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OBOFoundry / OBOFoundry.github.io

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
http://obofoundry.org
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Document the distinctions between active/inactive, orphaned, etc. #1126

Closed jamesaoverton closed 2 years ago

jamesaoverton commented 4 years ago

This builds on #733. We've done the work, but don't have clear documentation. Sources:

jamesaoverton commented 4 years ago

This is the most informative bit of https://github.com/OBOFoundry/OBOFoundry.github.io/issues/733#issuecomment-430312155:

'active': The ontology project has a contact person who is responsive. Terms are being added or edited in response to community requests.

'inactive': The ontology project has a contact person who is responsive. A static version of the ontology is available, but no edits are being made.

'orphaned': The ontology project does not have a contact person who is responsive. A static version of the ontology exists.

'obsolete': The ontology project is not in active development, and the past developers do not recommend using existing versions of it, either because another project is available that supersedes it, or because previous produced versions have serious issues that make them less usable, and/or are not available at all.

util/validate-metadata.py classifies into five levels, which drive the sorting of the main table (although not all distinctions are obvious in the table):

  1. foundry: activity_status: active and in_foundry_order: 1 (that's ugly)
  2. active: activity_status: active
  3. inactive: activity_status: inactive
  4. orphaned: activity_status: orphaned
  5. obsolete: activity_status: inactive and is_obsolete: true; the latter should imply the former
pbuttigieg commented 4 years ago

That's a pretty good starting point. I think that the foundry/library classification is orthogonal, which is why it could cause confusion. We should separate the two.

Also, we'd need some sort of time threshold (or similar) on an "inactive" status. When will it be considered static? Consider that some small ontologies may be "inactive" because they accomplished their aim and new terms may only come in very occasionally. Being labelled "inactive" gives the wrong impression here.

Suggested revisions:

Ontology Development Status

OBO Alignment Status

mellybelly commented 4 years ago

I think that having the ontologies organized by Foundry status is disadvantageous to OBO. I continue to hear that people come to the OBO page and disregard the ontologies that are not "Foundry"; e.g. the OBO Foundry does not have many production ontologies." However, many of the non-Foundry ontologies have had extensive review and adoption in the community outside the context of the OBO committee review.

All of the ontologies in the library aim to adhere to the principles and this is evaluated in the context of their request. Meanwhile, a dated Foundry review admitting an ontology into the Foundry does not indicate that the ontology is of better quality. IMHO, being a Foundry ontology only means that there has been an internal OBO review, it is not an indication of quality, interoperability, or any other functionality.

I suggest that the OBO reviews become a linked attribute in the table, similar to other attributes. The reviews should also be dated.

jamesaoverton commented 4 years ago

@pbuttigieg We haven't set time threshold for "inactive". When @rvita was emailing all contacts over the past year, some voluntarily classified their projects as inactive, so we had to add this category (see the rest of #733). There's been discussion of scheduled manual reviews of project status, but no firm plans.

Foundry status is not orthogonal, because foundry projects must be active.

@mellybelly This issue is about documenting existing metadata on project status. We're doing a ton of work on automated tests for "quality, interoperability, or any other functionality" with the OBO Dashboard, and there are other open issues about dated reviews.

cmungall commented 4 years ago

Actually we don't have a dedicated ticket about dated reviews AFAICT. I added one: #1140

Regarding:

I suggest that the OBO reviews become a linked attribute in the table, similar to other attributes. The reviews should also be dated.

We have this ticket that @wdduncan is working on: #1088

yongqunh commented 4 years ago

I agree with @pbuttigieg. Some ontology may be inactive due to their maturation or lack of more feature request or use cases for further improvement. Different situations may need to be considered.

jamesaoverton commented 4 years ago

See also #300 about hiding obsolete ontologies by default.

cmungall commented 3 years ago

I note that orphaned status isn't showing up on the site

http://obofoundry.org/ontology/rex

should show up as orphaned

yongqunh commented 3 years ago

REX: an ontology of physico-chemical processe. It's different from Orphaned, right?

cmungall commented 3 years ago

I think you mean Orphanet? I am talking about the status field!

On Wed, Jun 23, 2021, 18:27 Yongqun Oliver He @.***> wrote:

REX: an ontology of physico-chemical processe. It's different from Orphaned, right?

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yongqunh commented 3 years ago

I see. thanks for explaining.

nlharris commented 2 years ago

are there still things to be done here?

matentzn commented 2 years ago

For now this is enough:

https://obofoundry.org/docs/OntologyStatus.html

We can iterate in smaller portions. We are waiting for @ddooley and his team to provide a new front page for sorting ontologies better.