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Code freeze
Create a new release candidate
We will be testing vivo-ontology-lab pull request. https://github.com/vivo-project/VIVO/pull/63
Is it good to go in production?
- Preparing documentation for release (LEAD - Mike)
- Create release notes
- Create release upgrade instructions regarding Jena2/Jena3
- Does ingest documentation need to be revisited?
- See Preparing Documentation for Release
- Evaluation of Jena2 and Jena3 tools
- Work through and document upgrade from 1.7
Team: Mike Conlon (VIVO) Muhammad Javed (Cornell) Benjamin Gross LEAD (Clarivate) Ralph O'Flinn (UAB), Jim Blake (Cornell), Don Elsborg ( CU Boulder )
DELIVERABLES:
Pull request merge in dev (and merge to master??)
Updated documentation following evaluation of current state of 1.10 documentation. Don Elsborg volunteered to assist as 1.7 persona.
Upgrade a CU Boulder 1.7 dev instance with local customizations to 1.9 — updating documentation as appropriate
Upgrade CU Boulder 1.9 dev instance to 1.10 with local customizations
Verify single vivo.owl file and address local customizations for CU Boulder instance.
VIVO ontology & Ontologies.owl file
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update - DONE
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Homework: Evaluation, what has been changed, what should be removed, what should be updated, building the VCARD ontology module file (Add/Retract).
Team: Tatiana Walther LEAD (TIB), Muhammad Javed (Cornell), Mike Conlon Co-LEAD (VIVO)
DELIVERABLES:
A file that contains list of VCARD entities that are used in vivo software but with a second column, specifying if the entity is current, changed or is deprecated (do not exist) in the current VCARD ontology. (current/deprecated/changed).
A new model to substitute the changed or deprecated VCARD terms.
A file that contains vcard graph that should be removed from vivo.owl
A file that contains vcard graph that should be added in vivo.owl.
Evaluate vivo_changed.owl
"SPARQL Construct Query" to find existing triples and to replace with new. - most likely a part of the next sprint
Comments:
04-27-2018: Created a file vcard.owl which I have extracted out of vivo.owl by means of robot. Then I've made the necessary changes: *1*. I've changed the URIs if necessary, *2*. I've modified datatype properties to object properties if it was required, *3*. I removed deprecated properties and classes. I have substituted the removed classes with rdfs:Resource in range assignments of affected properties. 4. I've added the owl:equivalentProperty axiome where it was required according to the spec. All of these changes are in the vcard_changed.owl. Both of the files as well as a vcard_diff.txt where all the differences are enumerated are in the Google Drive folder (https://drive.google.com/drive/folders/1Q6ZgmxyF0wDDgvNt0zm8OOgQfAud4ydM) I have also tried to make a new vivo.owl with the help of merge / unmerge functions of robot, but not all of the deprecated things could be removed this way. So, I need to figure out, how to do this with robot. Of course, it would be no problem to do it manually. I'm not that experienced with robot yet.
04-30-2018: As discussed and agreed upon the affected domain and range assertions recently , I've removed those, where the class for the range and domain no longer exists in the spek instead of substituting it with rdf:Resource. There were not only the range and domain assertions affected, but the values of owl:allValuesFrom in the assertions of vcard:Kind. So, I had to remove the affected assertions as well. All of these changes you can see in the vcard_changed_2.owl (https://drive.google.com/drive/folders/1Q6ZgmxyF0wDDgvNt0zm8OOgQfAud4ydM). After that I've created the vivo_changed.owl (also in the Google Drive folder) which contains all the changes on vcard terms. As it is obviously very necessary to test and evaluate, how the vivo_changed.owl affects the application, me and Javed considered it to be a new and only sub task which is to be finished by the end of the sprint 1. @marijane white it would be great if you could evaluate the vivo_changed.owl together with Javed. And everybody who wants to evaluate the updates on vcard is very welcome!
When reviewing Muhammad Javed detected some domain assertions which are still in vivo_changed.owl but not in the recent version of Vcard spec. After a further chek other numerous assertions were removed or added. A renewed review needed.
Preparation of ontology modules for the candidate ontologies/entities to be deleted. (Homework)
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