology
   Farshild, about 30m-1hr
   It is recommended to have information about
   (1) background (e.g., which group of people are using these, the origin of the ontology, etc.)
   (2) application domains (datasets) that are using this ontology.
   (3) the difficulties to finalize this ontology

-- break 15m (this break can be before 2, depending on the situation)

3. Introduction to the trait ontology
   Marie-Angelique, about 30m-1hr

   It is recommended to have information about
   (1) background (e.g., which group of people are using these, the origin of the ontology, etc.)
   (2) application domains (datasets) that are using this ontology.
   (3) the difficulties to finalize this ontology
  
-- 1-hr noon break around 12:00

Afternoon:
4. Introduction to SBC ontology
   Mark, about 30m-1hr

5. OBOE model changes
   Shawn, about 1hr

-- break 15m

6. Discussion:
   (1) How do the changes in the oboe core model affect your ontology building?
   (2) How to incorporate domain ontologies (plant and trait ontologies) with OBOE and use them well. Referencing SBC ontology,
   (3) Could any group either using plant ontology or trait ontology contribute to one of our use cases?

** Output:
(1) Design patterns (or practice guidelines) to create SONet domain models. e.g.,:
   (a). Conventions for naming classes, etc.
   (b). Conventions for organizing and naming ontologies.
   (c). Conventions for versioning ontologies.
   (d). How to "register" these with SONet.
(2) Two use cases for the demo project
   (a) SBC use case
   (b) One from plant/trait group???
(Note: if the time is not enough for all these discussions, we could move 1 hour to June 8 to wrap-up the discussion results. ) 

June 8, 2010, Tuesday

1. Demo or introduction to Marie-Angelique's registry tool
   (MA, 15-20m)

2. OBOE and O&M: Conceptual differences (and similarity)
   (Mark, or Shawn, or Huiping, 30m)

-- break 15m

4. Discussion
(1) What do you want to see in the demo of the system?
(2) If the re-factored "OBOE" is adopted as the core conceptual model, what factors you want to see in the demo out of OBOE?

**Output: a workable plan for the project demo.

-- 1-hr noon break around 12:00

The afternoon activities would be partitioned to two groups:
Group 1: Mark, Shawn, Huiping
Discuss the following:
1. Paper algorithm and progress, and several technical difficulties
   (about 2 hrs)
2. Annual report (about 1.5 hrs) discussion
3. Revising the SONet "mission" and organization (move subgroups to
"themes/areas"?) and plan for organizing the next SONet "community" meeting (2hrs)
4. Plan for Cornell meeting
This afternoon will not be enough to finish all these tasks. So, one or two hours will be used on Wed. afternoon.

Group 2: MA, Farshid: flexible discussion.

June 9, 2010, Wednesday

1. Data Annotation Language: Key constraints.
   Shawn, 45m-1hr

2. How to do annotation to data
   (Ben, 30m)

3. Data materialization and querying using OBOE model
   (Huiping, 30m)

-- break 15m

4. Discussion:
   (1) What parts are hard to understand to domain scientists if they need to use this system?
   (2) What are the queries that domain scientists may pose to the system?
   (3) What are the “Killer applications” for an observational approach – in particular for data integration and analysis? 

-- 1-hr noon break around 12:00

Afternoon:
1. More wrap-up on the discussion results
2. Group 1: finish the tasks on the previous day
3. Meeting with Margaret.

** Output:
(1) Benchmark queries for domain scientists using plant, trait, SBC ontologies. This is the input for the demo projects.
(2) Finalize the annotation language

Participants

Farshid Ahrestani, Shawn Bowers, Huiping Cao, Marie-Angelique Laporte,  Ben Leinfelder, Margaret O'Brien, Mark Schildhauer