[turbomam]

The mirror/uberon.owl rule ran wget with no -O, so uberon.obo landed in src/envo/. On a second build wget saved the download as uberon.obo.1 and owltools converted the old file. The rule now runs mkdir -p $(TMPDIR), downloads with -O $(TMPDIR)/uberon.obo, and owltools reads the file from there. That puts the download under make clean. The rule keeps its comment linking the PR below.

I checked this in obolibrary/odkfull:v1.6 on 2026-11-02. Two forced rebuilds with make -B mirror/uberon.owl both exit 0, write only tmp/uberon.obo, and leave no uberon.obo files in src/envo/. make clean then empties tmp/.

Related:

• Issue 1286: remove exact synonyms that match label #1289

Closes #1699

[Copilot]

🟢 Approval recommended

There are no active review issues for the UBERON temporary-path update.

No open issues 🎉

What changed in this PR

Fixes stale UBERON input reuse in the ontology build by downloading to a consistent temporary path, addressing #1699.

Changes:

• Creates $(TMPDIR) and uses wget -O to overwrite $(TMPDIR)/uberon.obo.
• Converts that downloaded file with owltools, keeping the input within the existing make clean scope.

File	Description
src/​envo/​Makefile	Updates the UBERON mirror rule to download and convert a fresh copy under $(TMPDIR).

_{Review effort: Balanced}

[pbuttigieg]

Looks cleaner. Could you confirm why we're working with the OBO vs the OWL (and perhaps add that as a comment in the makefile)?

@matentzn any insight there ?

[turbomam]

confirm why we're working with the OBO vs the OWL

I added the makefile comment. Good idea.

I don't know why the build read uberon.obo originally. The download-then-owltools step comes from

• Issue 1286: remove exact synonyms that match label #1289

where @cmungall explained that the OWLAPI inside owltools did not follow the PURL redirect and tried to parse the error page. The failing command there already read uberon.obo, so the OBO choice predates that fix. I added a Makefile comment saying this in

• 0fad1e3

It also notes that mirroring uberon-base.owl with ROBOT the way ODK does would remove the need for owltools and the OBO file. I opened an issue for that so it isn't lost, but the release doesn't need it:

• Build mirror/uberon.owl from uberon-base.owl with ROBOT instead of converting uberon.obo with owltools #1703

[turbomam]

Was using OBO instead of OWL a pragmatic solution to avoiding the numerous axioms that are imported into EnvO for Uberon?

Who else uses tmp/ ?

[turbomam]

If we decided to import OWL instead of OBO, would ROBOT has an elegant solution for not importing anything other than subClasssOf assertions?

[pbuttigieg]

Was using OBO instead of OWL a pragmatic solution to avoiding the numerous axioms that are imported into EnvO for Uberon?

Who else uses tmp/ ?

It may have been - this is some years back, so recollection is foggy and documentation wasn't so high on the agenda. If we can use the OWL file with ROBOT stripping away superfluous axioms (for import purposes), this would be better in my opinion.

[matentzn]

On the questions for me (@pbuttigieg, @turbomam):

Why OBO and not OWL? Historical. My guess is the usual one from back then: uberon.owl was heavy (imports, GCIs, taxon constraints) and the OBO was the lighter thing to grab. It hardly matters for the output, though. --make-subset-by-properties -f $(KEEPRELS), --remove-external-classes and the annotation stripping cut the mirror down to the same small graph from either format.

Can ROBOT strip it down to subClassOf? Yes. filter/remove take --axioms (subclass, equivalent, logical, annotation, external, ...), so something like robot merge -I .../uberon-base.owl remove --base-iri UBERON --axioms external filter --axioms "subclass" --trim false gets you subClassOf only. ODK goes further with extract -m BOT on the seed plus its minimal/"simple" import modes. That's #1703. I agree with @pbuttigieg that it's the better setup, but it doesn't need to block this.

Who else uses tmp/? validate-dl-profile (tmp/validate.ofn) and a few targets in envo.Makefile (tmp/envo-edit-merged.owl, tmp/tags-dosdp.*). They're all scratch files, src/envo/tmp is gitignored, and make clean empties it, so a downloaded OBO fits there fine.