Semantic eScience Meeting February 02, 2015

Printer-friendly version

Dates and Speakers

Date Feb 2 Feb 16 Mar 2 Mar 16
Weekday Monday Monday Monday Monday
Time 11amET 11amET 11amET 11amET
Speaker Linyun Stephan
Topic Ontology interest group Vocabulary Services
Date Mar 30 Apr 13 Apr 27 May 11
Weekday Monday Monday Monday Monday
Time 11amET 11amET 11amET 11amET

Possible Speakers and Topics for the first week:


Linyun Fu, etc

General Information

  • href="">This Meeting: Ontology of ontology
  • Previous Meeting (N/A)
  • Next Meeting: Vocabulary Services

Call In


  • Marshall (remote)
  • Linyun Fu
  • Congrui Li (Corey)
  • Hao Zhong
  • Anirudh
  • Yu Chen (Momo)
  • Apurva Kumar Sinha
  • Patrick West (remote)
  • Stephan Zednik (remote)
  • Xixi Luo (remote)
  • Peter Fox


  • Introduction to eScience meetings
    • in the beginning of each semester we send invitation to the escience email list and ask everybody to choose a time for the meeting for the semester.
    • for every escience meeting there will be a short talk. at the beginning of the semseter we are asking people to fill out their proposed topics to talk about.
    • the escience meeting is not made as a project meeting, but more as a discussion of general esicence and also particular intersets.
    • every new semester we will have a new organizer/chair for the meeting

  • Around the room (10-15 minutes max)
    • Hao: 1st yr phd student, starting on DCO project
    • lingyun: 5th yr phd student,,automatic capturing of provenance in research publications
    • Corey: 2nd year at TWC. research qualifier. a new project in material science. he said he will talk about that in the future
    • anirudh prabhu: document data dark metadata,NOCV
    • yu chen "slash" momo:  deep carbon observatory infrastructure, single sign on
    • xixi: postdoc working for deborah (DataOne project)
    • marshall ma: 3rd yr postdoc, use of semantic technologies in data management and publications; geoinformatics
    • stephan: software engineer. projects: NOCV; RDS; Dark Metadata
    • Patrick: work for Peter since 2002. Projects: DCO; RDESC; infrastructure for the lab
    • Prof. Peter Fox:
    • Apurva: 1st graduate student in IT, working for DCO
  • Linyun Fu: Proposing ontology interest group
  • Topics to discuss for meetings


Action Items


  • eScience meeting is a science meeting, not a project meeting
  • a short talk at each meeting (15-20 min talk, 5-10 min discussion)
  • discuss interesting research topics
  • place to talk about problems you are stuck on, interesting ideas...

Around the room

Hao: Deep Carbon Observatory (DCO)

Linyun: Provenance capturing for research publications

Corey: Material Science & Engineering Ontology

Anirudh: Dark metadata,NOCV

Yu Chen/momo: DCO, mobile sensor system

Xixi: DataONE --- build a data sharing network for earth scientist

Marshall: The use of semantic web technology for data publication and management, quantitative and qualitative modeling of geospatial data

Stephan: DCO-DS (dev-ops, s2s), NOCV (vocabulary services, possible RDA interest group), RDS (VIVO & CKAN for RPI datasets), Dark Metadata, BEDI

Patrick: DCO-DS, RDESC, lab infrastructure management


Apurva: new ITWS student on DCO.


  • DCO-DS (Deep Carbon Observatory - Data Science)
  • Dark Metadata
  • RDESC - Resource Discovery for Extreme Scale Collaboration
  • ToolMatch - Service to match tools with datasets
  • OPeNDAP Provenance - OPeNDAP - open source data access software
  • SemantEco
  • Jefferson Project
  • BEDI
  • NOCV - vocabulary services
  • RDS (RPI Data Services)
  • DataONE

Ontology Interest group within the eScience group

  • a lot of ontologies involved in these projects of us
  • an informal mailing list where people can put topics and questions.
    • useful across multiple projects
    • inspiring each other
  • later in the semester we can lead a ontology TWed talk & discussion
  • how do we publish ontologies in the lab? as the first problem to discuss on the list
  • can we take "ontology of ontologies" as the interest group name
    • what does ontology mean to each person?
    • ontology definition: a specification of a shared conceptualization
      • useful over beautiful
    • a Cmap to get some ideas on what to do and what should I take care of while using ontologies
  • Possible Discussions
    • Publishing an ontology in the Tetherless World Constellation
    • Is the term ontology synonymous with schema
    • Making assertions about ontologies defined by someone else.
      • foaf:Person subClassOf rdesc:Resource
    • Is Ontology Software?
    • Patrick’s experience with VSTO 1.0
      • The ontology was overkill-ish
        • restrictions
        • min/max
        • disambiguation
      • developed in Protege, which automatically generates java classes from the ontology
    • ontology -> explicit, take knowledge hidden in the code, people’s mind out and make it explicit in ontologies
    • Too much explicit details in a triple store? Unmanageable. Too slow. A lot of people turn off inferencing. Turn off restrictions and disambiguation.
    • implementability, expressibility, maintanability triangle for ontology design
    • difference: graph database vs relational database
      • open world vs closed world?
      • relational database could be a restricted graph database, more compact
        • relational database factors out common edges shared by instances in the knowledge graph, thus more restriction on data, more compact storage.
      • graph database has more expressivity
      • difference between graph database and directed graph database???
      • relational database is based on relational algebra, must be provable in math

  • what to do next
    • building up a group from the escience - marshall & prof. fox
      • When you go to, log in, create list, you can specify a list configuration to copy
    • talker in two weeks: stephan on vocabulary services