Uberon developers have converted Allen JSON hierarchies (structure graphs) for human and mouse brains to OBO/OWL ontologies and mapped these to Uberon (see Uberon bridge files & also xrefs in Uberon). The ontologised JSON files are available for download from GitHub, but are not released as official OBO ontologies (and so are not available via ontology search and browsing services such as the Ontology Lookup Service). They have not been maintained since they were first derived (in 2015), and so may have become out of date in some cases.
Mapping Table
| Ontology (OBO) | Uberon bridge ontology | Allen Ontology ID | Ontology name (Allen) | Allen StructureGraph ID | Atlases |
|---|---|---|---|---|---|
| allen-mba.obo | bridge/uberon-bridge-to-mba.owl (.obo) | 1 | "Mouse Brain Atlas" | 1 | 602630314 ("Adult Mouse, 3D Coronal"); 1 ("Mouse, P56, Coronal"); 2 ("Mouse, P56, Sagittal") |
| allen-dmba.obo | bridge/uberon-bridge-to-dmba.owl (.obo) | 12 | "Developing Mouse Brain Atlas" | 17 | 181276165 ("Developing Mouse, P56") 181276164 ... |
| allen-hba.obo | bridge/uberon-bridge-to-hba.owl (.obo) | 7 | "Human Brain Atlas" | 10 | 265297125 ("Human Brain Atlas Guide ") |
allen-dhba.obo |
bridge/uberon-bridge-to-dhba.owl (.obo) | 11 | "Developing Human Brain Atlas" | 16 | 138322605 ("Human, 34 years, Cortex - Gyral") 265297126 ("Human, 34 years, Cortex - Mod. Brodmann") 3 ("Human, 21 pcw") 287730656 ("Human, 21 pcw - Brainstem") 138322603 ("Human, 15 pcw") |
| allen-pba.obo | bridge/uberon-bridge-to-pba.owl (.obo) | 4 | "Non-Human Primate Brain Atlas" | 8 | ? |
Derived from Allen mapping tables here http://help.brain-map.org/display/api/Atlas+Drawings+and+Ontologies
Using the Uberon bridge files, we can programatically derive ontology files in which the ABA terms are classified under terms from Uberon.
Unlike node IDs in structureGraphs, the ontology versions of the ABA StuctureGraphs provide unambiguous identifiers (namespaced OBO / OWL URL) to refer to Allen brain regions. The ontology versions can also be used to:
-
Define cell types ontology terms precisely by
referencing spatial regions on standard atlases.
-
Annotate cell types precisely by referencing spatial
regions on standard atlases.
-
Map between species using Uberon.
We could also potentially use these ontologies and links to atlases to enhance information and links displayed for Uberon terms in ontology browsing tools such as the Ontology Lookup Service. For example, we might display thumbnail images of brain regions, linked to the relevant atlas at Allen. This would be extremely useful to experts wanting to use Uberon to annotate their data or wanting a visual reference for existing annotations. To realize this, we need recipes for links and for thumbnails. The former already work well, e.g. Uberon CA3 field of the hippocampus is linked to: MBA:463. This corresponds to an id in StructureGraph 1 which used by Allen reference atlas 602630314. Using this information we can use MBA:463 to roll the link: http://atlas.brain-map.org/atlas?atlas=602630314#structure=463.