slide1
Download
Skip this Video
Download Presentation
The Protein Identifier Cross-Reference (PICR) service

Loading in 2 Seconds...

play fullscreen
1 / 15

The Protein Identifier Cross-Reference (PICR) service - PowerPoint PPT Presentation


  • 52 Views
  • Uploaded on

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)

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'The Protein Identifier Cross-Reference (PICR) service' - karis


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
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

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 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

ad