Integration with neuroanatomical atlases

This page describes ongoing work to integrate Uberon with neuroanatomical sources of data

An ontology is not an atlas

Classes vs instances

Atlases are typically representations of a single individual brain (perhaps a hypothetical brain), and thus form partonomies.

An anatomical ontology uses classes, and thus the representation consists of (at least) SubClassOf and part_of.

For example, the classes 'rhombomere', 'neural nucleus' or 'white matter tract' may be instantiated in different locations of the brain.

In practice this is less of an issue that with other areas of anatomy, as we generally see less serial homology in the adult vertebrate brain (with the exception of metameric/left-right homology).

Multi-species vs single-species

Atlases represent a single individual in a single species. Uberon is a multi-species ontology. Thus the class 'forebrain' is applicable across vertebrates, the class 'hippocampus' across mammals, and the class 'nervous system' across most of the Eumetazoa.

All axioms are assumed to be true for the class they are applicable for. If taxon-specific exceptions are to be encoded, we use the Evolutionary-variability-GCIs pattern

Multiple partonomic axes

Atlases typically reflect a single partonomic division. There is no such restriction in an ontology, and we can divide my multiple criteria

E.g. for the hippocampus, there is nothing to prevent cross-cutting divisions into fields (CA1-4) and layers (pyramidal layer, etc)

Allen Adult Mouse Neuroanatomy

The following is taken from the Uberon paper, and is still current:

Augmentation using Allen Brain Atlas

We downloaded the OWL version of the Allen Brain Atlas (ABA) and aligned it using the methods described above. We took advantage of the fact that the ABA, like most atlases, provides a non-overlapping parcellation, and derived spatial disjointness axioms to add to Uberon. The ABA is a partonomy that is represented in OWL as a subclass hierarchy. For every axiom in ABA of the form A DisjointWith B, we derived an axiom (part_of some A') DisjointWith (part_of some B'), where A' and B' are the Uberon equivalents of A and B. We represented this in the ontology using the spatially_disjoint_from shortcut relation (see below). For example, ABA contains the axiom: ``` ABA:HPF DisjointWith ABA:Isocortex ``` We used this to derive an axiom: ``` (part_of some UBERON:0002421) DisjointWith (part_of some UBERON:0001950) ``` where UBERON:0002421 has the label 'hippocampal formation' and UBERON:0001959 has the label 'neocortex'. These axioms were used to detect problems in Uberon, some of which could be traced back to source ontologies -- see, for example, [This item](https://sourceforge.net/tracker/?func=detail&aid = 3291162&group_id=76834&atid=1205376)

Bridge and composite ontologies

The ontology uberon-bridge-to-aba.owl contains bridging axioms between Uberon and ABA. It follows the standard pattern of all inter-anatomy-ontology-bridge-ontologies. Because ABA is mouse-specific, the axioms are of the form

 ABA:Forebrain EquivalentTo UBERON:forebrain and part_of some NCBITaxon:10090

The composite ontology for ABA can be made available on request. For information on composite ontologies, see Multi-species-composite-ontologies

Integration with other Allen ontologies

Currently the ABA is the only version available in OWL, so it was the highest priority

Integration with Neurolex

Neurolex contains regions from multiple sources/atlases. Some of these are mapped to a generic brain representation (which came from NIF_GrossAnatomy, in NIFSTD, which is all currently represented in Uberon).

Unfortunately Neurolex uses a semantic mediawiki RDF representation which is technically challenging to integrate. We have started a project to map neurolex to a more usable representation:

• https://github.com/cmungall/nlx-pl