About
Chaos-XML is an file format based on the sequence modules of the chado relational schema. Chaos-XML is for representing sequences and sequence features in a graph-like structure, typed according to SO.
Bio-Chaos is a utility consisting of perl modules and xsl transforms to help import, export and manipulate sequence feature data.
Both Chaos-XML and Bio-Chaos is Free Software, available, licensed under the LGPL.
Bio-Chaos or Chaos-XML can be cited as [INSERT CGL REF HERE]
Chaos-XML
Chaos-XML is the file format at the core of the Bio-Chaos library, and is also used heavily by CGL. Chaos-XML is a simplified XML version of the sequence module of the chado relational schema, and is designed to be highly compatible with Chado. Chaos-XML can be seen as a lightweight alternative to Chado-XML. Chaos-XML is more suited towards bioinformatics data mining applications, and Chado-XML is more suited towards "enterprise level" and database related use.
More details can be found on the specification page
Bio-Chaos
Bio-Chaos is a perl module that helps import, export and manipulate Chaos-XML. Bio-Chaos is not a necessary requirement for using Chaos-XML. Bio-Chaos is bundled with some xsl transforms. These can be used in conjunction with the Bio-Chaos perl module, or they can be used independently. See the Bio-Chaos XSL documentation for more details.
One of the main uses of Bio-Chaos is to convert genbank files to Chaos-XML
Requirements
There are no requirements for using Chado-XML as a representation format. If you wish to use Bio-Chaos then the following perl modules are absolutely required:
- Graph
- Data-Stag
- Datastore-MD5 (available from Yandell Lab)
- BioPerl - You will need bioperl 1.5, or you can download this tarball
- XML-Parser-PerlSAX - This is required for parsing Chaos-XML. Note that if all you are doing is generating Chaos-XML for use with another library (eg CGL) then you do not need this
- xsltproc - This (or another XSLT processor of your choice) is required for doing some conversions of Chaos-XML files - for example, converting to Chado-XML and back. (Note that if you have installed libxslt or XML::LibXSLT then you will already have this)
Download
The Bio-Chaos library can be downloaded from CPAN. The current release is 0.02. See the instructions.
Etymology
The name "Chaos" was derived from "Chado". The name was used internally at the BDGP and then became fixed. There is no relation to Chaos plots