BrainStars (B*)

Web API

The database has a REST-like Web API interface for accessing from your Web applications. This document shows how to access the database via our Web API.

We have the following Web APIs:

• Search API
• List API
• Probe set API

You can get contents in HTML, JSON, YAML, and so on. (See below)

Search API

Search API is for keyword search and is based on Tokyo Manifesto and TogoWS REST interface.

URL for retrieving a list of hit entries

http://brainstars.org/search/(query+string)[/(offset),(limit)]

output:

If the result has at least one hit entries, a list of entry IDs is returned in text/plain format (each line corresponds to each hit entry). If not, 404 Not found error code is returned. The output format can be changed to JSON, and so on (see below). "offset,limit" can be used to retrieve a part of hit entries. If "offset,limit" is not given, all hits are returned.

URL for retrieving the count of hit entries

http://brainstars.org/search/(query+string)/count

output:

The count of hit entries is returned in text/plain format

samples

• http://brainstars.org/search/receptor
• http://brainstars.org/search/receptor/1,5
• http://brainstars.org/search/receptor/count

List API

List API is for retrieving a list of entries, such as genes in a specific gene category.

http://brainstars.org/(type)[/(category)[/(subcategory)[/...]]]/(offset),(limit) http://brainstars.org/(type)[/(category)[/(subcategory)[/...]]]/all
http://brainstars.org/(type)[/(category)[/(subcategory)[/...]]]/count

You can specify "type" in the following list:

• "marker": marker gene candidates
• "multistate": multi-state genes
• "onestate": one-state genes
• "ntnh": inferred connections among CNS regions by neurotransmitter/neurohormone
• "genefamily": gene family / categories

Marker gene candidates (marker)

[List of entries]: http://brainstars.org/marker/{high,low}/(region)/(offset),(limit)
[Count of entries]: http://brainstars.org/marker/{high,low}/(region)/count

{high,low}: "high": highly expressed regions, "low": low expressed regions.
(region): CNS region.

Multi-state genes (multistate)

[List of entries]: http://brainstars.org/multistate/{high,up,low,down}/(region)/(offset),(limit)
[Count of entries]: http://brainstars.org/multistate/{high,up,low,down}/(region)/count

{high,up,low,down}: "high": high state regions, "up": up state regions, "low": low state regions, "down": down state regions.
(region): CNS region.

One-state genes (onestate)

[List of entries]: http://brainstars.org/onestate/(offset),(limit)
[Count of entries]: http://brainstars.org/onestate/count

Inferred connections among CNS regions by neurotransmitter/neurohormone (ntnh)

[List of entries]: http://brainstars.org/ntnh/{high,low}/(ligand-region)/(receptor-region)/(offset),(limit)
[Count of entries]: http://brainstars.org/ntnh/{high,low}/(ligand-region)/(receptor-region)/count

{high,low}: "high": high state regions, "up": up state regions.
(ligand-region): Ligand CNS region.
(receptor-region): Receptor CNS region.

gene family / categories (genefamily)

[List of entries]: http://brainstars.org/genefamily/(category)/(keyword)/(offset),(limit)
[Count of entries]: http://brainstars.org/genefamily/(category)/(keyword)/count

(category): gene family / category name

• "tf": transcription factors
• "transmem": transmembrane genes
• "channel": channel genes
• "gpcr": GPCR genes
• "adhesion": cell adhesion genes
• "excellmat": extracellular matrix genes
• "structural": structural protein genes
• "neurogenesis": neurogenesis related genes
• "hox": homeobox genes
• "nucrcpt": nuclear receptor genes
• "ntnh": neurotransmitter/neurohormone genes
• "axon": axon guidance genes
• "fox": forkhead genes

(keyword): keyword. If no keyword search required, make this omited or blank.

samples

• http://brainstars.org/marker/low/SCN/all
• http://brainstars.org/multistate/up/SCN/20,10
• http://brainstars.org/onestate/count
• http://brainstars.org/ntnh/high/SCN/ME/all
• http://brainstars.org/genefamily/tf//1,20
• http://brainstars.org/genefamily/tf//count
• http://brainstars.org/genefamily/tf/terminal/all
• http://brainstars.org/genefamily/tf/terminal/count

Entry API

Entry API is for obtaining information (annotation, expressions, links) about each entry

http://brainstars.org/probeset/(id)

samples

• http://brainstars.org/probeset/1450371_at
• http://brainstars.org/probeset/1450371_at?content-type=application/json

Content type

How to designate a content type

You can get information in another format rather than default format (default: text/plain in search/list API; text/html in entry API).

1. Using a "content-type" parameter in the query string of the URI.
   Example: http://brainstars.org/marker/high/LS?content-type=application/json
2. Using an "Accept" header of your HTTP request.
   Example: curl -H "Accept: application/json" http://brainstars.org/marker/high/LS
   Example: wget --header "Accept: application/json" http://brainstars.org/marker/high/LS

Supported content type

• JSON (text/x-json or application/json)
• YAML (text/yaml, text/x-yaml, or application/x-yaml)
• Perl Data::Dumper (text/x-data-dumper)
• Perl Data::Denter (text/x-data-denter)
• Perl Data::Taxi (text/x-data-taxi)
• Perl Storable (application/x-storable)
• Perl FreezeThaw (application/x-freezethaw)
• PHP Serialization (text/x-php-serialization)

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Copyright © 2009 RIKEN Center for developmental Biology.