Documentation for the eFamilyService Schema

Version:1.0

Schema Version: 2004-06-17

Last Modification: 2010-09-21

Contributers: Sameer Velankar, Jose Dana, Rob Finn, Dave Howorth, Andreas Prlic

Background

The eFamily project is designed to integrate the information contained in five of the major protein databases (CATH, Interpro, MSD, Pfam and SCOP). The databases CATH, SCOP, Interpro, and Pfam contain information describing protein domains. The domain definitions of the former two databases are based on protien structure, while the latter two databases are based on protein sequence. The MSD database is the primary data warehouse for data exchange and integration, containing the fundamental mapping from protein sequence (UniProt) to structure (PDB).

Although the different domain databases perspectives on proteins are related, it is often difficult for biologists to navigate from protein sequence to protein structure and back again. The aim of this project is to provide the scientific community with a coherent and rich view of protein families that allow users to seamlessly navigate between the worlds of protein structure and protein sequence. In this project we are developing data exchange mechanisms and services that exploit grid utilities.

The aim of the eFamilyService schema is to allow multiple database entries that have been wrapped up in the eFamily schema, to be returned as a list of entries. This is particularly important for webservices where you only want to open up a single transaction to return the results from a query.

The Schema

Below we describe the eFamilyService schema.

The eFamilyService schema imports the following two schemas:

dcmes-rdf.xsd, under the namescape rdf.
efamily.xsd

Schema Location:http://www.ebi.ac.uk/pdbe/docs/sifts/eFamilyService.xsd

The Root: resultList element

resultList element

Format:

<resultList>
	<rdf:RDF>see below</rdf:RDF>
	<ef:entry>see below</ef:entry>
</resultList>

Element:<entry>

(required; one or more) The root element is entry. This represents any database entry. As such, the attributes for this element define the database source.

The ef:entry element

The is the location of the imported eFamily schema. Thus, refer to the eFamily schema documentation.

The rdf:RDF element

The Resource Description Framework (RDF) is an imported schema that allows the encapsulation of metadata. It is beyond the scope of this documentation to describe the imported schema, but more information can be found out here.

Some Examples

A Pfam domain query service output. In this example, a user has submitted a novel sequence to Pfam. A list of Pfam domains on this sequence have been returned.

A SCOP domain query service output. In this example, a user has submitted the PDB accession code 1CGP. A list of SCOP domains in this structure have been returned.