2019-03-21 Ontology Interest Group Call

Thursday, March 21, 2019, 10 AM US Eastern Time

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Ontology Interest Group Google Folder https://drive.google.com/drive/u/0/folders/1RGBh4fDZdzpJdwyiUMO8OPWwkcmVYrI0


  1. Updates
    1. Melissa Haendel – working to schedule
    2. Updated documents since our last meeting:
      1. New: Degree types according to Anabin (Thanks Christian Hauschke)
      2. New: Early Thoughts on representing Academic Degrees http://bit.ly/2Jo4ws9
      3. New: Early Thoughts on Ontologies Used in VIVO: http://bit.ly/2F5z2Bx
      4. Improved figure and text: Early Thoughts on Related Domains: http://bit.ly/2Jn3MTV
      5. Comments addressed in revision: VIVO Ontology Version 2 http://bit.ly/2R8gYuI
      6. Other documents revised to standardize formatting
  2. Conference
    1. Workshop?  Presentations?
  3. Finishing the white paper

Google doc for notes:  http://bit.ly/2Jud40G


  1. Updates

    1. Mike will reach out to Melissa and suggest a few possible times to discuss.  Then Mike will be on the road for 12 days after the end of next week.

      1. Mike: Anabin in Germany maps between equivalent degrees from different countries.  Not good coverage for the U.S.: only 22 degrees.

      2. Mike: Tatiana made a comment on the academic degree document: points out that there is no StudentRole in VIVO currently, and one of the ontologies we’re considering reusing -- ERO -- does have a StudentRole.

        1. Deeper issue of domain orthogonality:  ERO is a resource ontology; not clear why it has a StudentRole.  IAO, however, seems cleanly orthogonal. Things related to scholarship should be in the VIVO ontology; shouldn’t necessarily reuse everything, especially when entities are defined in ontologies where they don’t belong to the domain.

        2. Marijane notes that Eagle-i doesn’t even seem to be using roles:  why are they in there?
          https://search.eagle-i.net/model/ (ontology browser)
          https://search.eagle-i.net/model/#q=Matriculation%20Status&t=http://purl.obolibrary.org/obo/ERO_0000783&of=score (Student role, which is relabeled as Matriculation Status)
          Also note -- it’s being used as a “referenced taxonomy”, not in the BFO sense of a role.

        3. Javed: My understanding was that VIVO 2.0 would be entirely under its own namespace: was that not correct?

          1. Mike:  I’ve softened on that position.  We could include ontologies that are either required by general ontology practice (e.g. RDF terms, DC metadata) or the upper-level ontology (BFO).  We’re in good contact with BFO, IAO, and ERO. Feel comfortable collaborating with them, and they’re OBO compliant and actively maintained.

          2. Mike made notes for each ontology about the license, whether it is actively maintained, and whether it is OBO compliant.  Software ontology meets all the criteria. Could we work with them? Probably could.

        4. Mike:  Some ontologies, including ours, have vocabularies that could be maintained separately from the ontology itself (e.g. list of academic degrees).

          1. Concept vocabularies (GEMET, AGROVOC):  clearly, the maintenance is not in our domain.  Can effectively “outsource” certain subdomains.

          2. Academic degrees are a good example:  we’re not in this business, but would be very useful to us.  See Anabin (1-b-i) .

          3. Worked with Digital Science to create 90K organizations for OpenVIVO.  Could think about an automatically-maintained ontology from Digital Science data.

          4. Journals:  have a large list (44K) thanks to Violeta’s work.  ISNI list (65K) is proprietary.

          5. Can do a query in Dimensions to get a list.

        5. Mike: Awards and honors and academic degrees end up with a very similar structure: rewarding to see those patterns emerging.

  2. Conference

    1. Javed: Poster or presentation?

      1. Mike:  Maybe both?  Maybe a workshop?  For people who are new to ontology, or to the idea of a version 2 ontology, a workshop might make them more accepting and less fearful of what initially sounds like a radical idea.

      2. Javed:  If we go with a workshop, we could divide into four one-hour sessions:

        1. What is ontology?  (General principles of using vocabularies, etc., could be here instead of strictly linked to VIVO 2.0)

        2. Current VIVO ontology

        3. Current interaction with the application

        4. VIVO 2.0

          1. Way too early to talk in detail about VIVO 2.0

          2. Mike:  might have quite a bit more in six months.

      3. Mike will reach out to invited speakers to see if they want to participate in a workshop.

Action Items

  • Review all open ontology tickets
  • Early thoughts on covering the domains
  • Short description of what we are proposing, with white paper as a reference
  • Folder focusing on new work
  • VIVO community project
  • Proposals for the VIVO conference
  • Melissa regarding OBO, ERO, VIVO, VIVO-ISF

In Progress or Review Ontology Issues

Key Summary T Created Updated Due Assignee Reporter P Status Resolution

Open Ontology Issues

Key Summary T Created Updated Due Assignee Reporter P Status Resolution