About

OBD Phenotype data is available for download in a number of file formats. The core exchange format will be pheno-XML; generic ontology tools will use OBO or OWL instance format.

Representing Phenotypes

Document in progress:

pheno-syntax

Pheno-syntax is a compact syntax for the representation of phenotypes using ontologies.

xml-format

Pheno-xml format. For a definition of this format, see the schema description in the following languages:

Autogenerated documentation (derived from XSD) is also available. Current version: 0.11

The master version is maintained in RNC - RNG and XSD are generated from this. (For RNC mode, emacs users may be interested in RNC Mode). I recommend the RNC format as the best way for new users to get a handle on pheno-xml

obo

OBO 1.2 format can be used to represent generic instance data. See obo-format. Should correspond directly to OWL export (below)

There are a number of ways to map phenotypes to OBO/OWL instances - the current mapping may change. More details coming soon.

owl

RDF/OWL instance data. See OWL for more on OWL.

pro

Prolog database file. This uses a relational schema that is similar to the pheno-xml schema. This format is also suitable for loading into SQL databases with minor syntactic transformations.

For predicate definitions, see [COMING SOON]

tbl

Simple tabular summary (lossy format)

chado-xml

Chado-XML is an isomorphic mapping of the Chado relational schema to XML. More details here when the new Chado phenotype module is finalised