Uberon bridge files

Uberon provides bridge files for several foreign ontologies, especially species-specific anatomy ontologies (ssAOs). Each bridge file contains bridging axioms that establish a relationship between a Uberon term and a term from the foreign ontology.

For example, the uberon-bridge-to-zfa bridge contains axioms such as this one:

ZFA:0001262 EquivalentTo: UBERON:0005564 and (BFO:0000050 some NCBITaxon:7954)

which states that ZFA’s gonad primordium (ZFA:0001262) is equivalent to a Uberon’s gonad primordium (UBERON:0005564) that is part of a Danio (NCBITaxon:7954).

Such a bridge may be used by anyone who wants to merge Uberon and ZFA to obtain an integrated ontology in which the Danio-specific terms in ZFA are properly linked to their taxon-neutral counterparts in Uberon. Internally, Uberon itself is using those bridges to produce the combined multispecies ontologies such as composite-metazoan.

In addition to the bridging axioms proper, the bridges also contain an additional annotation for each bridged term: a “OBO Foundry unique label” (IAO:0000589). That label is automatically derived from the standard rdfs:label of the term, to which a suffix indicating the taxon is appended (for example in the case of ZFA:0001262, the unique label is “gonad primordium (zebrafish)”). This is to ensure that, upon merging Uberon with taxon-specific ontologies, all the terms in the merged ontology will have a distinct label.

Note that the bridges between the Cell Ontology (CL) and the species-specific anatomy ontologies are also provided by Uberon, rather by CL directly. This is because the pipeline that produces those bridges (briefly described below) is entirely hosted in the Uberon repository.

The latest bridge files can be found on GitHub.

Sources of truth

Each bridge has one source of truth which may be:

• cross-references in Uberon or CL;
• cross-references in the foreign ontology;
• an externally provided mapping set;
• an externally provided custom bridge.

Cross-references in Uberon or CL

Cross-references are currently the source of truth for most bridges. For such bridges, a Uberon or CL term will carry a oboInOwl:hasDbXref annotation (aka a “OBO-style cross-reference”) whose value is the short identifier of the foreign term that is, by virtue of this cross-reference, being mapped to the Uberon or CL term.

For example, Uberon contains the following annotation assertion:

AnnotationAssertion(oboInOwl:hasDbXref UBERON:0005564 "ZFA:0001262")

by which Uberon’s gonad primordium is mapped to the equivalent term in ZFA.

The annotations are present directly in the -edit file and may be edited by curators as they wish, using e.g. Protégé.

Note that for an annotation such as the one above to be used when producing the bridge files, the prefix used in the annotation (in this example ZFA) must be declared in an ontology-level annotation that will indicate the signification of the mapping. In the case of ZFA, the declaration is as follows:

Annotation(oboInOwl:treat-xrefs-as-reverse-genus-differentia "ZFA part_of NCBITaxon:7954")

and it indicates that any mapping between a Uberon term and a term from ZFA should result, when producing the bridge files, in a axiom that states that the ZFA term is equivalent to the intersection of the Uberon term and the existential restriction part_of some Danio.

Curators should not normally have to worry about declaring the prefixes of foreign ontologies that Uberon provides bridges for, unless they want to create a completely new bridge (which presumably should not be needed often). But for reference, here are the other possible declaration annotations and the meaning they give to the mappings:

• oboInOwl:treat-xrefs-as-equivalent "PFX": indicates that terms in the PFX namespace are equivalent to the Uberon or CL terms they are mapped to;
• oboInOwl:treat-xrefs-as-is_a "PFX": indicates that terms in the PFX namespace are parents of the Uberon or CL terms they are mapped to;
• oboInOwl:treat-xrefs-as-has-subclass "PFX": indicates that terms in the PFX namespaces are subclasses of the Uberon or CL terms they are mapped to.

Cross-references in the foreign ontology

Some foreign ontologies maintain their own mappings with Uberon and/or CL, using the same cross-reference-based system as used in Uberon and CL and described above. In such cases, when generating the bridges Uberon obtains the cross-references from the foreign ontologies and then derives the bridging axioms from them in the same way as is done for cross-references maintained internally in Uberon and CL.

Uberon or CL editors wishing to amend the mappings with an ontology that maintain its own mappings should contact the editors of that ontology directly, as the mappings cannot be edited directly within Uberon or CL. Adding a cross-reference in Uberon or CL is possible but will have no effect on the bridges.

Externally provided mapping sets

Some foreign ontologies maintain their own mappings with Uberon and/or CL, and provide the mappings in the form of a SSSOM mapping set. For such ontologies, Uberon simply uses the mapping set as provided and derives the bridging axioms from it. In that case, Uberon or CL editors wishing to amend the mappings should contact the editors of the foreign ontology, as the mappings cannot be edited directly within Uberon/CL. Adding a cross-reference in Uberon or CL will have no effect.

Externally provided custom bridges

Some foreign sources provide “custom” or “complex” bridge files that they generate on their side using whatever pipeline they need. Uberon simply uses those bridge files as they are. As for the case of externally provided mapping sets, Uberon or CL editors wishing to amend those bridges should contact the upstream source.

The bridges

The following is a list of all the current bridges, along with their current source of truth.

Bridges with Uberon

Bridge name	Foreign ontology	Source of truth
uberon-bridge-to-aeo.owl	Anatomical entity ontology (AEO)	AEO xrefs in Uberon
uberon-bridge-to-bfo.owl	Basic formal ontology (BFO)	BFO xrefs in Uberon
uberon-bridge-to-caro.owl	Common anatomy reference ontology (CARO)	CARO xrefs in Uberon
uberon-bridge-to-dhba.owl	Developing human brain atlas (DHBA)	DHBA xrefs in Uberon
uberon-bridge-to-dmba.owl	Developing mouse brain atlas (DMBA)	Externally provided custom bridge, maintained here
uberon-bridge-to-ehdaa2.owl	Human developmental anatomy (EHDAA2)	EHDAA2 xrefs in Uberon
uberon-bridge-to-emapa.owl	Mouse developmental anatomy ontology (EMAPA)	EMAPA xrefs in Uberon
uberon-bridge-to-fbbt.owl	Drosophila anatomy ontology (FBbt)	FBbt-maintained mapping set
uberon-bridge-to-fbdv.owl	Drosophila development ontology (FBdv)	FBdv xrefs in Uberon
uberon-bridge-to-fma.owl	Foundational model of anatomy ontology (FMA)	FMA xrefs in Uberon
uberon-bridge-to-go.owl	Gene ontology (GO)	GO xrefs in Uberon
uberon-bridge-to-hao.owl	Hymenoptera anatomy ontology (HAO)	HAO xrefs in Uberon
uberon-bridge-to-hba.owl	Human brain atlas (HBA)	HBA xrefs in Uberon
uberon-bridge-to-hsapdv.owl	Human developmental stages (HsapDv)	HsapDv xrefs in Uberon
uberon-bridge-to-kupo.owl	Kidney and urinary pathway ontology (KUPO)	KUPO xrefs in Uberon
uberon-bridge-to-ma.owl	Mouse adult gross anatomy (MA)	MA xrefs in Uberon
uberon-bridge-to-mba.owl	Mouse brain atlas (MBA)	Externally provided custom bridge, maintained here
uberon-bridge-to-mmusdv.owl	Mouse developmental stages (MmusDv)	MmusDv xrefs in Uberon
uberon-bridge-to-ncit.owl	NCI thesaurus OBO edition (NCIT)	NCIT xrefs in Uberon
uberon-bridge-to-oges.owl	?	OGES xrefs in Uberon
uberon-bridge-to-pba.owl	Primate brain atlas (PBA)	PBA xrefs in Uberon
i	uberon-bridge-to-sctid.owl	SNOMED CT (SCTID)
uberon-bridge-to-spd.owl	Spider ontology (SPD)	SPD xrefs in Uberon
uberon-bridge-to-tads.owl	Tick anatomy ontology (TADS)	TADS xrefs in Uberon
uberon-bridge-to-tgma.owl	Mosquito gross anatomy ontology (TGMA)	TGMA xrefs in Uberon
uberon-bridge-to-wbbt.owl	C. elegans gross anatomy ontology (WBbt)	WBbt xrefs in Uberon
uberon-bridge-to-wbls.owl	C. elegans development ontology (WBls)	WBls xrefs in Uberon
uberon-bridge-to-xao.owl	Xenopus anatomy ontology (XAO)	XAO xrefs in Uberon
uberon-bridge-to-zfa.owl	Zebrafish anatomy ontology (ZFA)	ZFA xrefs in Uberon
uberon-bridge-to-zfs.owl	Zebrafish developmental stages (ZFS)	ZFS xrefs in Uberon

Bridges with CL

Bridge name	Foreign ontology	Source of truth
cl-bridge-to-aeo.owl	Anatomical entity ontology (AEO)	AEO xrefs in CL
cl-bridge-to-caro.owl	Common anatomy reference ontology (CARO)	CARO xrefs in CL
cl-bridge-to-ehdaa2.owl	Human developmental anatomy (EHDAA2)	EHDAA2 xrefs in CL
cl-bridge-to-emapa.owl	Mouse developmental anatomy ontology (EMAPA)	EMAPA xrefs in EMAPA
cl-bridge-to-fbbt.owl	Drosophila anatomy ontology (FBbt)	FBbt-maintained mapping set
cl-bridge-to-fma.owl	Foundational model of anatomy ontology (FMA)	FMA xrefs in CL
cl-bridge-to-go.owl	Gene ontology (GO)	GO xrefs im CL
cl-bridge-to-kupo.owl	Kidney and urinary pathway ontology (KUPO)	KUPO xrefs in CL
cl-bridge-to-ma.owl	Mouse adult gross anatomy (MA)	MA xrefs in CL
cl-bridge-to-ncit.owl	NCI thesaurus OBO edition (NCIT)	NCIT xrefs in CL
cl-bridge-to-sctid.owl	SNOMED CT (SCTID)	SCTID xrefs in CL
cl-bridge-to-wbbt.owl	C. elegans gross anatomy ontology (WBbt)	WBbt xrefs in CL
cl-bridge-to-xao.owl	Xenopus anatomy ontology (XAO)	XAO xrefs in CL
cl-bridge-to-zfa.owl	Zebrafish anatomy ontology (ZFA)	CL xrefs in ZFA, maintained here

Producing the bridges

This section is a (very) brief overview of the pipeline that generates the bridge files.

The pipeline may be triggered by invoking the Make target refresh-bridges (whilst in the in src/ontology directory, where the Makefile is located). Here is what happens then:

1. Production of a SSSOM mapping set from the Uberon cross-references. Cross-references are extracted directly from the Uberon -edit file and turned into a SSSOM mapping set. This takes care of all the mappings with the foreign ontologies for which Uberon is the source of truth.
2. Production of a SSSOM mapping sets from ontologies that maintain their own mappings as cross-references. The foreign ontologies are downloaded and their cross-references are extracted in the same way as the Uberon cross-references are. Note that currently there is no such ontology.
3. Fetching of externally maintained mapping sets. For ontologies that maintain their own mappings and provide a SSSOM mapping set directly, we fetch the mapping set as it is. This currently concerns FBbt and CL (the CL set brings with it the mappings between CL and all the species-specific ontologies).
4. Merging of all the mapping sets. We merge the SSSOM mapping set that was derived from the Uberon cross-references (step 1), the sets that were derived from the cross-references of foreign ontologies (step 2), and the sets that we obtained directly from foreign ontologies (step 3).
5. Production of the bridges. We apply a large SSSOM/T-OWL ruleset (in tmp/bridges.rules, derived from a M4 source in bridges/rules.m4) to produce bridging axioms from the mappings in the combined mapping set obtained at step 4.
6. Dispatching into individual bridges. The axioms produced at step 5 are written to different bridges depending on the ontologies they are bridging (e.g., an axiom that bridges a Uberon term and a ZFA term will be written to the uberon-bridge-to-zfa.owl bridge file).
7. Fetching the custom bridges. Independently of all the previous steps, the “custom” bridges are fetched from their upstream source.

Note that steps 2, 3, and 7 only happen when the Make variable IMP is set to true (which is always the case when the pipeline is explicitly triggered with make refresh-bridges). When IMP is set to false, the bridge files are re-generated using only locally available resources previously committed to the repository.

Uberon maintainers should run make refresh-bridges periodically to refresh external resources and commit refreshed versions to the repository, similarly to what is needed to refresh the imports.