[ <Chado> <Difference> <Chado-XML> <Relational bridge> ]

Chado

Chaos-XML is based on the Chado relational model. For a full explanation of the meaning of the elements in Chaos-XML, please refer to the chado documentation, in particular The Chado sequence module

Difference

For the most part, Chaos-XML maps isomorphically to the Chado relational schema. Differences are listed below.

Coordinates
Chaos uses nbeg/nend as opposed to fmin/fmax, as descibed above
Dbxref flattening
Chaos collapses the normalised chado table "dbxref" into a single "dbxrefstr" PCDATA element. See the specification for more details.
Type flattening
Chaos uses a PCDATA element "type" in both feature and feature_relationship. In Chado, types are represented as a foreign key into the cvterm table In Chaos the type string is implicitly mapped to cvterm with the same name as the type, from the Sequence Ontology (SO) CV
Organism flattening
Chaos uses an "organismstr" PCDATA element to represent the normalised chado table "organism". See the specification for more details.

Chado-XML

Chaos-XML can be seen as a lightweight alternative to Chado-XML. The two XML formalisms are intended to be complementary rather than competing. They were developed independently, with different aims. Conversion between the two is simple and well-defined, involving no ad-hoc code, since they both map to the same semantic model

Chaos-XML contains several denormalisations with respect to the chado relational schema, detailed above. This makes the representation more tractable, whilst at the same time making it harder to access certain kinds of data. This is because Chaos-XML is aimed primarily at bioinformatics data mining, whereas Chado-XML is aimed at keeping a high-fidelity representation of normalised database structures. Chaos-XML users may be working solely with file-based databases and datastores, whereas Chado-XML users will typically be working with a Chado database.

The Bio-Chaos collection includes transforms for going back and forth between both representations. The Bio-Chaos distribution also includes some scripts for making the conversion.

Relational bridge

The chado relational schema contains a bridge layer to the chaos model. For more details, see the chado distribution, look in

schema/modules/sequence/bridges