Data Access Web Service

 The Data Access Web Service is the application interface (API) of the BIOFAB's electronic datasheets. It is a RESTful web service that provides the design and performance of BIOFAB parts and constructs.  The data and information are provided in machine-readable formats.

Collections

Collections are sets of annotated parts and constructs that contain the annotated parts. You can access information about collections with the following URL template:

http://io.biofab.org/services/data/collections?format=[ json ]

The words between the brackets describe the values expected for a particular parameter.  For example, a working URL for the template described above is:

http://io.biofab.org/services/data/collections?format=json

Collections Data Fields
Name Field Label Data Type Description
Numeric Identifier id integer Numeric identifier for a collection.
BIOFAB Identifier biofabID String Alphanumeric identifier for a collection.  The BIOFAB identifier is intended to be more user-friendly than the numeric identifier.
Chassis chassis String Biological chassis where the components of a collection are expected to function correctly.
Name name String Name of the collection.
Version version String Version of the collection.  The alphanumeric value of the version has the pattern "##.#.#".  A valid version is, for example, "1.0.1".
Release Status releaseStatus String The maturity of a release.  This field has three possible values: "alpha", "beta", "production".  The alpha status indicates that the data and information provided are correct, but are being curated and enhanced.  The beta status indicates that the data and information provided are correct and complete, but we are collecting user feedback to further enhance the user experience.  The production status indicates that the data and information provided are correct, complete, and unlikely to change till the next release.
Release Date releaseDate Date Date when a collection was released.
Description description String Short description about a collection.

Annotated Parts

Annotated Parts are DNA sequences with one known biological function.  For example, J23101 is a known constitutive promoter.  You can access a collection of annotated parts with the following URL template:

http://biofab.jbei.org/services/data/parts?collectionid=[ collection numeric identifier ]&format=[ json or csv ]

If you do not provide a collection identifier (collectionid) then the web service will return all the available annotated parts.  A working URL for the template described above is:

http://io.biofab.org/services/data/parts?collectionid=2&format=csv

The annotated part data and information in JSON format are organized in a structure that is moving towards compliance with the emerging Synthetic Biology Open Language (SBOL) standard

Constructs

Constructs are DNA sequences that contain one or more annotated parts inserted into a plasmid vector.  You can access a collection of constructs with the following URL template:

http://io.biofab.org/services/data/constructs?format=[ json ]

A working URL for the template described above is:

http://io.biofab.org/services/data/constructs?format=json

The construct information in JSON format is organized in a structure that is moving towards compliance with the emerging Synthetic Biology Open Language (SBOL) standard

Construct Design

Construct design is the complete DNA sequence of a construct with annotations. You can access construct design information with the following URL template:

http://io.biofab.org/services/data/constructs?id=[ construct identifier ]&format=[ insd or genbank ]

A working URL for the template described above is:

http://io.biofab.org/services/data/constructs?id=pFAB314&format=genbank