h1. {color:#807f83}Allen Brain Atlas API{color}

The Allen Institute for Brain Science offers access to its published data through an application programming interface (API). The API, documentation, sample applications, and [2012 Allen Brain Atlas Hackathon|http://community.brain-map.org/display/hackathon/2012+Allen+Brain+Atlas+Hackathon] materials are made available to the community under the Allen Institute's [Terms of Use|http://www.alleninstitute.org/Media/policies/terms_of_use_content.html] in hopes of facilitating discovery.

Learn about the API with these atlas and resource overviews:

h5. Atlases

!mouse_brain.png|width=32!*Mouse Brain*
!developing_mouse_brain.png|width=32!*Developing Mouse Brain*
!mouse_connectivity.png|width=32!*Mouse Connectivity*
!human_brain.png|width=32!*Human Brain*
!developing_human_brain.png|width=32!*Developing Human Brain*
!nhp.png|width=32!*Non-Human Primate*

h5. Resources

| [Atlas Drawings and Ontologies |api:Atlas Drawings and Ontologies] | Download colorized and labeled atlas images, histological images, SVG atlas graphics and the associated structure ontology. |
| [api:Data Model] | The data model includes entities from molecular biology, anatomic atlases, laboratory artifacts, experiments, and annotations. |
| [Downloading 3-D Expression Grid Data |api:Downloading 3-D Expression Grid Data] | Download 3-D expression grid data packaged into a compressed archive file (.zip). |
| [Downloading and Displaying SVG |api:Downloading and Displaying SVG] | The SVG download service returns annotations associated with the specified SectionImage as scalable vector graphics. |
| [api:Downloading an Image] | The image download services serves whole and partial two-dimensional images presented on the Allen Brain Atlas Web site. |
| [Downloading an Ontology's Structure Graph |api:Downloading an Ontology's Structure Graph] | Download a hierarchical XML or JSON document containing each of the Structures in the requested StructureGraph. |
| [Example Queries for Experiment Metadata |api:Example Queries for Experiment Metadata] | Commonly requested queries for experiment metadata. |
| [Image-to-Image Synchronization|api:Image-to-Image Synchronization] | Image synchronization services based on the image alignment results. |
| [Quantified Data by Structures |api:Quantified Data by Structures] | Gene expression and projection statistics. |
| [RESTful Model Access (RMA) |api:RESTful Model Access (RMA)] | An HTTP service designed along RESTful principles to allow access to data in the Allen Institute API. |
| [api:Searching Annotated SectionDataSets] | Search expert annotations of the Developing Mouse Brain Atlas' ISH data. |
| [Searching a Specimen or Structure Tree |api:Searching a Specimen or Structure Tree] | The Structure and Specimen Tree Search services return flat lists of ancestors and/or descendants for a specified structure or specimen. |


For more detailed information, please refer to the [Allen Brain Atlas Data Portal |http://www.brain-map.org].

h6. Example Applications

The [example applications |http://www.brain-map.org/api/1.html] demonstrate several features of the API for the following studies:

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* Mouse Brain
* Human Brain Microarray
* Developing Mouse Brain
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h6. Accessing Data and Services

In the spirit of [REST|http://en.wikipedia.org/wiki/Representational_State_Transfer], the Allen Institute publishes its data model as documents that can be requested using the standard HTTP method, GET. Use RESTful Model Access (RMA) with the following services for searching and downloading data:

* [RESTful Model Access (RMA)|api:RESTful Model Access (RMA)] for searching and retrieving data in JSON, XML and CSV
* [SectionImage, AtlasImage, and ProjectionImage download services|api:Downloading an Image] for whole or partial images
* NeuroBlast Service for finding genes with a similar spatial expression profile to a seed gene when compared over a user-specified domain
* Differential Search Service for finding genes with higher expression in 1..n structures when compared to another 1..n structures
* [Image-to-Image Synchronization Service|api:Image-to-Image Synchronization] uses alignment results to find corresponding position between SectionDataSets, the 3-D reference model and structures
* [Structure Graph Download Service|api:Downloading an Ontology's Structure Graph] for downloading anatomic structure ontologies
* [3-D Expression Grid Data Service|api:Downloading 3-D Expression Grid Data] for a 3-D gene expression summary re-sampled to a canonical reference space