Registry API

Revision as of 10:43, 15 November 2022 by Vinoo (Talk | contribs)

The iGEM Foundation operates the Registry of Standard Biological Parts (Registry), an open community that runs and grows on the "Get, Give, & Share" philosophy. Users get parts, samples, data, and tools from the Registry to work on their synthetic biology projects. They give back to the Registry the new parts they've made, as well as data and experience on new and existing parts.

The Registry has made part information available to software tools developers through a series of API's (Application Programming Interface) to foster this open community.

All Registry content falls under Creative Commons Attribution-ShareAlike.

Before you start, please read through our API Guidelines.


XML Part Information

The database information about each part is now available as XML. You can get information about a part by entering a URL like this one. If your browser parses and displays XML in a formatted way, it will make some sense. The URL ends ...xml/part; you can follow with a list of part names separated by periods.

https://parts.igem.org/xml/part.BBa_B0034

The information for a part includes:

  • Part name, type, nickname, short description, status, rating, date entered, authors, quality
  • Lists of subparts (as specified by the designer, at the basic part level, and with scars)
  • Sequence
  • Features
  • Parameters
  • Categories
  • DNA Samples (not enabled not)
  • References (not enabled now)
  • Groups (not enabled now)

If you enter 'recursive' as the first part name, the returned XML will include details about all the subparts of this part.


DAS - Distributed Annotation System

"The distributed annotation system (DAS) is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up genome annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers." - Wikipedia

FASTA Formatted Sequences

We will provide a daily update of part sequences, types, subparts, status, and short description for each part and for all parts. Go to https://parts.igem.org/fasta/parts/BBa_C0040 (substitute our desired part name for BBa_C0040) and you will receive a FASTA formatted file with the part's sequence. The header line has this format:

'>'[Part name] [First character of status] [Part Id Number] [Part type] [Short description]

Note: the short description has unusual characters converted to their two-digit hex value.

You can also get all of the parts in a single download (about 30 megabytes) as https://parts.igem.org/fasta/parts/All_Parts.

We are not yet updating these files on a daily basis. -- Randy May 30, 2009


POINT-IN-TIME DATABASE DUMP

We now have a point-in-time database dump of the parts as a gzipped XML file or a sql file. This file is a direct dump of the parts table and the sequence and features table of the Registry using mysqldump. This dump was made 11 November 2022.

XML: Download

SQL: Download

We also have an evaluation of the number of times a part is used in other parts. This will be found in the field 'uses'. Note that we have excluded B0015, B0010, B0012, and B0034 from the calculation since they are so often used. We have also excluded construction intermediates since they are neither basic nor final parts. This information is now included in the part download above.