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Protein Identifier Cross-Reference

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News
March 2013: New EBI Website!

On 4 March, the EMBL-EBI website was relaunched, hoping to give all our visitors a warmer welcome. We?ve been working behind the scenes to give you a more consistent experience, because a big part of our mission is to make molecular data available ? and accessible ? to everyone.

July 2011: New features and databases

We have implemented searching by protein fragments using a homology search (BLAST). In addition queries can be mapped against subsections of Ensembl Genomes corresponding to various taxa. Support for mapping against geneIDs present in Ensembl and Uniprot has also been added.

January 2009: Addition of SEGUIDs

We have implemented the SEGUID algorithm to generate sequence-based unique identifiers, as described in Babnigg, 2006.

January 2009: New databases and bugfixes

We have added the KIPO database as well as several ENSEMBL genome databases to the mapping algorithm. We have also improved the PICR codebase to make it more robust. PICR has been the victim of its own success in recent months and has had problems coping with the demands put on the web application. These problems should now be resolved.

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Just as it is possible to query PICR using SOAP, as described in the WSDL and detailed in the webservice documentation, it is also possible to use RESTful URLs to query the service and obtain XML in return.

RESTful URLs are useful in that there is no need for any external dependency. You simply need to build a well-formatted URL and you will retrieve an XML document that you can consume with your preferred technology platform. The XML document that is returned will contain elements defined in the WSDL schema.

The methods available in the REST service are very similar to those available via SOAP, save for one major difference: only one accession or sequence can be mapped per request.

Method: getUPIForAccession

Base URL: http://www.ebi.ac.uk/Tools/picr/rest/getUPIForAccession

Parameters:

  • accession - the accession to map [required]
  • version - the version of accession to map [optional]
  • database - the database to map to. At least one database is required, but multiple databases can be queried at once.
  • taxid - the NEWT taxon ID to limit the mappings [optional]
  • onlyactive - if true, only active mappings will be returned. If false, results may include deleted mappings. [optional, default is true]
  • includeattributes - if true, extra attributes such as sequence and taxon IDs will be returned if available. If false, no extra information returned. [optional, default is false]

Notes:

Parameter names are case sensitive.

If version is not specified but the accession is of the form P29375.1, the accession and version will automatically be split to accession=P29375 and version-1.

If a taxid is submitted, includeattributes will be true.

Example: http://www.ebi.ac.uk/Tools/picr/rest/getUPIForAccession?accession=P29375&database=IPI&database=ENSEMBL

Method: getUPIForBLAST

Base URL: http://www.ebi.ac.uk/Tools/picr/rest/getUPIForBLAST

Parameters:

  • blastfrag - the AA fragment to map to map [required]
  • database - the database to map to. At least one database is required, but multiple databases can be queried at once.
  • taxid - the NEWT taxon ID to limit the mappings [optional]
  • onlyactive - if true, only active mappings will be returned. If false, results may include deleted mappings. [optional, default is true]
  • includeattributes - if true, extra attributes such as sequence and taxon IDs will be returned if available. If false, no extra information returned. [optional, default is false]
  • BLAST search parameters: These should not be changed unless you are sure that you know what you are doing.
    • filtertype - which parameters should the BLAST results be filtered by, valid values are ORGANISM, IDENTITY, ORGANISM_AND_IDENTITY, and NONE. [optional, defaults to NONE]
      • identityvalue - the minimum score to accept as a BLAST hit. [required if filtertype is IDENTITY or ORGANISM_AND_IDENTITY]
      • identitytaxon - the target organism that BLAST is filtering for. [required if filtertype is ORGANISM or ORGANISM_AND_IDENTITY]
    • program - which BLAST program to use for mapping [optional, defaults to blastp]
    • matrix - specifies which protein scoring matrix to use. [optional, defaults to BLOSUM62]
    • alignments - specifies the number of alignments to find pre-filtering (there is probably no need to change this.) [optional, defaults to 100]
    • scores - sets the maximum number of scores to display in output. [optional, defaults to 100]
    • exp - sets the E-value cutoff. [optional, defaults to 10]
    • dropoff - Amount score must drop before extension of hits is halted. [optional, defaults to 0]
    • gapopen - sets the gap opening penalty. [optional, defaults to 11]
    • gapext - sets the gap extension penalty [optional, defaults to 1]
    • gapalign - perform gapped alignment. [optional, defaults to true]
    • filter - specifies filters to be used to mask query sequence. See table 3.2.7 for details. [optional, defaults to F, ie none]
    • align - sets the alignment view. [optional, defaults to 0]
    • stype - sets the type of submission. [optional, defaults to protein]
    • blastdb - set the database against which to query the protein fragments. [optional, defaults to uniprotkb]

Notes:

Parameter names are case sensitive.

If a taxid is submitted, includeattributes will be true.

Example: http://www.ebi.ac.uk/Tools/picr/rest/getUPIForBLAST?blastfrag=MSVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS&database=SWISSPROT

Method: getUPIForSequence

Base URL: http://www.ebi.ac.uk/Tools/picr/rest/getUPIForSequence

Parameters:

  • sequence - the sequence to map [required]
  • database - the database to map to. At least one database is required, but multiple databases can be queried at once.
  • taxid - the NEWT taxon ID to limit the mappings [optional]
  • onlyactive - if true, only active mappings will be returned. If false, results may include deleted mappings. [optional, default is true]
  • includeattributes - if true, extra attributes such as sequence and taxon IDs will be returned if available. If false, no extra information returned. [optional, default is false]

Notes:

Parameter names are case sensitive.

Some servers, browsers and other clients may have restrictions on the length of the query string, so long sequences might cause errors. If this is the case, use a POST request rather than a GET.

If a taxid is submitted, includeattributes will be true.

Example: http://www.ebi.ac.uk/Tools/picr/rest/getUPIForSequence?sequence=MDSTNVRSGMKSRKKKPKTTVIDDDDDCMTCSACQSKLVKISDITKVSLDYINTMRGNTLACAACGSSLKLLNDFAS&database=IPI&database=ENSEMBL&database=SWISSPROT

Method: getMappedDatabaseNames

Base URL: http://www.ebi.ac.uk/Tools/picr/rest/getMappedDatabaseNames

Parameters: None

Example: http://www.ebi.ac.uk/Tools/picr/rest/getMappedDatabaseNames spacer
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