oneallenbrainontology v0.1.9

OneAllenBrainOntology

OneAllenBrainOntology provides a set of convenience methods related to searching and indexing mouse brain region from the 1.json of the Allen Institute for Brain Science (AIBS). It contains only static methods, thus no object needs to be instantiated and methods can be called directly.

In addition, this library contains the listing of all the brain region computed volumes from the volumetric files annotation_10.nrrd and annotation_25.nrrd for both ccfv2 (2014) and ccfv3 (2017). The method getRegionVolume(...) makes it easy to get the volume of any given brain region (in cubic micrometer) and let you specify the version and resolution of the atlas.

Example:

import oneallenbrainontology from 'oneallenbrainontology'
let allRegionNames = oneallenbrainontology.getAllRegionNames()

When querying a specific brain region, the returned value if found will be of the form:

{
  "id": 567,
  "atlas_id": 70,
  "ontology_id": 1,
  "acronym": "CH",
  "name": "Cerebrum",
  "color_hex_triplet": "B0F0FF",
  "graph_order": 2,
  "st_level": 2,
  "hemisphere_id": 3,
  "parent_structure_id": 8,
  "children_structure_id": [
    688,
    623
  ],
  "isLeaf": false,
  "slug": "cerebrum"
}

Where

• id: number the identifier of the brain region (given by AIBS)
• acronym: string is the short unique name for a region (given by AIBS)
• name: string full name of the brain region (given by AIBS)
• color_hex_triplet: string the color of the brain region in hexadecimal (given by AIBS)
• parent_structure_id: number the id of the parent brain structure (given by AIBS)
• children_structure_id: number list of region ids this region is the parent of (AIBS gives a list of nodes instead of a list of id, but here the whole tree has been flattened)
• isLeaf: boolean says if the brain region is a leaf of the tree (true, it does not have child region) or if it has child brain region (false). Not that this could easily be deduced from length of the children_structure_id list.
• slug: string a URL compatible name
• atlas_id: number some field given by AIBS (no more info about it)
• ontology_id: number some field given by AIBS (no more info about it)
• graph_order: number some field given by AIBS (no more info about it)
• st_level: number some field given by the AIBS (no more info about it)
• hemisphere_id: number some field given by the AIBS (no more info about it)

Methods

getRawData

Get the raw data (1.json) that contains nested nodes

Examples

let rawData = oneallenbrainontology.getRawData()

Returns object the raw data

getRootNode

Get the root node, which is the most top level node and has no parent.

Examples

let rootNode = oneallenbrainontology.getRootNode()

Returns Object the node

getAllRegionNames

Get the full list of region names (lowercase) as an array

Examples

let allRegionNames = oneallenbrainontology.getAllRegionNames()

Returns Array

getAllRegionAcronyms

Get the full list of region acronyms (lowercase) as an array

Examples

let allRegionAcronyms = oneallenbrainontology.getAllRegionAcronyms()

Returns Array

getAllRegionId

Get the full list of region ID (integers) as an array

Examples

let allBrainRegionId = oneallenbrainontology.getAllRegionId()

Returns Array

getRegionByFullName

Get a region by its strict full name (case insensitive)

Parameters

• name string full name of the brain region

Examples

let visa23 = oneallenbrainontology.getRegionByFullName('anterior area, layer 2/3')

Returns Object the brain region metadata

getRegionByAcronym

Get a region by its strict acronym (case insensitive)

Parameters

• ac string acronym of the brain region

Examples

let visa23 = oneallenbrainontology.getRegionByAcronym('visa2/3')

Returns Object the brain region metadata

getRegionBySlug

Get a region by its strict slug (case insensitive)

Parameters

• slug string slug of the brain region

Examples

let orbL23 = oneallenbrainontology.getRegionBySlug('orbital_area_layer_2_3')

Returns Object the brain region metadata

getRegionById

Get a region by its id

Parameters

• id number id of the brain region

Examples

let visa23 = oneallenbrainontology.getRegionById(312782554)

Returns Object the brain region metadata

getChildRegionsFromId

Get the list of child regions given the ID of the parent region.

Parameters

• parentId (string | number) the id of the parent node

Examples

let children = oneallenbrainontology.getChildRegionsFromId(997)

Returns Array array of regions, alphabetically sorted by name. If the parentId does not exist or if it has no children, then an empty array is returned.

getParentRegionFromId

Get the parent region given the id of a child.

Parameters

• childId (string | number) the id of the child region to get the parent of

Examples

let parent = oneallenbrainontology.getParentRegionFromId(304325711)

Returns (Object | null) the parent region or null if no parent (aka. root node)

getAscendantsFromId

Get the list of IDs of all the brain regions that are at a higher level than the one given.

Parameters

• id (number | string) id of the brain region to find the ancestors of
• options object the options object (optional, default {})
  • options.omitChild boolean if true, the id provided as argument will not be part of the list (dafault: false, the one provided is part of the list)
  • options.rootFirst boolean if true, the order will be starting with the root node, if false, the list will be ending by the root (default: false)

Examples

let ancestors = oneallenbrainontology.getAscendantsFromId(159, {
  rootFirst: true,
  omitChild: false
 })

Returns array of region IDs in ascending order (default) or descending order

getDescendantsFromId

Get all the descendants from a given brain region. The descendants are the children and all the children of the children recursively until the leaf nodes are reached.

Parameters

• id (number | string) id of the region to list the descendants of
• options opbject the option object (optional, default {})
  • options.keepCurrent boolean if true, the region given as argument will also be added, if false, only the descendants will be added (default: false)
  • options.leafOnly boolean if true, only the leaf region will be added (a leaf is a region that has no child) (default: false)

Examples

let allChildren = oneallenbrainontology.getDescendantsFromId(997, { // 997 is the top region, the one that contains all the others
  keepCurrent: true, // this one will actually not apply as 997 is not a leaf
  leafOnly: true     // and here we want only the leaf
})

Returns array the descendants

getRegionVolume

Gives the volume in um^3 (cubic micro-meter) of the given brain region, using some builtin atlas data. Pro-tip: divide by 1E9 to get the volume in mm^3 and again by 1E3 for cm^3.

Parameters

• id (number | string) the id of the brain region to get the volume of
• options object the option object (optional, default {})
  • options.atlas string 'ccfv2' or 'ccfv3' (default: 'ccfv3')
  • options.resolution string the resolution of the voletric data the volume were computed from. '10um' or '25um' (default: '10um')

Examples

let volume = oneallenbrainontology.getRegionVolume(997, {
  atlas: 'ccfv3',
  resolution: '10um'
})
console.log(`The whole mouse brain has a volume of ${volume/1E12} cm^3`)

Returns number the volume of the brain region in cubic micro-meter

findRegion

Search a region using multiple words. There is possibly multiple matches when all the words of the query are found in the full name + acronym + id of a brain region

Parameters

• query string possibly multiple words

Examples

let cerebellumRelated = oneallenbrainontology.findRegion('cerebel')
let layer23Related = oneallenbrainontology.findRegion('layer 2/3')

Returns array brain regions or empty if not found, or an empty array if the query was not succesful

buildNestedTree

Rebuild the tree with nested objects (non-flat) from the list of nodes. Internally, the path to the root is found for each node and children list of ids are replaced with child nodes. The tree is built bottom-up, meaning all the node that match the query willl be added to the tree as well as their parent, up to the root node.

Parameters

• nodes array list of nodes to build the partial tree on (optional, default [])

Examples

let partialTree = oneallenbrainontology.buildNestedTree(oneallenbrainontology.getRegionById(140)))

Returns (Object | null) the tree starting with the root node, or null if the query was not succesful

buildNestedTreeFromQuery

Build a tree in a nested way, based on the query. The tree is built bottom-up, meaning all the node that match the query willl be added to the tree as well as their parent, up to the root node.

Parameters

• q string query, a substring of the region name, not case sensitive. (optional, default '')

Examples

let partialTree = oneallenbrainontology.buildNestedTreeFromQuery('layer')

Returns Object the tree starting with the root node