Inventory of current bridges between Uberon/CL and foreign resources #3047
Comments
gouttegd
added
mapping
bridge-files
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What I am considering to do (unless there is objection):
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Another piece of information: The following bridges are used to build the
In addition:
Those last two products are typically not built in recent releases. |
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I looked through the empty ones, and I agree they can be all excluded. |
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FYI, here is what I plan to do with the current bridges when overhauling the pipeline that generates them:
In addition, the bridge to OlatDv will be removed as well; that ontology is only inactive and not deprecated, but since MFO is deprecated, I am not sure there is a point in keeping OlatDv if we drop MFO (OlatDv is the ontology of life stage terms for the same taxon as MFO; basically, OlatDv is to MFO what FBdv is to FBbt).
If you think one (or more!) of the bridges slated for removal should be kept, please say so. |
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Final list of bridges about to be deprecated Uberon bridges
CL bridges
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The overhaul of the bridge pipeline is over, so we can close here. |
I will soon overhaul the way the bridges between Uberon/CL and foreign resources (mostly foreign ontologies but not only) are handled. Before I do that, here is an inventory of those bridges as they currently exist. Some of them may not be relevant anymore, so I’d like people to weigh in on whether they can be removed or not.
“Last updated” refers to the last time the bridge file had any changes committed to the repository (regardless of whether those changes were significant or not; for example, merely changing the version IRI without any edit to the bridging axioms still counts as an “update” and indicates the bridge file is actively maintained); when the last update is “ODK migration (2021)”, it means the history of the bridge cannot be traced back any further than PR #1798 because of the huge repository-wide changes in that PR – the real last update may be much older.
The “source of truth” indicates where the mappings that underlie the bridging axioms come from. A “?“ means that the source of truth is unknown: we have the bridge file, but we have no indication of how that file was generated in the first place.
The “bridge types” are:
equivalent: the mapped foreign term is said to be equivalent to the Uberon/CL term (FOREIGN:YYYY EquivalentTo: UBERON:XXXX);has-subclass: the mapped foreign term is said to be a subclass of the Uberon/CL term (FOREIGN:YYYY SubClassOf: UBERON:XXXX);is-a: the Uberon/CL term is said to be a subclass of the mapped foreign term (UBERON:XXXX SubClassOf: FOREIGN:YYYY);reverse genus differentia (NCBITaxon:ZZZZ): the mapped foreign term is said to be equivalent to the intersection of the Uberon/CL term and an existential restriction with the indicated taxon (FOREIGN:YYYY EquivalentTo: UBERON:XXXX and (BFO:0000050 some NCBITaxon:ZZZZ)in most cases, except when the Uberon term represents a life stage, in which case the property is BFO:0000066 instead of BFO:0000050);complex: custom-made bridge that does not obey simple rules like the previous ones.Uberon bridges
CL bridges
Of note, it is completely expected that the CL bridges with foreign ontologies such as FBdv, HsapDv, MFO, MmusDv, WBls, or ZFS are empty: those ontologies only contain terms representing life stages, and CL has no such terms (all terms representing life stages are in Uberon).
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