Thursday, February 8, 2019, 10 AM US Eastern Time
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Google Doc: http://bit.ly/2DgHUDK
- Updates, intros, review agenda
- Current ontology
- Vocal http://vocol.kbs.uni-hannover.de:8087/documentation
- Table of entities http://mconlon17.github.io/table.html
- Next steps
- New ontology
- White paper http://bit.ly/2DrAhKP
- Discussions with constituents – Andrew, Julia
- Other discussions?
- Review of document
- Some preliminary analysis
- Next steps – Trello?
- Next call – Feb 21,
- Mike out – CTSA ontology workshop – Barry Smith, Bill Hogan, organizers. http://ncorwiki.buffalo.edu/index.php/Ontology_for_Precision_Medicine:_From_Genomes_to_Public_Health#Organizers
Since we are an IG now, we should no longer take notes in the OpenRIF GitHub wiki.
VoCol test (see http://vocol.kbs.uni-hannover.de:8087/documentation)
exchange the ontology file (CH)
Mike will give it a try and reply with comments
Perhaps we could set it up with ontology from VIVO 1.10 distribution so we have a common base ontology (Christian updated after the meeting)
It started out as a PhD project (by some of Sören Auer’s PhDs back at Bonn, at his previous affiliation)
We’d like it to be useful, so it needs to be used -- with a real project and experienced people
Bugs in Vocol can be reported here: https://github.com/vocol/vocol/issues
Mike showed a simple list of the entities in the VIVO ontology. http://mconlon17.github.io/table.html 870 entities (annotation properties, object properties, datatype properties and classes). Perhaps a new ontology covering the same domain would need about 400 entities once duplicates and entities outside the domain are removed.
The scope of the VIVO ontology has to be evaluated and newly defined
A lot of entities in the VIVO ontology are not from the VIVO domain. See the VIVO ontology domain definition
Examples: vCard stuff, geopolitical ontology
A lot of the URIs are not resolving, because the ontologies are broken
Mike started the discussion that the ontology will eventually change
Two primary questions: how? Why?
Ontological perspective: The ontology we have is not a good one, and we run into barriers when changing the ontology. VIVO is used in the real world, it’s not a PhD project. We have different ownerships in the VIVO world - devs, ontologists, etc.
The vivo ontology should be free to be a good ontology
Currently we have a working ontology, so what more do we need to represent, why would we change it?
Much of scholarship can not be represented using the current VIVO ontology. Some things could be added to the existing ontology, but many things need refactoring so that we have a firm foundation.
Furniture and house analogy --- we are building a new house with new furniture. We’ll fix things in the house currently own. People need to be comfortable in the new house. Will take time and communication.
How to write. We have pent up ideas to remodel parts of the ontology – people, orgs, papers. We have the general notion of using more roles and less types. We need to review local ontologies to see what extensions people have made. We need to review other ontologies in domains similar to VIVO such as IAO, FABIO, EuroCRIS, SPAR and many others. Where are the edges of the domain, for example, where does research end and research administration begin? VIVO has been focused on research and scholarship.
How to convert: 1) build a new ontology, 2) review/test/prove out the new ontology – this involves representing data using the new ontology, querying. 3) Train and tool around the new ontology. Architects and developers are considering how best to accommodate the need for a new ontology. All these take significant time. Three years? How to convert: Time, tools, training.
- Follow up about Trello. Anyone using?
- What ontologies we should review?
In Progress or Review Ontology Issues
Open Ontology Issues