Improvements to composite pipeline

[anitacaron]

Note that there are still things that can be improved, including:

• The “merge species” step leaves behind a bunch of class declaration axioms for the taxon-specific classes that have been “merged“ into their taxon-neutral equivalent. That is, when (for example) EMAPA:17443 is replaced by UBERON:00005695 and (BFO:0000050 some NCBITaxon:10090), we still have a class declaration axiom for EMAPA:17443:

<!-- http://purl.obolibrary.org/obo/EMAPA_17443 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/EMAPA_17443">
    <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
</owl:Class>

• General class axioms are not translated. If we have, say, a GCA that says

FBbt:X and (BFO:0000050 some FBbt:Y) SubClassOf BFO:0000050 some FBbt:Z

and upon merging FBbt:X is merged into UBERON:X and (BFO:0000050 some NCBITaxon:7227), the GCA will still refer to FBbt:X.

• We have a bunch of FBgn pseudo-terms from the FlyBase ontologies, which in my opinion don’t belong to composite-metazoan.

Those problems are not new – they already existed in previous versions of composite-metazoan. They should be easier to fix now, but I’d rather do that as a separate PR (possibly several separate PRs). My aim for this PR was strictly to replace the existing pipeline by one that is easier to maintain, but that is otherwise equivalent (including in its bugs! :P ).

Originally posted by @gouttegd in #3129 (comment)

[anitacaron]

Sorry, it's the same as #3132