Closed gouttegd closed 8 months ago
What I am considering to do (unless there is objection):
Remove the CL bridges to the life stage ontologies. This shouldn’t be controversial. Unless we start putting some life stage terms in CL (why whould we ever do that?), those bridges will always remain empty, so they serve no purpose at all.
Remove the bridges to ontologies that are deprecated (e.g., AAO, BILA, EHDAA, EMAP, EV, etc.). We may keep the existing cross-references on the Uberon/CL terms (though I’be keen to remove them as well), but they would no longer be used to generate bridge files.
I’d be inclined to do the same for ontologies that are inactive (e.g. AEO, MFA, OlatDv, etc.), but maybe this is going a bit too far.
For prefixes that are “unknown to the OBO Foundry” (e.g. ABA, BSD, OG, OGES, etc.): unsure. All those prefixes are also unknown to Bioregistry. If someone knows which resources these prefixes refer to, please share your knowledge and indicate whether you think having bridges with these resources is still relevant.
For the bridges where the source of truth is currently unknown (meaning we have the bridges, but no idea where they come from), I’d suggest moving the source of truth to cross-references in Uberon/CL, to align them with most of the other bridges. That would concern at least BFO, and possibly ABA, NIFSTD, VAO, KUPO (if we decide to keep the bridges with those).
Another piece of information:
The following bridges are used to build the composite-metazoan
product:
In addition:
composite-mouse-with-stages
;composite-vhog
.Those last two products are typically not built in recent releases.
I looked through the empty ones, and I agree they can be all excluded.
FYI, here is what I plan to do with the current bridges when overhauling the pipeline that generates them:
1) The following bridges will be removed (they will no longer be produced and will be removed from the repository; the cross-references in the -edit file will be left untouched, so no information will be lost – if we later decide to reactivate those bridges, we can do so in a matter of seconds) as the ontologies they bridge to are formally deprecated:
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).
2) The following bridges will also be removed since they are, by construction, empty (they are supposed to bridge CL to ontologies of life stage terms; as mentioned above, CL has no such terms):
3) The following bridges will be removed for the indicated reason(s):
vao
as an alternative prefix for vsao
)4) The following bridges will be maintained and have their source of truth moved to the -edit file:
If you think one (or more!) of the bridges slated for removal should be kept, please say so.
Final list of bridges about to be deprecated
Bridge name | Foreign end | Reason for deprecation |
---|---|---|
uberon-bridge-to-aao |
Amphibian gross anatomy ontology | AAO is deprecated |
uberon-bridge-to-aba |
Allen Brain Atlas | Redundant with the MBA/DMBA bridges |
uberon-bridge-to-bila |
Bilateria anatomy ontology | BILA is deprecated |
uberon-bridge-to-bspo |
Biological spatial ontology | Bridge is empty |
uberon-bridge-to-efo |
Experimental factor ontology | Bridge “makes no practical sense” (©️ @matentzn) |
uberon-bridge-to-ehdaa |
Human developmental anatomy, abstract version | EHDAA is deprecated |
uberon-bridge-to-ev |
eVOC (expressed sequence annotation for humans) | EV is deprecated |
uberon-bridge-to-mfo |
Medaka fish anatomy and development | MFO is deprecated |
uberon-bridge-to-nifstd |
NIF standard ontology | Unknown source of truth, only contains pointless bridging axioms |
uberon-bridge-to-og |
? | Bridge is empty |
uberon-bridge-to-olatdv |
Medaka developmental stages | OlatDV is inactive and tied to MFO which is deprecated |
uberon-bridge-to-tao |
Teleost anatomy ontology | TAO is deprecated |
uberon-bridge-to-vhog |
Vertebrate homologous ontology group | VHOG is deprecated |
uberon-bridge-to-vsao |
Vertebrate skeletal anatomy ontology | VSAO is deprecated |
uberon-ext-bridge-to-zfa |
Xebrafish anatomy ontology | Uberon “ext” no longer exists (note that this is not the uberon-bridge-to-zfa !) |
Bridge name | Foreign end | Reason for deprecation |
---|---|---|
cl-bridge-to-aao |
Amphibian gross anatomy ontology | AAO is deprecated |
cl-bridge-to-bila |
Bilateria anatomy ontology | BILA is deprecated |
cl-bridge-to-bspo |
Biological spatial ontology | Bridge is empty |
cl-bridge-to-dhba |
Developing human brain atlas | Bridge is empty |
cl-bridge-to-dmba |
Developing mouse brain atlas | Bridge is empty |
cl-bridge-to-efo |
Experimental factor ontology | Bridge “makes no practical sense” (©️ @matentzn) |
cl-bridge-to-ehdaa |
Human developmental anatomy, abstract version | EHDAA is deprecated |
cl-bridge-to-ev |
eVOC (expressed sequence annotation for humans) | EV is deprecated |
cl-bridge-to-fbdv |
Drosophila development ontology | Bridge is empty |
cl-bridge-to-hao |
Hymenoptera anatomy ontology | Bridge is empty |
cl-bridge-to-hba |
Human brain atlas | Bridge is empty |
cl-bridge-to-hsapdv |
Human developmental stages | Bridge is empty |
cl-bridge-to-mba |
Mouse brain atlas | Bridge is empty |
cl-bridge-to-mfo |
Medaka fish anatomy and development | MFO is deprecated |
cl-bridge-to-mmusdv |
Mouse developmental stages | Bridge is empty |
cl-bridge-to-nif_grossanatomy |
? | Bridge is empty |
cl-bridge-to-og |
? | Bridge is empty |
cl-bridge-to-oges |
? | Bridge is empty |
cl-bridge-to-olatdv |
Medaka developmental stages | OlatDV is inactive and tied to MFO which is deprecated; also, the bridge is empty |
cl-bridge-to-pba |
Primate brain atlas | Bridge is empty |
cl-bridge-to-spd |
Spider ontology | Bridge is empty |
cl-bridge-to-tads |
Tick anatomy ontology | Bridge is empty |
cl-bridge-to-tao |
Teleost anatomy ontology | TAO is deprecated |
cl-bridge-to-tgma |
Mosquito gross anatomy ontology | Bridge is empty |
cl-bridge-to-vsao |
Vertebrate skeletal anatomy ontology | VSAO is deprecated |
cl-bridge-to-wbls |
C. elegans development ontology | Bridge is empty |
cl-bridge-to-zfs |
Zebrafish development stages | Bridge is empty |
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).