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Published 20 hours ago • verified publisher icon OBOFoundry

Update information on VariO

Open cthoyt opened this issue 3 years ago • 3 comments

This PR does the following:

  1. Add the ORCID and email given by @maunov in https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2090#issuecomment-1259470698
  2. Adds the CC BY 4.0 license as given by @maunov in https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2090#issuecomment-1259470698
  3. Removes the redundant body text as the short description.
  4. Adds the 3 publications listed on the VariO homepage
  5. Add missing domain annotation
  6. Switches VariO's activity status from "orphaned" to "inactive" and annotates a to-do list for how to proceed
    • needs a public issue tracker
    • needs to update PURL configuration to reflect new artifacts (see http://www.variationontology.org/vario_download/)
    • needs to make OBO version of new artifacts

cthoyt avatar Sep 27 '22 11:09 cthoyt

Ok will wait for confirmation

matentzn avatar Sep 27 '22 11:09 matentzn

@matentzn is there official policy on whether a public issue tracker is required?

cthoyt avatar Oct 01 '22 10:10 cthoyt

@matentzn is there official policy on whether a public issue tracker is required?

100%, see https://obofoundry.org/principles/fp-020-responsiveness.html A discussion mailing list and issue tracker are required to obtain an OBO Foundry PURL. The discussion mailing list requirement should probably be removed.

matentzn avatar Oct 01 '22 14:10 matentzn

@maunov please confirm that the information in this PR is all accurate.

matentzn avatar Oct 24 '22 13:10 matentzn

Thanks, The details seem to be correct. We will fix the issues with tracker and PURL redirects. Have to see how to make the tracker to work.

All the best,

Mauno

maunov avatar Oct 24 '22 19:10 maunov

@maunov could you check this PR please?

matentzn avatar Nov 15 '22 12:11 matentzn

@maunov could you check this PR please?

He already checked and approved in https://github.com/OBOFoundry/OBOFoundry.github.io/pull/2103#issuecomment-1289498381, we haven't made any changes since beside discussion - you might want to ping him specifically in the threads if you want him to check them

cthoyt avatar Nov 15 '22 12:11 cthoyt

@maunov sorry, to be clear, there are some issue with the PR which need to be sorted out, could you comment on the various open threads please?

matentzn avatar Nov 15 '22 12:11 matentzn

Ping @maunov

matentzn avatar Dec 08 '22 10:12 matentzn

@maunov It would be great to get your inputs on the conversation threads above.

To summarize:

  • vario.owl: One of the products of VariO is 'VariO in OWL Functional notation' but this is not inline with OBO Principles, as @matentzn pointed out. Could you change this on your end? Or provide an OWL version of the ontology with RDF/XML syntax?
  • vario.owx: OWX format is for OWL/XML whereas RDF/XML is what is recommended and required to satisfy 'Principle 2: Common Format' of the OBO Principles
  • Requirements to become active: In this PR we have 'Requirements to become "active"' directly in the markdown which would be useful for you and your team to know what additional work needs to be done for your ontology (thanks to @cthoyt). If you would like to remove it from vario.md then please let us know your plans towards the listed requirements. (for example, creating tickets on VariO issue tracker to keep track of the requirements)

deepakunni3 avatar Dec 12 '22 15:12 deepakunni3

@deepakunni3 @matentzn I think we should accept the changes in this PR and leave this ontology marked as orphaned, since we've been relatively unsuccessful at contacting @maunov. I moved the todo list into the title of this PR for later reference.

cthoyt avatar Feb 26 '23 01:02 cthoyt

I think the contact is not very active on GitHub, I emailed them once more now. I don't want to merge this PR as is as it partially violates the OBO Principles

matentzn avatar Feb 26 '23 07:02 matentzn

@matentzn Did you get a response from @maunov ?

deepakunni3 avatar Mar 20 '23 12:03 deepakunni3

I sent another follow up and cced you in!

matentzn avatar Mar 20 '23 12:03 matentzn

@matentzn @deepakunni3 we're well past the suggested window from https://obofoundry.org/docs/SOP.html#META - I think we should take executive action and denote this ontology as either orphaned or inactive, then call it done

cthoyt avatar May 25 '23 08:05 cthoyt

Thank you @cthoyt for bringing this up.

Yes, it has been 2 months our email to @maunov .

@matentzn What do you recommend here? Should we mark the ontology as inactive/orphaned or just accept the changes in this PR as-is and merge?

deepakunni3 avatar May 25 '23 15:05 deepakunni3

Thanks @matentzn

deepakunni3 avatar May 29 '23 12:05 deepakunni3