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- Updates
- Updated documents since our last meeting:
- New: Early Thoughts on representing People in VIVO http://bit.ly/2KWR7rY
- Updated: Early Thoughts on Representing Organizations http://bit.ly/2KJZ8jx . Mike Conlon spoke with the creators of ROR (child of GRiD) at RDA and at CNI.
- Updated: Early Thoughts on Ontologies Used in VIVO: http://bit.ly/2F5z2Bx
- Updated: Early Thoughts on Related Domains: http://bit.ly/2Jn3MTV
- Updated: VIVO Ontology Version 2 http://bit.ly/2R8gYuI
- Other documents revised to standardize formatting
- Github
- I spoke with Andrew – perhaps we break out vivo.owl to its own repo in the VIVO Project now so we can 1) continue maintenance; 2) clarify dependency of software on ontology, and 3) establish versioning practices based on 1.x
- Create a vivo-community project for the version 2 work
- Updated documents since our last meeting:
- Conference
- A talk introducing the ideas / work / rationale on Ontology version 2 based on VIVO Ontology Version 2 http://bit.ly/2R8gYuI
- A poster on VIVO ontology domains based on Improved figure and text: Early Thoughts on Related Domains: http://bit.ly/2Jn3MTV
- An workshop based on Javed's outline:
- Introduction to ontology (no VIVO content)
- Introduction to current use of ontology in VIVO
- Introduction to work of the interest group on version 2
Google doc for notes: http://bit.ly/2KJbEQq
Notes
- Approach to the work
- Comments on existing documents
- One page description of the VIVO Version 2 ontology work.
- Document coming on scholarly works
- Document coming on grants / projects
- Revision of Early Thoughts on Representing Roles and Relationships
- Analysis coming on open tickets
- Additional analysis of IAO and ERO for reuse/intersection
- Some simple working models corresponding to existing models – people,
Google doc for notes: http://bit.ly/2KJbEQq
Notes
Updates
Updates
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.
Mike: Anabin in Germany maps between equivalent degrees from different countries. Not good coverage for the U.S.: only 22 degrees.
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.
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.
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.Javed: My understanding was that VIVO 2.0 would be entirely under its own namespace: was that not correct?
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.
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.
Mike: Some ontologies, including ours, have vocabularies that could be maintained separately from the ontology itself (e.g. list of academic degrees).
Concept vocabularies (GEMET, AGROVOC): clearly, the maintenance is not in our domain. Can effectively “outsource” certain subdomains.
Academic degrees are a good example: we’re not in this business, but would be very useful to us. See Anabin (1-b-i) .
Worked with Digital Science to create 90K organizations for OpenVIVO. Could think about an automatically-maintained ontology from Digital Science data.
Journals: have a large list (44K) thanks to Violeta’s work. ISNI list (65K) is proprietary.
Can do a query in Dimensions to get a list.
Mike: Awards and honors and academic degrees end up with a very similar structure: rewarding to see those patterns emerging.
Conference
Javed: Poster or presentation?
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.
Javed: If we go with a workshop, we could divide into four one-hour sessions:
What is ontology? (General principles of using vocabularies, etc., could be here instead of strictly linked to VIVO 2.0)
Current VIVO ontology
Current interaction with the application
VIVO 2.0
Way too early to talk in detail about VIVO 2.0
Mike: might have quite a bit more in six months.
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
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