Make OFN the canonical intermediate format; emit RDF/XML & OBO only at release

[matentzn]

Summary

Preliminary consensus from Slack (@balhoff, @gouttegd, @matentzn): Use OWL Functional Syntax (OFN) for all intermediate OWL artifacts in ODK builds. Convert to RDF/XML and/or OBO only as terminal release outputs.

Rationale

• RDF/XML parsing is slower; OFN speeds up builds/CI.
• OFN is easier to diff/grep during reviews.
• Cleaner, centralized prefix handling before final conversion. In fact, RDF-XML and OBO Format cannot currently handle prefixes in all cases we need them to, for example OBO Format outputs should have CURIES for exact Matches monarch-initiative/mondo#9681.

Proposal

• Update ODK Makefile so intermediate targets read/write .ofn.
• Keep .owl (RDF/XML) and .obo only in for final release targets.

[gouttegd]

What about things like import modules or components? Do you consider them as “intermediate artefacts” for the purpose of this proposal?

[matentzn]

What about things like import modules or components? Do you consider them as “intermediate artefacts” for the purpose of this proposal?

Yes but I think they are already ofn by default.. But yes, I do.

[gouttegd]

Fine by me.

I asked because the distinction between an “intermediate” artefact and a “final” artefact can sometimes be blurry. For example, the “bridge files” in Uberon are nominally only intermediate artefacts used to produce composite-metazoan.owl (the real final artefact), but they are also used by third parties (e.g. Ubergraph) – so they are intermediate artefacts from the point of view of Uberon but final artefacts from the point of view of said third parties.

[gouttegd]

Update ODK Makefile so intermediate targets read/write .ofn.

Do you want to also update the correspond filenames so that they use the .ofn extension? (E.g. rename merged_import.owl to merged_import.ofn, etc.)

Pros:

• It’s nice to have consistency between the extension of a file and its format, even though it is strictly speaking not necessary.
• It’s slightly easier when working with ROBOT because then the simple fact of passing a --output file.ofn option is enough to tell ROBOT that the output should be in OFN format – if the extension is .owl then you need an explicit convert --format ofn --output file.owl.

Cons:

• Such a switch has a potential to break a lot of things when people will update their repos.

[matentzn]

I would prefer not to update the file extensions, but could be swayed.

[gouttegd]

I would prefer not to update the file extensions

So would I (too much trouble for not enough benefits), so let’s not do it then. :)