Semantic eScience Meeting October 21, 2011

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General Meeting Information


  • Status of eScience Projects
    • first as Deborah needs to be up campus by 12:30
  • Joanne Presentation on Ontology Evaluation followed by discussion


  • Deborah (needs to leave at 12:30)
  • Peter Fox
  • Joanne Luciano
  • Eric (needs to leave at 12:30) (remote)
  • I (Arun) will not be able to make it to the meeting as I will be interviewing this morning at NYC. Will follow up on the notes.
  • I (Rajashree) am in Boston for a job interview today, and I won't be able to come to

the meeting. Sorry for being so late to notify this to you. But these
past few weeks have been crazy. I'll meet you on Monday to give you an
update on my work. I met Eric last Thurs and discussed my Siren
implementation. Right now, I am looking into Virtuoso bif.

  • Stephan
  • Patrick
  • Le
  • Katie
  • Linyun
  • Han
  • Yu
  • Sapan
  • Naveen

Past Action Items

  • Create tickets at for problems to solve
  • HW & ER: problem populating the calendar given instrument and/or parameter
    • It seems older version of Virtuoso has a problem of inference working with multiple named graphs
    • Eric helped install Virtuoso 6.1.4 on escience, which promises to fix that bug
      • BCO-DMO and CEDAR data are being/have been loaded
  • SESF: By Friday, October 14: take a look at all d working groups at sesf. updating working group page. plan for the workin group, tasks, timeline
  • PW: plan meeting end of this month, production planning, timeline, who needs to go end of month, etc...
  • PW: sync up NEON trip via email

Action Items

  • (DONE) PF: Add Weijing to escience list (DONE - also added Sapan, Yu, Naveen)
  • (DONE) PW: Need heather Powell email address = Heather Powell
  • PW: Put up pictures from NESDAA Meeting - Ticket
  • NESDAA: Next Steps, look at different tasks for the projects, working groups
  • (DONE) DLM: Alvaro slides for LODSpeaKr
  • (DONE) PW: Eric on schedule for next meeting re time
  • PF & PW: ontology components and someone to work on them (very bottom) - Ticket
  • (DONE) PW: titan pad for notes on evaluation, how we're doing it, etc... TitanPad



  • NEON - Non-Specialist Use Case
    • Successful meeting in Boulder last week (10/12-10/14)
    • Heather Powel and Brian Wee from NEON
    • James Wilson from James Madison
    • Non-specialist Use Case development: making a lesson plan for upper-level high school or lower level undergrad.
    • Increase Narative
    • Actors
    • Information Modeling
    • Mockup of an implimentation interface
    • Use Case
    • Group cmap
    • Stephan's cmap
    • Connecting specialist vocabularies w/ non-specialist vocabularies
    • stream health is a focus (and everything (other than oceans and lakes - streams are moving) including the mississippi river) is a stream
  • Deborah is interested in keeping in touch with this project due to connection with other projects, same with SemantAqua
    • Ontology conversion fixed:
    • S2S Faceted Browse 2.0 Demo:
    • BCO-DMO Linked Data:
      • e.g., Linked Data for Person instance:
      • RDF Example:
      • BCO-DMO Template:
      • intended to look like:

^^ Please try all these links later (they are currently broken)

    • Bo Jin and Stephen McCaulife (undergrads) working on accessing triple store and displaying information much like what we do with the web site
    • Using Alvaro's LODSPeaKr (simple publishing kit for linked open data) for Linked Data (html or rdf)
      • (
    • Patrick, Le, and Eric going down next week
    • Virtuoso on escience for BCO-DMO, accessible now

  • VSTO
    • VSTO triple store from aquarius to escience, virtuoso
    • Calendar issue is now solved
    • Working with Le regarding VSTO look and feel with Cynthia
    • new testbed
    • COMP data being integrated
      • Need extensions to ontology
      • Focus should be on getting COMP data into VSTO
    • CSAC is also available, new scientist leading effort
      • Need extensions to ontology
  • SeSF
    • Joanne Presentation on Ontology Evaluation
    • Three testbeds
    • Six other areas of work
  • Stephan "the kid" Zednik - next visit sometime in November
  • Patrick next visit to Boulder November 14-18

Joanne's Presentation - Ontology Evaluation

MITRE budgets funds for internal projects, ontology evaluation work part of that.

Separating what you are evaluating from how you evaluate it.

  • Recast the problem into its components
  • evaluate components using objective metrics

Three criteria for evaluation - slide 8

  1. Correctness
  2. Completeness
  3. Utility

Additional 2

  1. Extensibility
  2. ???

Review is more of a correctness and binding to a specific language encoding

Three triangle approach

Modularity/Refactor/Extending would come out of evaluation (part of result)

Still need to develop discovery ontology and integration ontology

First need to break apart the ontology, components, and determine where we want to evaluate first.

  • time
  • facets
  • datasets
  • application integration
  • discovery

four performance categories (use cases) - in IEEE paper or Computers and Geosciences 2009

  • inventory search services
  • data access services
  • data product return
  • web service