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The Scourge of Neuroanatomical Nomenclature: A Rational Strategy


Maryann E. Martone (University of California, San Diego), Fahim T. Imam (University of California, San Diego), Stephen D. Larson (University of California, San Diego)

The brain is perhaps unique among major organ systems in the multiplicity of naming schemes for its major and minor regions. The brain can be divided based on topology of major features, cyto- and myelo-architecture, developmental boundaries, evolutionary origins, histochemistry, gene expression and functional criteria. The gross anatomy of the brain reflects the underlying networks only superficially, and thus any parcellation reflects a somewhat arbitrary division based on one or more of these criteria.

One of the core aims of the Neuroscience Information Framework (NIF; is to establish an interoperable semantic framework for searching and integrating data across diverse systems. As for neuroanatomy, NIF and other projects, e.g., NeuroNames [1], BAMS, have established the means to translate among different available nomenclatures. The NIF project, in collaboration with the INCF Program on the Ontologies of Neural Structures (PONS), has established the NeuroLex (, a semantic wiki for developing a knowledgebase around the core concepts of neuroscience.
As part of the NeuroLex, we have defined a standard reference vocabulary for mammalian neuroanatomical structures, based on the classical structure hierarchy of the NeuroNames and common terminology found in neuroanatomy textbooks. As verified by text mining of neuroanatomical names [2], these terms tend to be common across species. We have also defined “parcellation schemes”- delineations made on a particular species by a specific author in the context of an atlas or a paper - that reference these core structures. In order to relate brain regions and different parcels, we have defined the ‘overlap’ property in NeuroLex. The term ‘overlap’ in NeuroLex implies some degree of spatial co-localization, although it does not, at this point, specify the degree.

We have worked with the PONS group to implement a reasonable strategy for defining brain structures and relating them with different parcellations that is useful for implementation within information systems like the NIF. This poster presentation will depict the overall NIF strategy in details.

[1] D. M. Bowden, E. Song, et al.: NeuroNames: An Ontology for the BrainInfo Portal to Neuroscience on the Web. Neuroinformatics 10 (1): 97-114, 2012
[2] L. French, P. Pavlidis: Using text mining to link journal articles to neuroanatomical databases. J Comp Neurol. 2011, doi: 10.1002/cne.23012
Preferred presentation format: Poster
Topic: Computational neuroscience