Registry API

Revision as of 13:01, 25 October 2010 by Jcnossen (Talk | contribs) (→‎Part query service)

The information in the Registry is being made available to software tools developers through a series of API's (Application Programming Interface). These interfaces will change with time.

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. 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 6 April 2010. We will put it on a cron job in the future.

All of the database parts information (including sequences and features): 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. A subset of the part information and the number of parts using this part: Download


Part query service

I have set up an automated mirror of the parts.igem at http://igempartview.appspot.com (Running on [http://code.google.com/intl/nl-NL/appengine/ Google AppEngine]). Also see the description at our team wiki: [http://2010.igem.org/Team:TU_Delft/Software/part-search Part search server]

It can be used to query parts based on various properties such as the categories. See the [http://igempartview.appspot.com/api.jsp API description] for more details about using it. However, the mirror is limited by the parts reported by the DAS server 'parts.igem.org/das/parts/entry_points', which returns some older snapshot of the part IDs.

-- Jelmer Cnossen, Oct 23, 2010. (TU Delft 2010 Team)