Brain Regions Template

From Program on Ontologies of Neural Structures

Proposed Template

with modifications from Karl and Doug Fall of 08, and a few additional updates as of June 2010:

• Name (e.g., area V1; middle temporal area)- it must be unique or there must be another way to distinguish it from other entries (e.g. area 12 of Walker to distinguish it from area 12 of Brodmann, etc.).
• Synonyms or acronym(e.g., for area 17; BA 17, or area striata, or primary visual cortex, or area Oc1; V5)
• Short name (V1; MT)
• Source creator
  • the original reference or person contributing the information
  • need the ability to have multiple creators-it may be an attribute for each attribute
  • need a way of deciding when the definition is no longer the same as that created by the source
• Creator (date)
• Version (curation status), question arose if this should also be an attribute for each attribute
• Species
• Species equivalents; interspecies mapping
• Partitioning scheme (publication)
• Link to publications (or source): PMID, DOI + specific text, figure(s).
  • there is some debate in this category as to whether website should be referenced here. This entry might only include links to online journals and references. We may wish to include a “database/atlas” category that links to databases with some long-term stability (i.e. not just a lab web-site).
  • need ability to reference a source(s) (publication) for each attribute
• Definition-is this redundant? or would this be an Aristotelian definition?
• Defining criteria (cyto-, myelo-, chemo-architecture, connectivity, topography,functional imaging, lesion…)
  • suggestion that this should be part of definition; however, if definition is Aristotelian not sure if this would be possible
• Profile (expression, binding, physiology, etc…)
• Coordinates (stereotaxic space, registration algorithm; range; variability) (coordinates much be referenced to a particular atlas, so “coordinates” and “atlas” belong in the same attribute)
• Atlases that show area (probabilistic and/or individual) (name of atlas-see link to publication for discussion of links to specific databases and atlases)
• Instances (e.g., map of area in one or more individuals)
• Synonyms (e.g., area 17; V5)
• Partially overlaps: (this might need to be within a larger class of “degree of overlap”: identity, contains, is contained by, partially overlaps, no overlap)
• Connectivity (links)
  • does this refer to others areas which neurons in this area connect?
• Tracts/pathways (links) (this may not differ from connectivity)

May also wish to include:

• Cell types found in this region:
• Genes expressed in this region:
• The system should be designed for extension to other attributes desirable in the future, e.g., ‘models that include the region’, ‘functions’ (behavioral, physiological, etc.), ‘public data sets that involve the structure’ (gene expression atlases, fMRI, MRI and PET datasets (e.g., fMRIDC, IBVD, etc.).

Note from Maryann: The above information can be generated from the ontology that underlies the Wiki and does not need to be added by hand in the same way as the supporting information for each structural concept. There are efforts underway, e.g., WikiNeuron that are creating prototypes that will query dynamic databases for this type of information.

13- This list is appropriate for metadata in the Brain regions domain. An overlapping but different list would be more appropriate for metadata in the Cell domain. That list would not include such attributes as Partitioning scheme, Coordinates, Atlases, Overlaps, and resident ‘Cell types ’, On the other hand, it WOULD include a number of attributes not pertinent to the Brain regions domain, such as Canonical shape category, Receptors (dendritic, somal, axonal, terminal), Organelles, myelinated vs. unmyelinated axons, Neurotransmitter(s), Structures in which the cells are found, and other features important to nerve net modelers