Integration with neuroanatomical atlases

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

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)

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