Ontology Improvement in VIVO
Background
Following the convergence of the eagle-i and VIVO ontologies into a combined VIVO-ISF ontology in 2013, a manual extraction from VIVO-ISF to produce the “VIVO Core” ontology has been used for VIVO 1.6 through 1.9.2. Changing the VIVO Core ontology betwen VIVO 1.5 to VIVO 1.6 had significant impact on the VIVO community. Some sites never upgraded. As a result, no ontology changes have been made since 2013. In 2015, OpenRIF, an open source organization, was created to maintain and develop the VIVO-ISF. Several commits have been made to the OpenRIF repository, but none involving the VIVO Core.
The VIVO Project would like to consider how to make improvements to the VIVO Core. To facilitate the conversation, the following questions appear to be pertinent (these appeared in VIVO Updates February 19:
What is the purpose of any ontology improvement? What kinds of improvements are there? Why would any improvements be needed? What impacts would ontology changes have on the community? How can we know the impact of any particular ontology change?
If we were great at ontology improvement, what form would that greatness take? What would be included? Can you picture a world in which we were great at ontological improvement? What would that world look like?
How would we get from where we are now to what we want? What would we do first?
Notes from the Meeting of Monday, February 27
Attendees:
Brian Lowe
Benjamin Gross
Christian Hauschke
Damaris Murry
Dong Joon (DJ) Lee
Graham Triggs
Huda Khan
Javed
Julianne
Linda Rowan
Marijane White
Matt Meyernik
Mike Conlon
Tatiana Walther
Tenille Johnson
What would success look like?
Marijane - If we were really successful
Everyone could update
Automating changes in upgrade
Automated extraction process
Able to contribute local extensions
Funding for an ontology role
Damaris - we have a lot of customisations for artistic works
Christian - not transparent where the discussion takes place
Who is in charge?
Javed - start with defining the scope of the VIVO Core ontology
Who asked for the change and where
Who analyze the need of this change
Who analyze the impact of the change
How do we communicate the change
Damaris - what is the goal of the VIVO ontology? To use established ontologies?
DJ - how can we handle grey literature, which isn’t covered by the existing ontology
Javed - Found at Cornell that people had added extensions to the VIVO core
Tenille - How do we keep up with changes in external ontologies?
Mike - two versions of SKOS in VIVO.
Mike - for VIVO, changes in ontology relate to changes in the software that need to be kept in step
Graham -- ontology changes have different impacts on the software -- some are readily handled by existing software. Some require minor changes. Some require significant changes.
Benjamin - we need confirmed set of changes in order to change the software
Mike -- to be good at change, we need to manage community change. Changes to the ontology impact SPARQL queries and deep knowledge of the ontology. When the ontology changes, these external processes break. This can be ameliorated by communication of changes, lead time, examples and training, testing platforms.
Graham -- can there be a means of getting data in regardless of ontology changes. Can there be a means of extracting data that does not require knowledge of the ontology.
Mike -- There is an eagle-i ontology. Should there be a VIVO ontology?
Marijane -- Yes, this would likely help with extraction
The chat
from Mike Conlon to Everyone:
Google doc for notes: https://goo.gl/cELuXJ
from Mike Conlon to Everyone:
Google doc for notes: https://goo.gl/cELuXJ
from Mike Conlon to Everyone:
Google doc for notes: https://goo.gl/cELuXJ
from Christian Hauschke to Everyone:
"Ontology impact evaluation", important points by Javed
from Benjamin Gross to Everyone:
I think this is where we make ontology suggestions for VIVO-ISF? https://github.com/openrif/community
from Christian Hauschke to Everyone:
I think so, too, but it's not clear to everyone, I fear.
from marijane white (OHSU) to Mike Conlon (privately):
it is the place intended for suggestions, but i agree, it is not clear.
from Mike Conlon to marijane white (OHSU) (privately):
No impact analysis, no work, no governance, no pathway to the software. It is an issue tracker. :-)
from Mike Conlon to Everyone:
http://www.vivoweb.org/sites/vivoweb.org/files/vivo-isf-public-1.6.owl
from marijane white (OHSU) to Mike Conlon (privately):
your audio is breaking up mike
from Mike Conlon to Everyone:
I have heard there is a tool used by eagle-i for VIVO-ISF extraction to eagle-i. Is this tool publically available? Can it be used by VIVO?
from marijane white (OHSU) to Mike Conlon (privately):
https://www.eagle-i.net/get-involved/for-developers/
from marijane white (OHSU) to Mike Conlon (privately):
there is a tool, but i think it might only exist in Harvard's SVN?
from marijane white (OHSU) to Mike Conlon (privately):
The OBO community has some tools we might be able to use, like https://github.com/ontodev/robot
from Tenille Johnson to Mike Conlon (privately):
Yes, Shahim set it up and I believe the plan was for it to be used by VIVO as well, although I'm not sure what would be required on the technical end to make that happen. There is some documentation here: https://docs.google.com/document/d/1HO0s1C9D9f5gh2puS8_B3i_U2n78KB0uKnxbhoVzboI/edit
from marijane white (OHSU) to Everyone:
https://www.eagle-i.net/get-involved/for-developers/
from marijane white (OHSU) to Everyone:
The OBO community has some tools we might be able to use, like https://github.com/ontodev/robot
from Tenille Johnson to Everyone:
Yes, Shahim set it up and I believe the plan was for it to be used by VIVO as well, although I'm not sure what would be required on the technical end to make that happen. There is some documentation here: https://docs.google.com/document/d/1HO0s1C9D9f5gh2puS8_B3i_U2n78KB0uKnxbhoVzboI/edit
Marijane also took notes at the OpenRIF github wiki:
https://github.com/openrif/vivo-isf-ontology/wiki/20170227-Ontology-Change-Improvement-Call
