Fix taxon constraint violations #3455
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Recently introduced terms describing some crustacean nerves have been asserted to be simultaneously 'in_taxon some Astacidea' and 'in_taxon some Brachyura'. Astacidea (NCBITaxon:6712) and Brachyura (NCBITaxon:6725) are *sibling* taxa, so such assertions are contradicting each other: a term that is 'in_taxon some Astacidae' or it is 'in_taxon some Brachyura', but it cannot be 'in_taxon' both taxa simultaneously. Remember that 'in_taxon some X' means that the term is *specific to the X taxon*, exclusive of any other taxon that is not X itself or a descendant of X. Assuming that the terms refer to nerves that are in fact present both in Astacidea and Brachyura, we replace for all affected terms the faulty 'in_taxon' assertions by a single assertion 'in_taxon some Pleocyemata', where Pleocyemata (NCBITaxon:6692) is the parent taxon of both Astacidea and Brachyura. We also explicitly import NCBITaxon:6692, since it is used in those assertions.
The -edit file contained some weirdly formatted line with trailing spaces, some tags improperly ordered, and some incorrectly formatted xrefs (possibly the result of some manual editing with a text editor?), so we re-serialize it.
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#gogoeditdiff |
Here's a diff of how these changes impact the classified ontology (on -base file):Ontology comparisonLeft
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Ontology importsOntology annotationsNCBITaxon_6692
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Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotationsNCBITaxon_6712
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Since STG is an abbreviation for "stomatogastric ganglion", it is more appropriate to make it a RELATED synonym (rather than an EXACT synonym), and to explicitly flag it with the "abbreviation" (OMO:0003000) synonym type (as per the Uberon editor SOP). Likewise for similar abbreviations on crustacean nerves.
This PR fixes some problems introduced by the recent #3445 PR, the most important being that the new terms for crab and lobster nerves are causing taxon constraint violations as explained in #3454. We fix that by replacing:
with
We also explicitly import the Pleocyemata term from NCBITaxon, and fix a few incorrectly formatted cross-references (such as
[PMID: 17009928], with a spurious space after the colon).closes #3454