Update gaz.md #2269

lschriml · 2023-01-24T20:39:21Z

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 · 2023-01-25T11:19:09Z

@deepakunni3 postpone merging until I have had a chance to think this over.

matentzn · 2023-02-01T11:25:12Z

@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 · 2023-02-01T19:33:39Z

@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 · 2023-02-02T10:25:44Z

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

http://purl.obolibrary.org/obo/gaz.owl points to https://github.com/EnvironmentOntology/gaz/blob/master/src/ontology/gaz_countries.owl
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 · 2023-02-02T20:20:50Z

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 · 2023-02-02T20:59:53Z

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 · 2023-02-03T06:45:42Z

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 · 2023-02-03T15:35:37Z

@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 · 2023-02-03T15:39:56Z

@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 · 2023-02-06T16:59:31Z

ENVO does not have any imports or dependencies on GAZ.

…

On Thu, Feb 2, 2023 at 10:45 PM Nico Matentzoglu ***@***.***> wrote: 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! — Reply to this email directly, view it on GitHub <#2269 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOKRMBRLH3KJI663KULWVSSSDANCNFSM6AAAAAAUFRKKCQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

cmungall · 2023-02-06T17:03:26Z

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.

cmungall · 2023-02-06T17:59:29Z

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

See:

GAZ is inconsistent EnvironmentOntology/gaz#35

lschriml · 2023-02-06T18:31:07Z

Thanks Chris. Looking over the old ticket. I see what you mean. And how this occurred. BFO-big of GAZ. For GAZ countries, it will not contain BFO terms. Lynn

…

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On Feb 6, 2023, at 12:59 PM, Chris Mungall ***@***.***> wrote: First time I had heard that it was considered logically inconsistent. See: EnvironmentOntology/gaz#35 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

bpeters42 · 2023-02-06T20:43:43Z

Thanks all for re-raising this! As I was tagged, I wanted to weigh in: As part of the IEDB and other projects, we have been using GAZ to identify countries of birth for human subjects. That has worked fine for us, but we would be happy to transition to another solution that is recommended and vetted by the OBO community. - Bjoern

…

On Mon, Feb 6, 2023 at 10:31 AM lschriml ***@***.***> wrote: Thanks Chris. Looking over the old ticket. I see what you mean. And how this occurred. BFO-big of GAZ. For GAZ countries, it will not contain BFO terms. Lynn Sent from my iPhone > On Feb 6, 2023, at 12:59 PM, Chris Mungall ***@***.***> wrote: > > > First time I had heard that it was considered logically inconsistent. > > See: > EnvironmentOntology/gaz#35 > > — > Reply to this email directly, view it on GitHub, or unsubscribe. > You are receiving this because you were mentioned. — Reply to this email directly, view it on GitHub <#2269 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJX2IW5PWE4WKYBHRLRCTLWWE7PPANCNFSM6AAAAAAUFRKKCQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

See: - #2269 Do not merge until the PURL is available: - OBOFoundry/purl.obolibrary.org#897

* 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 · 2023-02-22T16:02:40Z

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 · 2023-03-06T20:00:58Z

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
- Keep GAZ inactive in the metadata
- 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

@lschriml does this sound like an ok compromise?

lschriml · 2023-03-06T23:37:36Z

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 · 2023-03-07T05:33:10Z

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 · 2023-10-02T10:52:24Z

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

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

Thanks!
Nico

Update gaz.md

6ccb994

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

lschriml requested a review from matentzn January 24, 2023 20:39

nlharris added the attn: OFOC call Issue to discuss on fortnightly OBO Operations meeting label Feb 6, 2023

nlharris mentioned this pull request Feb 6, 2023

Re-activate gaz - gaz_countries #2108

Open

cmungall added a commit that referenced this pull request Feb 7, 2023

Adding GAZ-countries (DO NOT MERGE YET)

bdaeae0

See: - #2269 Do not merge until the PURL is available: - OBOFoundry/purl.obolibrary.org#897

cmungall mentioned this pull request Feb 7, 2023

Adding GAZ-countries (ready to merge) #2284

Merged

1 task

Merge branch 'master' into lschriml-patch-1

8edfe96

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

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

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Update gaz.md #2269

Update gaz.md #2269

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Update gaz.md #2269

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Update gaz.md #2269

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