FYPO:0000512

[manulera]

Once annotations in https://github.com/pombase/curation/issues/3251 are re-assigned.

[ValWood]

I followed the steps for "deprecate" but it does not look like the ones Midori has obsoleted previously (it appears as deprecated, not 'obsolete')

At one point there were 3 options Basic GO or OBI (I chose "Basic" but I do not know if this was the correct option)

@matentzn @nicolevasilevsky

I guess I will see if something goes terrible wrong...

[matentzn]

I am not sure why I was tagged here, but I think we should try to consolidate deprecation here: https://oboacademy.github.io/obook/howto/obsolete-term/

Indeed, we should not use the word "deprecate" at all - just obsolete!

[nicolevasilevsky]

@ValWood I can't see what was done, is there a PR that you'd like me to look at?

You can also use the Protege 'Make entity obsolete' function, which is described here (and this is missing in the OBO Academy documentation, I will add it.

[ValWood]

Hi Nicole. I don't know how to point to a pull request. It was part of the edits I did in the branch with the linked issues above, and is now in the current release. We recently switched from the editing in a branch, rather than master, as advised, but we only do one pull request for the release (following the protocol of our legacy pipeline). The branch containing this edit was successful and is now deleted.

Essentially, I looked for an "obsolete option" in Protege, but could not see it. But I found depracate, so I assumed it must be the same thing. I can follow the obsolete instructions that you provided here in future.

Presumably I can 'undeprecate' this term somehow, and obsolete it instead. I will look at this when I am next editing FYPO (Likely the week beginning 6th June). If I get stuck I'll let you know. Thanks!

[nicolevasilevsky]

@ValWood in my protege, I have an open to Make entity obsolete (see screenshot below).

I think you chose the Deprecate entity option - do you not have the option Make entity obsolete? I don't know why that is, but I have seen that before with another colleague (and their version of Protege was the most recent version).

In the future, it is fine to use the Deprecate entity option, but you should choose GO, as it will prepend the label with 'obsolete [label]' instead of 'deprecate [label]'.

Alternatively, you can follow the directions here, as @matentzn pointed out: https://oboacademy.github.io/obook/howto/obsolete-term/#obsoletion-process-manual

That being said - I just looked at your fypo.owl file and the term does not appear to be obsoleted (unless I am looking in the wrong place). Do you see that it has been obsoleted?

[manulera]

Hello, @nicolevasilevsky, I was revisiting this issue. In protege 5.5 I only have the deprecate option in the edit menu. Which protege version are you using? Also, in the help search I am not able to find any menu option to obsolete a term.

[matentzn]

@nicolevasilevsky is it possible this is because you have the protege OBO plugin installed?

https://github.com/monarch-initiative/protege-obo-plugin

[ValWood]

Right, so we likely need OBO plugin and Elk plug-in. Anything else? Is there a list of things we should have in our set-up?

Thanks, v

[matentzn]

Can you as this question on the obook issue tracker? We should have / make a page for it.

[ValWood]

https://github.com/OBOAcademy/obook/issues/197

[nicolevasilevsky]

I don't think I have that plugin, do I?

I feel like when I downloaded Protege, it had that option. But when I worked with Kallia a while back, her Protege didn't have it either (even though we had the same version) and I never understood why.

[manulera]

But the obo plugin description on github does say:

A plug-in for Protege that provides entry fields for standard OBO annotation properties, as well as menu actions such as term obsoletion.

[manulera]

I changed the term from deprecated to obsolete following the pattern of other obsoleted terms:

• I used the Edit > Make entity obsolete:
• Restored the old definition from a previous version, and added OBSOLETE. in front of it.
• Removed DEPRECATED from the term label
• owl:deprecated true is still there, as by the guidelines
• Made the annotation that points to 'abolished nuclear fusion during mating' consider instead of seeAlso, as by the guidelines.