Difference between revisions of "irefindex-new"
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| [http://wodaklab.org/iRefWeb/ '''iRefWeb'''] | | [http://wodaklab.org/iRefWeb/ '''iRefWeb'''] | ||
| − | iRefWeb provides a searchable web interface to the iRefIndex. | + | iRefWeb provides a searchable web interface to the iRefIndex. This interface was developed as part of a collaboration with the Wodak group at the hospital for Sick Children in Toronto, Canada. |
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| [[iRefIndex#Contact|'''Contact info''']] | | [[iRefIndex#Contact|'''Contact info''']] | ||
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iRefIndex assigns a global unique identifier (rigid) which looks like 'tjWXXjgPyHyT2J6EwED8zK2x18U' to identify interactions that are identical (according to the sequence and taxon ids of the interactors). iRefIndex also assigns similar looking keys to protein interactors. These keys are global meaning they can be generated by anyone using the method described in the paper. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. | iRefIndex assigns a global unique identifier (rigid) which looks like 'tjWXXjgPyHyT2J6EwED8zK2x18U' to identify interactions that are identical (according to the sequence and taxon ids of the interactors). iRefIndex also assigns similar looking keys to protein interactors. These keys are global meaning they can be generated by anyone using the method described in the paper. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. | ||
| − | + | A listing of those responsible for developing and maintaining the database, iRefIndex related publications, references for source databases and works citing and using the iRefIndex is provided here: [[iRefIndex_Citations]] | |
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:During the process of data consolidation, iRefIndex uses a sophisticated method to keep track of potential problems with source records such as outdated or unfound protein identifiers or incorrectly assigned taxonomy identifiers. These data are provided as feedback files to source interaction databases for correction, clarification or improvements to our own system. This process will help to harmonize data representation and improve the overall quality of interaction records for all source databases. This process will also help source databases to exchange data with one another. | :During the process of data consolidation, iRefIndex uses a sophisticated method to keep track of potential problems with source records such as outdated or unfound protein identifiers or incorrectly assigned taxonomy identifiers. These data are provided as feedback files to source interaction databases for correction, clarification or improvements to our own system. This process will help to harmonize data representation and improve the overall quality of interaction records for all source databases. This process will also help source databases to exchange data with one another. | ||
| − | ==iRefIndex availability | + | == iRefIndex availability == |
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| − | + | iRefIndex is made available in a number of formats. See the links at the top of this page. | |
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=== iRefWeb in the NCBI LinkOut programme === | === iRefWeb in the NCBI LinkOut programme === | ||
Many [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] records provided by NCBI contain links to iRefWeb in the [http://www.ncbi.nlm.nih.gov/projects/linkout/index.html LinkOut] section, allowing users to consult iRefWeb for related protein interactions when browsing gene information. The software which exposes iRefIndex information to the LinkOut programme can be found on the [[iRefWeb LinkOut Generator]] page. | Many [http://www.ncbi.nlm.nih.gov/gene Entrez Gene] records provided by NCBI contain links to iRefWeb in the [http://www.ncbi.nlm.nih.gov/projects/linkout/index.html LinkOut] section, allowing users to consult iRefWeb for related protein interactions when browsing gene information. The software which exposes iRefIndex information to the LinkOut programme can be found on the [[iRefWeb LinkOut Generator]] page. | ||
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---- | ---- | ||
| − | == License == | + | == License and disclaimer== |
Data released on the public FTP site is released under Creative Commons Attribution License http://creativecommons.org/licenses/by/2.5/ | Data released on the public FTP site is released under Creative Commons Attribution License http://creativecommons.org/licenses/by/2.5/ | ||
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Data is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. | Data is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. | ||
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== Other Resources == | == Other Resources == | ||
Revision as of 01:20, 15 October 2011
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About iRefIndex
iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. |
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Download
Download iRefIndex version 8.0 in PSI-MITAB tab-delimited format via FTP. |
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iRefScape
iRefScape is a plugin for Cytoscape that exposes iRefIndex data as a navigable graphical network. |
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iRefWeb
iRefWeb provides a searchable web interface to the iRefIndex. This interface was developed as part of a collaboration with the Wodak group at the hospital for Sick Children in Toronto, Canada. |
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iRefR
An R package providing access to iRefIndex data. |
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Web-services
iRefIndex PSICQUIC web services are now running on release 8.0 of iRefIndex |
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iRefIndex Videos |
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Contact info
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Additional information on the iRefIndex database
Source data sets: http://irefindex.uio.no/wiki/Sources_iRefIndex_8.0 Statistics: http://irefindex.uio.no/wiki/Statistics_iRefIndex_8.0 Build process: iRefIndex_Manual Feedback files: README_iRefIndex_Feedback_8.0 Normalization of MI cv terms: Mapping_of_terms_to_MI_term_ids_-_iRefIndex_8.0 Canonicalization: Canonicalization All iRefIndex pages and Archived releases: see below License and disclaimer: see below |
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Credits, publications, citing, and citations
A listing of those responsible for developing and maintaining the database, iRefIndex related publications, references for source databases and works citing and using the iRefIndex. Details here: iRefIndex_Citations
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DiG: Disease Groups http://donaldson.uio.no/wiki/DiG:_Disease_groups The Disease Groups project groups together phenotypically related disease-gene associations found in OMIM's Morbid Map. The resulting map of disease genes may be used to explore relationships between disease genes in the human protein-interactome. Disease groups can be searched on using the iRefScape plugin for Cytoscape. |
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iRefIndex is a PSIMex partner: |
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Contents
A reference index for protein interaction data
iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein.
iRefIndex assigns a global unique identifier (rigid) which looks like 'tjWXXjgPyHyT2J6EwED8zK2x18U' to identify interactions that are identical (according to the sequence and taxon ids of the interactors). iRefIndex also assigns similar looking keys to protein interactors. These keys are global meaning they can be generated by anyone using the method described in the paper. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once.
A listing of those responsible for developing and maintaining the database, iRefIndex related publications, references for source databases and works citing and using the iRefIndex is provided here: iRefIndex_Citations
Long term goals of the iRefIndex project
We believe that protein interaction data hold incredible potential for biomedical research. Presently, these data are collected and archived by multiple groups around the world and the number of groups taking part in this work is growing rather than diminishing.
As such, it is important that these databases have the means to effectively exchange and compare data and that they are curating and representing data using similar standards in order to make their data accessible and allow effective use.
To this end, the iRefIndex project has three long term objectives:
- 1) to facilitate exchange of interaction data between interaction databases.
- The iRefIndex paper describes a method for assigning unique and global identifiers to protein interactors, interactions and complexes. This method is independent of the iRefIndex resource and may be used by anyone to facilitate exchange and consolidation of data.
- 2) to consolidate interaction data from multiple sources.
- The method has been used by to index interaction records from multiple sources. The resulting iRefIndex may be used search for the existence of interaction data for any protein regardless of the original resource. Nine interaction databases have been incorporated so far, others will follow.
- 3) to provide feedback to source interaction databases.
- During the process of data consolidation, iRefIndex uses a sophisticated method to keep track of potential problems with source records such as outdated or unfound protein identifiers or incorrectly assigned taxonomy identifiers. These data are provided as feedback files to source interaction databases for correction, clarification or improvements to our own system. This process will help to harmonize data representation and improve the overall quality of interaction records for all source databases. This process will also help source databases to exchange data with one another.
iRefIndex availability
iRefIndex is made available in a number of formats. See the links at the top of this page.
License and disclaimer
Data released on the public FTP site is released under Creative Commons Attribution License http://creativecommons.org/licenses/by/2.5/
Data is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Other Resources
A collection of resources related to finding and working with protein interaction data: Protein Interaction Resources.
Contact
Suggestions, requests and comments are welcome. Please email
ian.donaldson at biotek.uio.no.
Visiting and mail address info is here.
iRefIndex Google Group
Join the iRefIndex Google group and receive announcement emails and discuss issues related to iRefIndex. Sign up at irefindex google group.
All iRefIndex Pages
Follow this link for a listing of all iRefIndex related pages (archived and current).
