The Protein Identifier Cross-Reference (PICR) service
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The Protein Identifier Cross-Reference (PICR) service. Overview. The problem… What is PICR? Access via web and web services. -No direct comparison of the results can be done. -Both groups used different Protein DB to report their results. The problem…. Protein list A (DB Search vs. IPI)

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The Protein Identifier Cross-Reference (PICR) service

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The protein identifier cross reference picr service

The Protein Identifier Cross-Reference (PICR) service


Overview

Overview

  • The problem…

  • What is PICR?

  • Access via web and web services


The problem

-No direct comparison of the results can be done.

-Both groups used different Protein DB to report their results.

The problem…

  • Protein list A

  • (DB Search vs. IPI)

  • IPI000001

  • IPI000002

  • IPI000003

  • Protein list B

  • (DB Search vs. UniProt)

  • P00001

  • P00002

  • P00003


The problem1

The problem…

  • -No direct comparison of the results can be done.

  • -Both groups used different Protein DB to report their results.

  • Protein list A

  • (DB Search vs. IPI)

  • IPI000001

  • IPI000002

  • IPI000003

  • Protein list B

  • (DB Search vs. UniProt)

  • P00001

  • P00002

  • P00003

We would need to use the PICR tool to be able to make a direct comparison


Databases are all different

Databases are all different


Databases evolve

Databases evolve


Why do you need id mapping

Merging datasets to a common identifier space

Finding all aliases/synonyms for an identifier

(data integration – submissions!)

Mapping from secondary IDs to more recent primary IDs

(data “freshness”)

Preparing data sets for specific tools

Querying in various primary databases

(data format requirements)

Why do you need ID mapping


Protein identifier mapping is hard

The basic problem: the same protein sequence is referred to by multiple accession numbers assigned by multiple databases.

No universal identifier scheme

Redundant databases – multiple identifiers for the same sequence in the same database

Unstable identifiers (ex: gi numbers)

Obsolete and deleted identifiers (hypothetical proteins)

Different production cycles for major databases

Tools exist, but are limited in important their database and species coverage and in their usability and availability.

Protein identifier mapping is hard


Picr home page

PICR Home Page

BLAST functionality for protein fragments

Limit search by taxonomy (pessimistic)

Submit accessions OR sequences (FASTA) with 500 entry interactive limit (no batch limit)

Choose to return all mappings or only active ones

Select output format

Select one or many databases to map to in one request

Run search


Picr result page simple view

Logical xref

(hyperlinked)

Secondary

Identifier

Active xref

(hyperlinked)

Inactive xref

PICR Result Page – simple view


Picr result page detailed view

PICR Result Page – detailed view


Picr result page xls view

PICR Result Page – XLS view


Picr services

PICR services

  • PICR offers both SOAP and REST web service interfaces.

  • Documentation is available online:

  • SOAP: http://www.ebi.ac.uk/Tools/picr/WSDLDocumentation.do

  • REST: http://www.ebi.ac.uk/Tools/picr/RESTDocumentation.do

  • Sample client code and URL examples are provided from the PICR website.


Do you want to know more

Do you want to know more?

Wein et al., NAR, 2012


Questions

Questions?


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