Structural lexicon

The Structural Lexicon task force is establishing defining criteria for neural structures across scales. The recommendations for the standard metadata to be included are still being solidified but are currently:

• Unique identifier
• Unique label
• Creator or contributor (including date of contribution)
• Version or curation status
• Human readable definition
• Abbreviation or acroynm
• Synonyms
• Defining citation (and link)
• Defining criteria
• Superclass from "classical" anatomy
• Part of relationships
• Overlaps relationship
• Pictorial or spatial definition from atlas or image in a paper
• Organism at taxon rank to which it applies, e.g. mammal, vertebrate, rodent

The content of the structural lexicon will be exposed through the Neurolex Wiki, and may also be browsed in Brain Info. The Neurolex Wiki has implemented a form for brain structures that provide a template input for the criteria. To add a brain region, just type one in on the Neurolex home page in the box labeled "Add a brain region" and the template will be generated. There is also a bulk upload option available to those interested.

Atlas representations are being linked to the Neurolex through the Scalable Brain Atlas, a 3D atlas viewer and query tool developed by Rembrandt Bakker of the NeuroPI group of the Donders Institute, Radboud UMC Nijmegen

A more detailed look at the template work can be found on this page Brain Regions Template.

The specifications for this system can be found on this page NeuroLex Specifications.

Common Pan Mammalian Brain Structures

To facilitate cross-species comparisons, the Structural Lexicon is defining a common upper ontology for structures commonly identified across primate and rodent species. This work is led by Drs. Doug Bowden and Laszlo Zaborsky. The current proposed hierarchy can be viewed at this link or at Brain Info by typing "brain" into the "Search by name" box, selecting "What, where and how big it is", then selecting "Models where it appears". A version of this hierarchy will also be posted on the Neurolex Wiki for comment in the near future.

Cortical parcellation schemes

As part of this program, the PONS is exploring different representations of anatomical nomenclatures to facilitate interoperability among different ways of parcellating the brain. Current recommendations:

• 1) Unique label:
  • Each brain region should be have a unique label in addition to a unique ID. The unique label should be of the form Brain region X of Nomenclature Y, where nomenclature may be an atlas or a paper.
• 2) Parcellation schemes: Each parcellation scheme is registered in the Neurolex under Parcellation scheme. Each parcellation scheme should have the year or edition from which it came.

Example: Perirhinal cortex of Burwell et al 1995

Note that this naming convention has not been followed consistently in the Neurolex. Once the final recommendation has been settled, the names will be changed:

Ongur, Price, and Ferry (2003) area AON

The R&D Task force is examining methods of representing overlap among these regions using spatial descriptions so that overlap relations among major brain structures can be inferred, e.g., BAMS

Other Links

Access the Structural Lexicon working pages