Semantic eScience Meeting June 29, 2012

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Welcome to TitanPad!

General Meeting Information


  • Off line meeting


  • Patrick "Uhhh" West
  • Deborah McGuinness
  • Stephan Zednik
  • Marshall X Ma
  • Peter Fox
  • Joanne Luciano (phase shifted)
  • Eric Rozell
  • Han Wang
  • Yanning(Yu) Chen
  • Massimo Di Stefano

Should be providing feedback as well

Amruta Akut
Patrice Seyed
Linyun Fu
Yang Li
Jay Sanghvi

Past Action Items

Action Items


Add your reports/ status/ etc/ here


Note, not EVERYONE will be able to go to AGU this year (at least at the present time) so please consult with Peter or Deborah when preparing abstracts.

Note there are TONS of Earth and Space Science Informatics sessions this year - a number of which are potentially of interest to us (and a number of which could be seen to overlap).
we need to think a bit about what makes sense to submit where.
i think patrick is putting up a page this weekend .
Deborah is co-convening one

 and giving an invited talk at another.  (I will list in a bit below)

Patrick West

  • TAF - The Asthma Files
    • Plone install on vserver on aquarius
    • new static IP address to point to tetherless machine
    • modularization of twsparql drupal module to use in other CMS
    • unit tests for twsparql module
    • command line app for using twsparql module
  • MetPetDB
    • installed on my laptop
    • working on documentation for web services
  • DCO - Deep Carbon Observatory
    • Setting up infrasturcture for the project
    • New project pages, collaboration environment
    • Will be working with John Erickson on this project (Le and Dan as well)
    • Changing the URI (DO WE REALLY WANT TO DO THIS)
    • Linked data with R2R
    • Web Services documentation like VSTO (
  • VSTO
    • version 3 of the ontology
    • annotations in the ontology
    • ontology review (behind schedule on this)
    • secure login to new site
    • Complete work on new portal implementation ( )
  • ESIP Federation
    • Upgrading MediaWiki and all of their extensions
    • Installed environment on my laptop to work on twsparq modules
  • ESIP Federation Summer Conference
    • attending, July 17-20
  • CMSPV - Coastal and Marine Spatial Planning Vocabularies
    • launch early June, setting up collaboration space, use case design and development
    • Stephan and I will be doing Information Modeling
  • HAO-CI
    • Working with Lance Jones on infrastructure support, backups, database work
    • OODT and Ramada investigation
    • SPCDIS provenance capture within HAO - (deborah is interested in keeping up with this. note james michaelis is in boulder now for 3.5 weeks . just wondering if we use any of his time there in an opportunisitic way)
    • Information modeling (using VSTO as basis)
    • databases crashed, no backups
    • been working to restore access for VSTO, CEDAR, and MLSO
    • lost three years of work on cedar administration wiki and cssc wiki
    • new portal development
    • Working with Massimo on installing to aquarius, making it public
    • Working with Massimo on documentation for installation, configruation, running
    • Working with massimo on C++ coding for GUI and iPython
    • Installing on laptop to help with documentation and coding
    • Busines Requirements document
    • Use Case 1 rework into smaller use cases
  • TW Web Site
    • Continuing to moderate the ENTIRE SITE
    • Continuing to work on editing capabilities
    • Continuing to add new style sheets, xslt, queries, etc
    • Will be starting call for knowledge updates (filling in descriptions for concepts, research areas, updated bios, etc...)
    • bug fixes (fileout_netcdf)
    • supporting new Grib handler
    • OPULS - OPeNDAP and THREDDS integration work
    • DAP4 specification meetings and documentation. - weekly meetings
    • new features to support server-side registration, individualized container support

Marshall X Ma

  • Status
    • Postdoc life at TWC started on Jun 11!
    • Catching up with meetings and projects at TWC
  • Papers
    • One paper almost done: Consensus on topic identification and diversity in modeling and encoding: pragmatics of building and using geoscience ontologies? -- to be submitted to Earth Science Informatics? will discuss with Peter
    • Will begin wrting another one in July if no heavy work loads from research projects
  • ESIP 2012 summer meeting
    • July 17-20, will meet Patrick and Stephan at the venue
    • Will see the progresses of DataOne (what are you doing with DataOne?) deborah would like to keep up with this and USGIN
    • Will present an abstract and a Demo (Jul 18 evening)
    • Abstract title: Beyond an image: using ontology and visualization to enrich Web Map Service for geosciences
    • Two initial videos related to the demo:

  • AGU 2012
    • Writing a abstract now, to be submitted to an ESSI session
  • Participating projects at TWC
    • Will review previous meeting minutes for progress
    • Will contact Patrick for participation and technical issues

Stephan Zednik

  • Recent Activities
    • Attended IPAW 2012 in Santa Barbara (June 19 - June 21)
    • Presented SPCDIS poster at IPAW
  • Attended W3C Prov WG F2F3 Meeting in Santa Barbara (June 22 - June 23)
    • Coordinating Implementation Report (deliverable required to become recommendation)
    • Coordinating a Note for a XML Schema of W3 Prov
  • Facilitated a USGS Semantic Web Working Group (SWWG) workshop in Denver (June 26 - 28)
    • Good progress, lead in to future USGS collaboration
    • Poster for project will be presented at internal USGS meeting in July
  • Upcoming Activities
  • ESIP - will attend, no presentation
    • Will be my top project priority in July
    • I will be developing the provenance presentation using Ajax
      • I need to learn Ajax ;-)
    • I will look into if we can add prov-o as a supported provenance encoding
      • Doing so would enable SPCDIS to get included in the list of implementations on the W3 Prov Implementation Report!!!
      • we could contemplate both this a s the 3rd supported provenance encoding and also we could write up what it takes to allow our infrastructure to take provenance encodings (including extension modules - prov essentially by definition will have extension modules)
  • MDSA
    • Finishing up documentation (javadoc, primers, ontology documentation, tutorial on extending ontology)
    • FInishing up refactor to using TDB as a persistent datastore (I *think* I worked out the major instability issue)
  • AGU 2012
    • Don't have an idea yet. What project?
      • SPCDIS? Focus on provenance as a vehicle for communication (rather than verification or reproducibility) - great - i would be happy to help with this.
  • PML Validator
    • I talked to Evren and Kendall at C&P, got instructions on how to develop custom Pellint Lints
      • I am interested in using cutom Lint's as PML integrity constraint tests. Could the PML Validator simply be a set of custom tests for Pellint? Deborah thinks we all think this is a promising route. We also have confirmation from C&P that they will give us the software required - stephan did you get what you are expecting from them? Deborah agreed that we will publish the PML axioms according to open source licensing

Deborah McGuinness ==
  • ESIP - Deborah will give a keynote on Wednesday (still contemplating title/theme)

(will be there tues night - friday morning) july 17 late night arrival, at meeting 18-19

  • AGU
    • deborah co-convening and promoting
    • does anyone have people they would like to see as an invited speaker in this session?)
    • deborah is invited speaker for AGU Session IN015: Data Interoperability and Inter-Use Solutions
    • can submit one other first authored paper of course but would like to get submissions in on a number of efforts...
  • DataOne - new postdoc Patrice Seyed is on board - YEAH!!!!!!
  • Microsoft Faculty Summit - Deborah is on a panel on monday - in seattle sun 7/15-16 night
  • Met with Mark Schildhauer of NCEAS (while at IPAW) (along with Stephan and Shawn Bowers). working on connections to LTER (long term ecological research network) data largely initially from Margaret Obrien at UCSB with out outreach to broader LTER holdings
  • IPAW meeting presentations (one led by Tim , another led by Jim M) and poster presentation (led by Stephan) went well. One of the most interesting posters was by curt tilnes - provenance of science going into reports for the us govt.
  • Attended VPR's research retreat. Interesting discussions with Kim Fortun - RPI - potentially about connecting SemantEco with the asthma files
  • writing up natural resource manager extensions to semantAqua with Ping and USGS for escience submission.
  • USGS hoping to have funding soon to scope continuation of semantic support for usgs data discovery, access, analysis, and dissemination soon through a cooperative agreement - Deborah is working with Sky Bristol

Massimo Di Stefano


  • Project page
  • Use Cases Page
  • Use Case
  • Conceptual map :
  • ontology development :
  • related rpi project :
  • Ipython notebook : (password: geohab ; notebook: ECO-OP)
  • GUI prototype :
    • Use case updates after first evaluation
      • web GUI prototype and Ipython Notebook to be avaluated by large group (waiting back from Jon H., demo is ready) demo available for download on drupal
      • iPython Notebook demo updated to new set of indicators
      • added iPython Notebook to show the possibility to derive plots using the BCODM repository as source dataset [ notebook: test_BCO-DMO ]
      • Activity diagram Update [ ]
      • draft DPSIR conceptual map to be revised by RPI group
      • documentation - ECOOP Build, install, configure, run []
      • ECOOP VServer on aquarius (Ipython notebook and GUI demo full running inside the VPN, needs to be exposed to the whole internet)
  • Note Ipython Notebook :
    • Ipyhon Notebook is too complicated for 'standard' user
    • Advanced Users are used to using (HA) matlab, R, IDL, and other utilities (the Ipython notebook will looks a familiar environment)
    • work with RPI to implement a better "provenance" system (using standard RPI - API?, provenance encoding?) to embed prvenance inside the data produxts
    • ISO 19115 investigation, (found online work already done on iso xsl schema and GUI/Mask to fill metadata entries)
  • Note Web-GIU
    • No document anywhere that describes what the admin interface is supposed to do
    • No document anywhere that describes what the user should be able to do

(there is a 2 slides pdf to be showed to the noaa group at the end of june that becomes with the video demo, a file is attached to the ecoop mailing list)

    • GUI development (C++ support/study needed to speedup its development)

  • ICES Conference
    • deadline poster submission 18 aug. (draft design started)
    • Mike F. Kim H. will attend too
    • work focused on zooplancton indicators and Satellite data (modis aqua, PP & Cl)
    • NOAA-DFO-IMR-workshop
      • Working on the poster draft, i had a chance to talk with Mike F. about it asking for some dataset to be included in the plots, looking fwd for his feedback too, before submission

Note :
- Interesting is the overlap of efforts between EU and US in multivariate statistical methods and spatial planning tools development.
- In Bergen i'll met some statistician working on marine spatial planning at IMR, in particular Dr. R. Bivand [ ]
- A tool for marine spatial planning that is capturing my interest : it is used wide on the US west coast.



  • NSF Earthcube community event June 12th-14th - see
    • Semantics Community Group is developing a roadmap (slowly)
    • Other groups on Interoperability, etc.
    • Umbrella solictiation for activities coming out in July.
  • NIST BigData June 13-14th -
  • It is NSF annual report writing season so I will be asking for inputs for all projects needing reports (SeSF, SPCDIS, ECOOP)
  • It is also proposal and paper writing season - so be prepared for requests - ready and willing!
  • Peter attending ESIP July 17-18
  • Peter on NRC study committee and will attend Symposium and mtg July 19-20 (- is there something we can give you for this? what is the focus?)


  • MetPetDB
    • Developing more services for alpha release
      • Bulk upload (chemical analyses, samples)
      • Image upload
      • Bibliographic upload
    • Migrating to WMS services
    • Mobile app support
    • Migrating to virtualenv/virtualenvwrapper for cleaner deploys
    • Documentation


  • Ontology Evaluation - page has been updated
    • Amruta was not funded, so work ceased.
    • Bharad met with Amruta and updated web page and notes.
    • Amruta said she is interested in contributing to the project when she completes her internship. She is willing to do this for the experience and will be credited on paper and demo.
    • Linyun and Amruta were working some on the use case formalization. I don't think it progressed very far, but perhaps if she does work more this summer, they can make progress.
  • Proposal to NIST to fund 20% of my time
  • NSF Proposal sumbitted in December was not successful
    • Aim to re-submit
  • Informal Meeting scheduled for ICBO Graz - may cancel if funding doesn't come through


  • S2S
    • Redeploying on aquarius virtual machine
    • IOGDS
      • Attempting to keep up with Greg and John's requests
    • DataOne
      • Working with Patrice to get an S2S instance set up
    • Made series of minor UI requests for Cyndy's presentations
    • Requests seem to have subsided
  • AGU
    • Co-convening session
      • IN031: Linked Data for Earth and Space Science
    • Potentially submitting abstract to:
      • IN014: Data Discovery and Access Services (ESSI-LOD)
      • IN028: Knowledge Networks and Collaborative Platforms in the Earth Sciences (SESF Discovery)
      • IN042: Semantic Web and Ontologies in Earth Science (S2S)
  • ESIP Summer Meeting - Discovery Cluster
    • Prepping Java mentor session for OpenSearch and xCasting specs
    • Setting up AWS instance for "hands-on" session
  • ESIP Summer Meeting - Semantic Web
    • Participating in ToolMatch Talkoot
    • Perhaps setting AWS instance with triple store, reasoning, SPARQL endpoint for session
  • Microsoft
    • Signed non-disclosure, so can't say much, but working in the Online Services Division
    • Working in the broad domain of knowledge representation
    • Getting experience for what it's like to work in a product team and work towards getting something shipped
    • Getting intimate with the Bing software stack
    • Playing with data from THE ENTIRE WEB GRAPH... muahaha (accompanied by evil grin) *note, it's not as fun as it sounds...
    • Juggling requests from multiple program managers, lead program managers, architects, user experience team, other engineers and the occasional edict from executive mgmt. that completely derails a course of action (who would've guessed, everyone has their own agenda)
    • Having fun! (kayaking, dodgeball, go-karting, orchestra, food, food, and lots of WA state wine).

Han Wang

  • MBL
    • Working with Nathan Wilson, Deborah, and Katie on Semantic Vernacular Fungi project
    • Learing Ruby on Rails
    • Sitting in Encyclopedia of Life development (EOL) team meetings
    • Working with Peter DeVries, who is playing with lots of EOL data and trying to put them in the linked open data cloud.
    • Go to the beach from time to time.
  • AGU
    • Trying to submit an abstract for the fungi project to IN041: Semantic Reasoning to Better Understand Complex Earth and Biological Systems
    • A little work on making maps.

Yanning(Yu) Chen

  • I've been working on sensor data, such as rainfall and sub-stream catchment, provided from CSIRO to do some prediction on the stream flow in the future days, and see whether there will be some disasters, such as flooding. The techniques I've been using are machine learning ways to to distinguish the data from disaster and non-disasters. Now I am adjusting the parameters of the machine learning tools, such as rbf in svm to optimize the solution. That's what I've been done. Thanks!