Overhaul taxon subsets

[gouttegd]

This PR updates the way we are building “taxon subsets”.

As explained in #3362, we currently have, for reasons unknown (to me at least), two slightly different methods to create taxon subsets: one producing the -view subsets (human-view, mouse-view, xenopus-view) and one producing the -basic subsets (amniote-basic, euarchotonglires-basic). Both methods rely on the use of OWLTools.

This PR replaces both methods by a single one (so that all taxon subsets are produced in the same way) that relies on a new command in Uberon’s custom ROBOT plugin.

The PR does not change which taxon subsets are produced and released by default (the five subsets aforementioned: human, mouse, xenopus, amniote, and euarchotonglires).

More subsets can be produced on demand, all that is needed is to define a TAXON_ID_subsetname Make variable pointing to the desired NCBITaxon ID.

For example, to create a subset for, say, insects, one can do:

sh run.sh make subsets/insect-view.owl TAXON_ID_insect=NCBITaxon:50557

The PR also adds a possibility to create, not a subset directly, but a small component containing only oboInOwl:inSubset annotations to “tag” classes that belong to a taxon subset. For example:

sh run.sh make subsets/human-tags.ofn

would create a human-tags.ofn component containing, for all Uberon classes that belong to the human subset, oboInOwl:inSubset <http://purl.obolibrary.org/obo/uberon/core#human_subset> annotation assertion axioms. Such a component can then be merged with the main ontology for downstream use (e.g., extracting all the classes of the subset).

closes #3362

[matentzn]

I have reviewed the code changes, they look great, - I would like to offer a single word of caution: renaming files, even subset files, may break existing pipelines somewhere on the deep web unless we also add a purl redirect to the OBO purl config.

[matentzn]

Can't imagine what this second relax does but well since it's there..

[gouttegd]

renaming files, even subset files, may break existing pipelines somewhere on the deep web unless we also add a purl redirect to the OBO purl config.

I know. But precisely, this is to be handled at the PURL level, which is here exactly for this purpose. There is no reason for us to refrain from renaming files if it brings better consistency (in this case, by having all taxon subsets consistently named something-view.owl instead of having some subsets being named something-basic).

[dosumis]

Hi @gouttegd - great to see this.

I'm especially excited to see this:

The PR also adds a possibility to create, not a subset directly, but a small component containing only oboInOwl:inSubset annotations to “tag” classes that belong to a taxon subset. For example:

sh run.sh make subsets/human-tags.ofn

would create a human-tags.ofn component containing, for all Uberon classes that belong to the human subset, oboInOwl:inSubset http://purl.obolibrary.org/obo/uberon/core#human_subset annotation assertion axioms. Such a component can then be merged with the main ontology for downstream use (e.g., extracting all the classes of the subset).

I would really like the tags to in incorporated into the release files. We can use them straight away in our autosuggest pipelines to boost for species relevant terms.

[gouttegd]

I would really like the tags to in incorporated into the release files.

I wasn’t sure whether this was your preferred option, so for now the idea was to merely produce the -tags file and leave downstream users of Uberon merge them with uberon.owl if they wanted.

But it certainly can be done directly upstream if preferred.

Do we want all release artefacts to include those tags (e.g. uberon.owl, oberon-basic.owl, but also all the organ-specific subsets such as nephron-minimal, sensory-minimal, etc)? Or just one supplementary artefact containing the taxon subset tags (e.g. something like uberon-with-subset-tags.owl)?

Based on your comment I assume the former (tags included in all release artefacts), in which case we’ll need a new intermediate file (upstream of uberon.owl) from which the subset tags can be generated before we produce the final uberon.owl with the subset tags included.