Semantic eScience November 17, 2010 Meeting

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eScience Meeting Notes:

Meeting Page

  • http://tw.rpi.edu/web/theme/SemanticeScience/meeting/101117
  • http://twc.titanpad.com/35

Attendance

  • Patrick West
  • Evan Patton
  • Linyun Fu
  • Daniel Souza
  • Peter Fox
  • Cynthia (call in)
  • Eric
  • Stephan
  • Deborah (will be late)
  • Yu Chen
  • Joanne
  • Jim McCusker
  • Tim

Agenda

  • Action item updates
  • ESG immediate gateway install
  • VSTO push
  • AMIA Summit on Translational Bioinformatics: http://jointsummits2011.amia.org/tbi-2011-initial-call-proposals (Abstract-only submission)
  • SPAR Ontology Work Updates - http://tw.rpi.edu/web/idea/SPAREvaluation
  • SOMEONE contribute a research discussion topic (yes, this is Peter typing).

Action Items

  • Patrick: Setting up new page for AGU
  • PW: push new VSTO (software) version
  • PW: Invite Katie down for next eScience meeting to talk about publishing semantic information, knowledge provenance, semantic documents within the library system instead of within the lab. "Kathryn M. Dunn"
  • Eric: meetings of interest, Twitter hashtag for TW@AGU
  • Eric: Summarize SRO work from Joanne for research ontology wiki
  • Eric: Summarize RDF compression work
  • Eric: Working Group for VSTO updates
  • Eric: Add DoCO content to SPAREvaluation
  • EVERYONE attending AGU - visit the page and add your details, talk/poster, day, time, etc.
  • EVERYONE attending AGU - also if you are to/ intend to attend someone's talk/ poster session

Past Action Items

  • Peter: check on Eric's first action item regarding SeSF publication (DONE)
  • Patrick: set up page for AGU visits, acceptance (DONE)
  • (old?)PW: push new VSTO (software) version (Working on)
  • (old?)PW: install and play around with LAS, TDS, FTDS, THREDDS in next week
  • PW: email to escience list for ESG meeting Thursday at 3pm (Linyun (maybe a little late due to a class), Jay, Evan at least)
  • PW: Yu Chen, does he have all of his accounts set up? (DONE)
  • PW: AGU 2010 directory in svn (DONE)
  • PW: Invite Katie down for next eScience meeting to talk about publishing semantic information, knowledge provenance, semantic documents within the library system instead of within the lab. (Working On)
  • PW: rename node 569 in idea repository (DONE)
  • Eric: discuss with professors about SeSF publication (DONE)
  • Eric: set up wiki page for research ontology (research companions) (Working On)

Notes

AGUFM

  • AGUFM10 - http://tw.rpi.edu/portal/AGUFall10
  • AGUFM10 Participation page - http://tw.rpi.edu/portal/AGUFall10_Participation
  • AGUFM10 SVN repository - https://scm.escience.rpi.edu/svn/private/papers/agufm2010/

VSTO

  • new version is working on Patrick's machine
  • Will push to Ligo for testing
  • By end of this week will have new VSTO live on escience
  • This is on version 2.0 of the VSTO ontology (not modularized, with new time ontology but not new time instances
    • http://escience.rpi.edu/ontology/vsto/2/0/vsto_all.owl

ESG

  • Assigned Linyun and Jay work to do for ESG
  • Patrick summarizes faceted browse for ESG (can only find full data files to download)
  • Can also do THREDDS browsing in ESG portal. Again, can only pull full files
  • No constraint evaluation, projections, aggregation, server-side functions, etc...

THREDDS

  • Can add additional attribute information
  • Is more of a configuration for the datasets than a catalog
  • can not query over

What are we doing

  • Working on OPeNDAP integration for requirements above

http://earthsystemgrid.org/browse/browseCollections.htm
http://www.opendap.org
Hyrax = OPeNDAP server - comprises Front-End (OLFS) and Back-end (BES).

For return as RDF - look at SADI http://code.google.com/p/sadi/
Also consider BITMAT

Future Work

  • Returning the data as RDF, either XML or turtle
  • ingesting the data files and adding semantic information to a semantic store
  • instead of using THREDDS, which can not be queried against, using a triple store that users can query
  • Additional server-side function work
  • Ability to commit virtual datasets and have them available/published

ESG Architecture

http://tw.rpi.edu/portal/ESG-CET_Broad_Design

Research Ontology

  • Research Ontology : http://tw.rpi.edu/web/idea/ResearchOntology

VSTO Push

  • Current Ontology http://escience.rpi.edu/ontology/vsto/2/0/vsto_all.owl
  • Have different versions installed on a machine
    • Current one that we can play with
    • Version using SESDI
    • Version using BCO-DMO
    • Modularized
    • Time Instances
    • Using external triple store and using SPARQL endpoint
      • Related is the Triple Store evaluation and SPARQL endpoint evaluations
      • Related to the Reasoner evaluatioon
  • Eric discussing data science class project
    • Link to CEDAR time instances: http://escience.rpi.edu/ontology/cedar/