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Update gaz.md #2269

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lschriml
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Update the GAZ project to active.
Make the gaz_countries.owl file the default file for the project.

Update the GAZ project to active.
Make the gaz_countries.owl file the default file for the project.
@matentzn
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@deepakunni3 postpone merging until I have had a chance to think this over.

@matentzn
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matentzn commented Feb 1, 2023

@lschriml can you tell me exactly which file this PURL should redirect to?

http://purl.obolibrary.org/obo/gaz.owl

and what the purl for the full, currently broken and not editable, gaz will be?

@lschriml
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lschriml commented Feb 1, 2023

@matentzn -
@lschriml can you tell me exactly which file this PURL should redirect to?

In the gas_countries.owl file, I had set the purl to be:
http://purl.obolibrary.org/obo/gaz/gaz_countries.owl/

The file is at:
https://github.com/EnvironmentOntology/gaz/blob/master/src/ontology/gaz_countries.owl

--> but perhaps it should be: 

http://purl.obolibrary.org/obo/gaz_countries.owl/

-- the purl for the full, currently too large to edit gaz is ?
http://purl.obolibrary.org/obo/gaz.owl

@matentzn
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matentzn commented Feb 2, 2023

Ok, I was hoping that we get rid of gaz.owl, and have it like this:

  1. http://purl.obolibrary.org/obo/gaz.owl points to https://github.com/EnvironmentOntology/gaz/blob/master/src/ontology/gaz_countries.owl
  2. http://purl.obolibrary.org/obo/gaz/gaz-full.owl points to the old main GAZ file.

I must have misunderstood you - my interest in this was to relegate the old gaz.owl into a secondary release artefact, and make your "gaz countries" the new, truly active, component. For example, OBO dashboard downloads http://purl.obolibrary.org/obo/gaz.owl, and I would have hoped it would, instead download, your gaz countries.

http://purl.obolibrary.org/obo/gaz.owl is the URL that matters, and if I understand you correctly, this does not become "active" again, right?

@lschriml
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lschriml commented Feb 2, 2023

Hello Nico @matentzn,
Can an OBO Foundry ontology have more than one purl ?
Could we keep the old gaz.owl purl
AND create a second purl for the project, for gaz_countries.owl ?

@bpeters42 @ddooley @pbuttigieg --
I would like to solicit feedback from the OBO Foundry group, on how to handle the full gaz.owl.
--> As the full GAZ (gaz.owl) is no longer editable, given it's size. However, it is being used.
Do we keep the old PURL, or create a new one for the Full GAZ ?

    --> Would changing the Full GAZ's purl to : http://purl.obolibrary.org/obo/gaz/gaz-full.owl  -- break current usages ? 
          Any objections to having the full gaz becoming a secondary release artifact ?
               I have no objection, but would like to hear from other users before making this switch. 

Cheers,
Lynn

@ddooley
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ddooley commented Feb 2, 2023

What happens to the OLS etc purl lookup of all the GAZ terms which are not countries? I.e. Is the proposal suggesting that OLS have two files they use to respond to GAZ purls? Or that we give OLS the gaz.owl file which happens to include all the countries; but going forward editing takes place to maintain the country list, and have it of course an easily included part of other ontologies? [edited]

@matentzn
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matentzn commented Feb 3, 2023

The assumption I had was that since GAZ is inconsistent, no one is using it; if ENVO is using GAZ that's problematic.. we should probably use something less OBO like wikidata in the long term for geography stuff.

In any case I don't have a long enough breath for this process now. I will defer to the operation committee as a whole to judge this case:

"GAZ is proposed to be changed to active status, with the argument that a subset of GAZ is actively maintained. The whole GAZ unmaintainable and logically inconsistent (not just unsatisfiable, inconsistent, which means it had no meaning)."

There is no precedence for this and this must therefore be passed back to the operations committee for vote.

Lynn, even if this vote is lost (my guess it's 50/50), we can still make a PURL for GAZ countries and make a note on the GAZ page that GAZ countries is actively maintained. Sorry about the hassle!

@lschriml
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lschriml commented Feb 3, 2023

@matentzn -- Nico - I greatly appreciate your efforts in moving this forward.
Will be good to get the operations committee to work on this.

--> First time I had heard that it was considered logically inconsistent.

The whole GAZ unmaintainable and logically inconsistent (not just unsatisfiable, inconsistent, which means it had no meaning)."

Cheers,
Lynn

@lschriml
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lschriml commented Feb 3, 2023

@ddooley

What happens to the OLS etc purl lookup of all the GAZ terms which are not countries? I.e. Is the proposal suggesting that OLS have two files they use to respond to GAZ purls? Or that we give OLS the gaz.owl file which happens to include all the countries; but going forward editing takes place to maintain the country list,

 and have it of course an easily included part of other ontologies? [edited]
         --> yes 

-- Good points to figure out.
I would suggest we leave the full gaz.owl alive in OLS, as it is used.
The issue is that is not editable.
Following earlier proposals, the first subset is to be gaz_countries.owl

Is the proposal suggesting that OLS have two files they use to respond to GAZ purls?
yes --> A new purl for this file, would be great.
Would be editable via GitHub pull requests/Gaz editors.

Lynn

@cmungall
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cmungall commented Feb 6, 2023 via email

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cmungall commented Feb 6, 2023

I just want to point out one thing if it helps: marking something as inactive in the OBO metadata does not remove an ontology from OLS or any other browser. It is simply an informative piece of metadata that informs users about whether the ontology is responding to term requests and has updates at some reasonable frequency. Something can be of high quality, useful, yet inactive.

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cmungall commented Feb 6, 2023

First time I had heard that it was considered logically inconsistent.

See:

@lschriml
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lschriml commented Feb 6, 2023 via email

@bpeters42
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bpeters42 commented Feb 6, 2023 via email

@nlharris nlharris added the attn: OFOC call Issue to discuss on fortnightly OBO Operations meeting label Feb 6, 2023
cmungall added a commit that referenced this pull request Feb 7, 2023
See:

- #2269

Do not merge until the PURL is available:

- OBOFoundry/purl.obolibrary.org#897
matentzn added a commit that referenced this pull request Feb 21, 2023
* Adding GAZ-countries (DO NOT MERGE YET)

See:

- #2269

Do not merge until the PURL is available:

- OBOFoundry/purl.obolibrary.org#897

* Update ontology/gaz.md

Co-authored-by: Nico Matentzoglu <[email protected]>

---------

Co-authored-by: Nico Matentzoglu <[email protected]>
@deepakunni3
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It looks like the QA is failing due to preferredPrefix missing for GAZ in gaz.md.

A quick look at gaz.owl and https://bioregistry.io/registry/gaz seems to indicate that the preferred prefix would be GAZ.

@matentzn
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matentzn commented Mar 6, 2023

Alright this is the state of this issue as I see it, correct me if I am wrong:

  • as GAZ is "partially active" again, we have created a proper PURL to the new subset of GAZ that is active: http://purl.obolibrary.org/obo/gaz/gaz-countries.owl
  • The "active" tag in the metadata means: "this ontologies is actively processing issues and dealing with term requests" - to not mislead users to think that all of GAZ is active, we

@lschriml does this sound like an ok compromise?

@matentzn matentzn removed the attn: OFOC call Issue to discuss on fortnightly OBO Operations meeting label Mar 6, 2023
@lschriml
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lschriml commented Mar 6, 2023

I would prefer that we : Keep GAZ active in the metadata
--> as that was my understanding while we were all discussing this on the call.
To 're-active' GAZ, not to partially do so.
Active: we are processing issue and dealing with term requests.
--> Which we are.

Make a comment in the GAZ metadata that clarifies that the Countries subset (http://purl.obolibrary.org/obo/gaz/gaz-countries.owl) is actively maintained. And that there are plans to create other GAZ subsets in the future.

Cheers,
Lynn

@matentzn
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matentzn commented Mar 7, 2023

The discussion in the call was pretty inconclusive as far as I understood it - we agreed to make a purl for the countries file, which we did. Ok, I will add GAZ to the new ontology dashboard now. We have already agreed a few months ago that reactivating an ontology means passing the OBO Dashboard, which will be extremely difficult to achieve for GAZ as right now as you can't even open the file and reason with it. I was hoping to spare the TWG this problem (which was a primary reason for setting it to inactive - it was broken and no one wanted to fix it), just so you understand why I am being so difficult here. Or do you want to activate GAZ despite it 1) being inconsistent and 2) not being able to pass the dashboard? remember that the dashboard does not know about the countries file, it will try to process the main GAZ.owl file because that is the file connected to the primary PURL.

@matentzn
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matentzn commented Oct 2, 2023

@lschriml as per OFOC call at some point in the past can you:

  1. Add yourself as the contact person
  2. Add a note in the ontology description which part of the ontology is actively maintained?

Thanks!
Nico

@cthoyt cthoyt added the ontology metadata Issues related to ontology metadata label Oct 19, 2023
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