The UniProt Protein DAS Server

The distributed annotation system (DAS) is a client-server system in which a single client integrates information from multiple servers. The UniProt DAS server provides access to sequence and annotation from UniProt, UniParc and IPI. Researchers can then provide annotation of their own results in the context of UniProt annotation, IPI annotation and UniParc cross references through the use of suitable DAS client such as Dasty2 , the Ensembl DAS client or SPICE .

The server also gives access to Gene Ontology Annotation of UniProt sequences (GOA) and theoretical tryptic digests of protein sequences in UniProt and IPI.

An extremely useful resource for users of DAS is the DAS Registration Server that supports registry and discovery of DAS services. The datasources provided by the UniProt DAS server are all registered with this service.

Access the UniProt DAS Server

This is a complete re-write of the UniProt DAS server. The server is now based upon the MyDas Java DAS Server Framework.

The data sources (DSN) available from the DAS reference server have been separated and extended. The previous version of the UniProt DAS server included only one DSN: 'aristotle'. This DSN is still available for services that rely upon it, with the same functionality as provided previously, however the three components of aristotle (UniProt, UniParc and IPI) are also available as separate data sources.

Please Note

The Aristotle das source will be taken offline at the beggining of 2010.

Another major change in the service is the use of the UniProt Java Remoting API (UniProtJAPI) to retrieve data from the UniProt Knowledgebase. This is used to provide sequence information for the UniProt, UniParc and IPI data sources and to retrieve the information for constructing features served from the UniProt and UniParc data sources.

The primary sources of the data avialable from the UniProt DAS reference server include: UniProt/Swiss-Prot , UniProt/TrEMBL , UniParc (The UniProt Archive), IPI (The International Protein Index) and GOA (Gene Ontology annotation of UniProt)

The individual data sources, together with some example queries are presented in the table below:

Data Sources

DSN (Data Source Name)	Type	Description	Coordinate Systems	Example Queries
DSN (Data Source Name)	Type	Description	Coordinate Systems	Sequence Request	Features Request
uniprot	Reference Server	UniProt	UniProt Accession numbers e.g. O35502	sequence	features
uniprot	Reference Server	UniProt	SwissProt ID e.g. A4_HUMAN	sequence	features
uniparc	Reference Server	UniProt Archive (UniParc)	UniParc ID e.g. UPI0000125656	sequence	features
uniprot-tryptic	Annotation Server	Theoretical tryptic peptides based upon a complete and successful digest of the requested UniProt protein with trypsin.	UniProt Accession numbers e.g. O35502	-	features
uniprot-tryptic	Annotation Server		SwissProt ID e.g. A4_HUMAN	-	features
uniprot-goa	Annotation Server	GO Annotation of UniProt	UniProt Accession numbers e.g. P99999	-	features
uniprot-goa	Annotation Server	GO Annotation of UniProt	SwissProt ID e.g. A4_HUMAN	-	features

The UniProt DAS server has been built using the MyDas Java DAS framework.

Project Support

The 'UniProt DAS Service Project' is supported by the Biosapiens Network .

The BioSapiens project is funded by the European Commission within its > FP6 Programme, under the thematic area "Life sciences, genomics and > biotechnology for health,"contract number LHSG-CT-2003-503265.

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