Semantic eScience Meeting July 13, 2012

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Welcome to TitanPad!

General Meeting Information

Agenda

  • Getting ready for ESIP
  • AGU abstracts due August 8th
  • Updates on Projects
    • ECOOP
    • BCO-DMO
    • VSTO
    • DCO
    • TAF
    • MetPetDB
  • What's everyone up to

Attendance

  • Deborah
  • Stephan
  • Marshall
  • Massimo
  • Patrick
  • Peter
  • Joanne
  • Le
  • Amruta (Titanpad)

Past Action Items

Action Items

  • PW: Conversation for meeting at ESIP
  • PW: Conversation for tabling at AGU
  • ALL: abstract submission ideas by the 27th of July
  • PW: Conversation for abstracts at AGU
  • PW,PF,CC: Conversation about URI "construction"
  • SZ: ontology version IRI, will share document
  • PW,DM: Deborah showing SemantAqua Monday morning at Seattle and Wednesday morning at ESIP keynote. Make sure they have access to aquarius.
    • Problem on aquarius, MDSA not running on aquarius,

Notes

ESIP

adam shephard and bob arko will be at esip. adam just joined bco-dmo at whoi working for cyndy chandler and arko is with r2r at lamont doherty.
cool - they want their uris to have meaning.. reminiscient of the paper "what's in a name" by bill woods ages ago....

  • http://tw.rpi.edu/web/event/ESIPFedSummer2012/Participation

possible dinner on wednesday, possible lunch wed or thurs.

AGU

  • http://tw.rpi.edu/web/event/AGU/FM/2012/Submissions
  • http://tw.rpi.edu/web/event/AGU/FM/2012/Participation
  • We want to have as many first authors to submit
  • Not everyone will be able to go this year
  • Someone who is going can present a paper/poster that you're first author on
  • We will have a table again this year
  • TW Abstract Process
    • Have abstract topics and targeted sessions determined by July 27th
    • Discuss/coordinate with group before submitting
    • Put abstract suggestions on http://tw.rpi.edu/web/event/AGU/FM/2012/Submissions
  • 47 informatics sessions ... WOW!!!
  • Maybe want to focus on Semantics and Provenance
  • Citizen Science submissions, potentially get started on the conversation this year and have more of a presence in future conferences

Projects

ECOOP

  • Previous titan pad, line 200, http://twc.titanpad.com/381
  • Working more on DPSIR
  • Meetings with different collaborators
  • Demo to be shown to larger group at some point?

(doodle poll to show the demo to the small group (days between 20/7 - 27/7 ) theme : A phone call with principals at their computers to view a project video and then discuss. The Eco-Op project is in collaboration with WHOI and RPI and seeks to improve the Ecosystem Assessment architecture of the NEFSC.)

  • ICES conference : http://www.ices.dk/iceswork/asc/2012/
    • ICES, submission deadline August 18th

 (which workshop is this going into? :  

The annual meeting between NOAA (USA), DFO (Canada) and the Institute of Marine Research (IMR) )
[agenda of that t meeting attached to the ECOOP mailing list, topic : annual meeting between DFO NOAA IMR]
    • will be submitting a Poster to the section "R" [Mapping and modelling of planktonic ecosystems for better monitoring and future projections of responses to global change ]

full session description : http://www.ices.dk/iceswork/asc/2012/themesessions/Session%20R.pdf,
Massimo will send around adraft

  • Implement provenance functions in Python Notebook (Deborah would like to stay up on plans - if there is a page to look at or a mailing list to get on, that is fine)
  • Diving into ISO 19115, group working on schema for this standard
  • Focus is still on prototype/demo. Later we'll get into information modeling, ISO standards, what metadata to collect, etc..
  • install documentation for webapp and python stuff is under svn (cover linux and osx)

BCO-DMO

  • Confefence coming up next week

VSTO/Ontology Review

  • The review wasn't to make changes to ontology, but to discuss the ontology, changes that we might want to make
  • Deborah had written up a document, we just need to go back and look at the document and discuss it
  • Can go ahead and make the changes to the ontology, don't have to wait for the review to be completed
    • Just make sure any changes go to
    • Use version IRI for the ontology
      • Specific owl property that shows the version of the ontology

Ontology Evaluation

  • See Amruta's status below on ontology evaluation

DCO

visit coming on tuesday the 24th of July with people from RI

TAF

  • The Asthma Files
  • project page on drupal ... http://tw.rpi.edu/web/project/TAF
  • Working with Erich and Erik to get Plone up and running on thetherless machine
  • have new static IP for taf.rpi.edu

MetPetDB

  • Moving to WMS services for maps, map server, used by mobile app development as well as main portal
  • working on GUI version of portal, http://leo.tw.rpi.edu/projects/metpetdb
  • integration with our modules for displaying information

SemantAqua

  • SemantAqua – SemantAqua - http://aquarius.tw.rpi.edu/projects/semantaqua/ is having trouble with system currently. (Deborah is getting inputs from Evan, Ping, and Linyun). Hoping to get things stable by my talk on Monday and Wednesday mornings. Evan says there is a heavy load on aquarius. It is also being updated with specialized queries to speed up processing. Patrice had a local copy with linyun’s help and that worked but the networked one is failing. Hoping to have cooperative agreement going with USGS in the fall.

MDSA

  • tech infusion
  • extending the ontology
  • working with someone new at GSFC
  • writing up documentation on the different systems of MDSA and how they work together
  • switched to TDB, had some issues, resolved now (AWESOME)
  • runs long time, all queries are working
  • left to do, push the source code to Goddard and have them take ownership

Status Updates

Amruta

Ontology Evaluation (GOEF)
Two Stages - Stage 1 is the preprocessing to extract the context as defined the use case, Stage 2 - is to evaluate the ontology in context of the use case by applying a set of metrics at every stage of the evaluation process.

  • HTML implementation completed
    • It was initially decided to extract the Function (F), Standard (S) and semantic Components (C) from the use case document. The use case documents are unstructured and therefore it is difficult to extract them. This task can even be more difficult since some documents may not express the F,S and C explicitly and hence parsing the use case document to extract the F, S and C will take time. We tried following the MIMV (http://tw.rpi.edu/media/latest/_MIMV.pdf) approach for extracting the F, S and C but this wont work since the use case document itself can be incomplete. We can use this as a reference for defining the minimum set of things which should be known in order to start ontology evaluation
    • Hence currently it is decided to accept the F, S and C directly in the UI from the user and then start the evaluation process.
  • The step 2 in the ontology evaluation process needs to begin and it will begin with the evaluation at the component level.
  • I will back in Troy around August 15th.

Joanne Luciano

  • Ontology Evaluation Methods and Metrics

    * RA funding ended May 2012 - so progress has been hindered
        - Bharad hired May-June (facilitatd coordination)- Proposal to NIST - looks promising (they requested the budget in a different (3-year) format
        - Amruta had 2 internships, and has volunteered to continue work when she returns in August.  See update above.
    * Remotely running Informal Meeting at ICBO - Graz / Robert Stevens from U Manchester will 

  • Citizen Science - Team: Robin Yue Liu, Linyun Fu, Yu Chen and Amar Viswanathan - Advised by Deborah and Joanne

    * current focus (For ISWC) is on driving the Ontology-driven UI 

  • What everyone's up to: working on various (other) projects:

    * Foundations and Trends Health Web Science Monograph (had the 2nd Health Web Science workshop at ACM Web Science Conference and meetings with co-authors, many were present)
    * Master's Thesis (Semantically Enabled Neural Network Modeling of Major Depressive Disorder - Yuezhang (George) Xian
    * TWC Distinguished Lecture Series for 2012-2013 - Future of the Internet (currently researching speakers and availability)
    * Web Science - Coordinating TWC WSTnet Lab activities - getting ready for fall kick off activities (with Deborah and John)
    * Invited talk at UAB Innovation Symposium: Big Data (June) - Data Driven Medicine: Data not Programs, Sharing not Hoarding, Personalized not Population (June 5th, 2012)
    * W3C Health Care and Life Science - integration of pharmacogenomic data for personalized medicine
    * FUSE - contributing to design and implementation/advising within RPI team and discussions with BAE sponsor - project to detect emerging trends in science / science technology
    * Battling with email
    * Continuting to recover from my experiment with gravity :-)
    * Getting my new house in Troy ready to live in

Deborah =

  • SemantAqua – SemantAqua - http://aquarius.tw.rpi.edu/projects/semantaqua/ is having trouble with system currently. (Deborah is getting inputs from Evan, Ping, and Linyun). Hoping to get things stable by my talk on Monday and Wednesday mornings. Evan says there is a heavy load on aquarius. It is also being updated with specialized queries to speed up processing. Patrice had a local copy with linyun’s help and that worked but the networked one is failing. Hoping to have cooperative agreement going with USGS in the fall.
  • FUSE – updated storyboard showing emergence of scientific trends (by looking for community of practice currently). Driving explanation environment updates
  • DataOne Use case evolving. integrating water data from Santa Barbara County LTER holdings, CUASHI data covering SBC, SemantAqua data covering SBC. Questions around what a water ecologist would ask (with slant for how they would leverage dataone and how dataone can use semantic technology and resources such as data-gov. Having a lot of trouble getting an instance of S2S up.
  • DataCube Explorer - work evolving presenting science data that statistics-literate scientists may want to see to look for trends and form hypotheses. Small demo (rough) using popscigrid tobacco data. Working on demo with Jeongmin and Chavon – deborah’s summer people – for iswc demo submission
  • Semantic Sea Ice - planning fall workshop to gather local knowledge