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Joint Working Group on Observational Data Semantics: SONet, DataONE, Data Conservancy

by jones last modified Apr 19, 2011 02:55 PM


Provisional agenda subject to some revision upon discussion among group.



Provide an overview of progress on inter-related projects focused on observational data semantics and advance co-development of observational data models, tools, and services across projects.

IMPORTANT: Survey and Background

  • Survey
    • Sorry this is so late.  However, if you have any time before the meeting, it would be great if you could fill out a quick (~15 minute survey) to gather information about your existing projects for background information.  The survey questions will also indicate what information we believe will be of great value for sharing as part of this Joint Working Group on Observational Data Models and Semantics.  Please take time to fill out the survey:
  • Use Cases
  • Report from prior JWG meeting
    • The JWG report has background on the previous JWG meeting in Cornell.


Monday, April 18, 2011

 9:00-9:10 Introductions
 9:10-9:30 Overview
Introduce Data Conservancy/DataONE and Joint Working Group; review original mission of SONet and update on JWG Ithaca meeting;  and provide overview of this meeting's goals  (20 mins; Schildhauer)
 9:30-10:30  Collaborating Projects Updates & Demonstrations; either brief live demos, screencasts or screenshots of products-- applications, schemas, result sets, etc. (15 mins each)
  • Semtools Semantics (Leinfelder/Jones)
  • O&M developments (Dibner via Simon Cox)
  • Data Conservancy Semantics (Lagoze-- delayed til afternoon)
  • DataONE Semantics (Vieglais/Horsburgh)
  • Phenoscape/EQ Semantics (Lapp)

10:30-10:45 Break
10:45-12:00 Progress Demonstrations (con't) (15 mins each)
  • BCO/DMO and ocean image Semantics (Maffei)
  • NSIDC Semantics (Duerr)
  • VSTO Semantics (Zednik/McGuinness/Fox)
  • HIS Semantics (Horsburgh)
  • SW Darwin Core (?Webb/Baskauf,delayed til tomorrow?)
12:00-1:30 Lunch

Session A: Observational data ontology co-development (Moderator: Mark Schildhauer); ~4 hrs

  • Product: 
    • Decide whether and how we can/should coordinate observational data ontology development across our projects?
    • If so, how would that be technically and procedurally facilitated? 
  • Details:
    • Are the components of observations and measurements (in our various observational data models) sufficient to model (any/most/some?) scientific data
    • OBO curated model versus autonomous communities (e.g. W3C LOD model)
    • Can we benefit from a shared corpus of:  Use Cases?  Code base?  Test data? Ontologies?
    • Identify tools to enable collaboration
    • Identify process for ontology submissions; reviews; revisions & versioning; formats & standards; citations;
3:15-3:30 Break
3:30-5:30 Session A: Observational data ontology co-development (cont)

  • Details (cont):
    • How enable sustained sharing of information regarding: implementation challenges; compatibility testing and cross-walks; capabilities/shortcomings of models, etc.
    • Are there specific (types of) ontologies that should be co-developed and shared?  Eg space, time, and units

Tuesday, April 19


Session B: Comparative Ontology review (Moderator: S. Bowers) ~4 hrs

  • Product: Identify relevant ontologies to be included in co-development activities, develop list of action items for ontology development
  • Details
    • Side-by-side comparisons of relevant ontologies
      • Identify areas of overlap and gaps
      • Identify dependencies
      • Identify Authority-- how are communities going to develop and adopt ontologies?
      • Identify structural differences: types of constructs used-- e.g. equivalence classes, class vs instance prevalence; object properties and other restrictions; reliance on natural language fields, etc.
    • Compare overlaps; deficiencies; structural differences; equivalence classes for:
      • OBOE-SBC
      • VSTO
      • SWEET
      • ENVO
      • PATO
      • PlantOntology (PO)
      • Trait Ontology (TO)
      • WaterML in O&M?
      • Semantic Darwin Core
      • Annotation Ontology (AO)
    • Need for "framework", process, and tools to enable collaboration (see Session A results)
    • Are there common pieces, strong design elements etc. that can be borrowed/shared among these?
    • How "compatible" are these?  Can we mix & match?
    • How will we deal with integrating dispare and/or complementary ontologies?-- multiple namespace references, or need for fully integrated "monolithic" ontology
10:30-10:45 Break
10:45-12:00 Session B: Comparative Ontology review (continued)
12:00-1:15 Lunch

Session B: Comparative Ontology review (Moderator: S. Bowers) (cont 1 hr more if needed)

  • Product: Identify relevant ontologies to be included in co-development activities, develop list of action items for ontology development

Session C: Creating and exchanging annotations to observational data (Moderator: M. Jones) ~3 hrs
  • Product: Identify shared mechanisms for binding semantics to raw data, and for storing, retrieving, and interpreting data via observational data semantics
  • Questions to be addressed:
    • How will/are observational data semantics (class/properties) used to describe or represent data relevant to our projects?
    • Is there a need for a standard, cross-domain approach for binding observational semantics to raw data?
      • If so, what are the technical requirements of an interchange format?
    • Is there a need for a standard, cross-domain approach for exchanging observational data?
      • If so, what are the technical requirements of an interchange format?
      • At what level(s) should observational data be exchanged? (E.g., concept descriptions, summaries, actual data?)
      • What information should be included in an exchange format (e.g., metadata about collector, ownership, quality?)
    • Would a semantics-based, common query language or API be beneficial for interoperability?
      • If so, what are the requirements of such a language or interface?
    • Details:
    • Are data being annotated? If so, using what annotation languages?
      • Are SPARQL "endpoints" used for providing access to observational data? Is this enough (e.g., what about sensor data?)
      • What about LOD?
      • Is the new W3C effort (AO) on developing an Annotation Ontology appropriate/sufficient for this task?
      • Are there other current or upcoming exchange standards that should be explored?
      • What current APIs or access mechanisms are being provided for retrieving data based on observational semantics?

3:15-3:30 Break
3:30-5:30 Session C: Creating and exchanging semantic annotations to observational data (continued)

Wednesday, April 20

Session C: Creating and exchanging semantic annotations to observational data (continued if needed)

Other topics  (time permitting) or Future topics--
  • Session D:  Semantic capabilities--Examples of semantic queries enabled by observational data model
    • nesting constructs in data (spatial containment; experimental plot design)
    • measurements on same instances
    • primary measurements vs associated or inferred measurements 
  • Session E: Ontology Design Patterns
    • Ontology design patterns (especially dealing with space/time and other aspects of "context"; recursive construction of "entities"; best practices with OWL or RDF-- e.g. complete definitions, equivalence classes) for modeling observational data
  • Session F: Managing complexity for scientist-users
    • How to enable scientists to semantically enhance/annotate and query data in these frameworks
10:00-10:30 Break; mingle in lounge with NCEAS Postdoctoral associates

Session G: Open Discussion, conclusions, and action items;

Conclusion of general meeting

12:00-1:00 Lunch

Session H: SONet Leaders' meeting

  • Plan for next working groups; way forward; products; new partnerships and opportunities


Shawn Bowers 

Corinna Gries 

Philip Dibner 

Deborah McGuinness 

Matthew B. Jones 

Mark Schildhauer 

Dave Vieglais 

Carl Lagoze 

Hilmar Lapp 

Jeff Horsburgh 

Margaret O'Brien 

Andrew Maffei

Ruth Duerr

Stephan Zednik

Ben Leinfelder

Chris Jones

Invited but unable to attend

Josh Madin - not attending

Steve Kelling  - not attending

Luis Bermudez   - not attending

Chris Mungall - not attending-- at European mtg

Cam Webb - not attending-- in Indonesian forest

Peter Fox - not attending

David Tarboton - not attending

Simon Cox not attending

Peter McCartney - not attending

Cyndy Chandler not attending

Mark Parsons not attending

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