Semantic eScience Meeting April 13, 2015

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General Information

Dates and Speakers

Date Weekday Time Speaker Topic
Feb 02 Monday 11am ET Linyun Fu Ontology Interest Group
Feb 16 Monday 11am ET Stephan Zednik Vocabulary Services
Mar 02 Monday 11am ET NA Catchups & Discussion
Mar 16 Monday 11am ET Linyun Fu Linked Vocabulary API
Mar 30 Monday 11am ET NA General Discussions
Apr 13 Monday 11am ET NA Ontology Versioning etc
Apr 27 Monday 11am ET
May 11 Monday 11am ET

Remote Users:

1.  Please join my meeting, Apr 13, 2015 at 11:00 AM EDT.

2.  Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (571) 317-3131

Access Code: 960-187-693

Audio PIN: Shown after joining the meeting

Meeting ID: 960-187-693


  • Hao
  • Peter
  • momo
  • Linyun
  • Han
  • Marshall
  • Corey
  • Apurva
  • anirudh
  • Deborah McGuinness
  • Benno Lee

Topics of Interests

  • Ontology Evolution (Versioning)
    • SYSE
    • -> ontology best practices hackpad
    • Never remove a concept or property
    • If a concept or property is modified then it receives a new URI, it’s a new concept/property basically
    • major/minor changes
    • provenance/relationships/hierachials
    • "deprecated" sign
    • vocabulary vesioning: Marshall for SKOS, there are "active" and "inactive" annotations to indicate whether elements are part of the current ontology
      • Stephan: there are?
    • the triangle? anybody can paste a picture?
    • software, database, provenance, schema, ... split tasks
    • Use Cases
      • change the description of a concept
      • add a new concept
      • remove a concept
      • simple typo in a description
    • ontology evolution literature, ISWC, ESWC, ASWC conference proceedings
    • RDA has an interest group related to this
  • Ontology versioning
    • versioning in software
      • Semantic versioning convention (for
        • Semantic Versioning Presentation, Software Versioning
        • major.minor.patch
          • major changes generally break backwards compatibility and usually involve interface or contract changes
          • minor changes generally add new functionality but do not break backwards compatibility
          • patch changes are generally bug fixes that do not make interface changes (but fix incorrect behavior)
        • difference from software engineering.
        • branching, different urls
        • ==> ontology best practises hackpad/email list.
        • ==> documentating ontologies
        • ==> an ontology in development for a small exercise?
        • stephan presentation (SKOS; versioning)
        • ==> PROV’O
        • ==> technology issues for the data set
    • versioning meriting from semantic tools, in RDF?
    • how to use provenance to describe versioning
    • other...?


  • Quick Recap
  • Discussion (15-20 min max)
  • Summary and What’s Next (3-5 min max)

Action Items from Last Time


  • Software versioning (major versions, minor versions, bug fixes...) does it work well with RDF versioning? What is missing? 
  • Versioning along with documentation and annotation
  • Difference between software and ontology 
    • Scope: ontology has global scope
    • Polymorphism not allowed in ontology for good reasons
    • NO Encapsulation in ontology (no private elements)
    • Software is defined by interfaces, ontology change is almost always interface change -- reasoning clients will break.
    • Annotating implications of a change to an ontology is hard.
  • How to define minor and major changes for ontologies (since almost every change in an ontology is considered a major (interface) change for software)?
    • Decoupled governance of ontology changes
      • e.g., OBO foundry governance arrangement
      • Use case: VSTO?
      • Benchmark/criteria for ontology evolution governance practices?
        • whether break client tools, how hard it is to fix these breaks, ...
  • Branching in ontology versioning
  • How datasets underpinned by an ontology are influenced if the ontology changes.

TWC Ontology Best Practices

Possible ontologies

  • DCO ontology needs to be reviewed so could have a discussion on versioning
  • Still have not switched to VSTO version 3
  • TW Ontology changing the tw:Concept and incorporating skos:Concept
  • skos, versioning of vocabularies

Action Items