|
|
| (28 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| | __NOTOC__ | | __NOTOC__ |
| | | | |
| | + | iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB, MPPI, Reactome, VirHostnet, and QuickGO. |
| | | | |
| − | <div class="floatleft">
| + | {|class="wikitable" style="text-align:left; clear: left" border="0" cellpadding="10" |
| − | <imagemap>
| |
| − | Image:iRefIndex_logo.png|120x120px
| |
| − | default [[iRefIndex#A_reference_index_for_protein_interaction_data]]
| |
| − | desc none
| |
| − | </imagemap>
| |
| − | </div>
| |
| | | | |
| − | iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, InnateDB, IntAct, MatrixDB, MINT, MPact, MPIDB and MPPI.
| + | <!--Download row row--> |
| | + | |- |
| | | | |
| − | [[iRefIndex#A_reference_index_for_protein_interaction_data|Read more]]
| |
| | | | |
| − | | + | <!--Download image--> |
| − | {|class="wikitable" style="text-align:left; clear: left" border="0" cellpadding="10"
| |
| | |<imagemap> | | |<imagemap> |
| | Image:Document-save-80x80.png | | Image:Document-save-80x80.png |
| Line 21: |
Line 15: |
| | desc none | | desc none |
| | </imagemap> | | </imagemap> |
| | + | |
| | + | <!--Download link and text--> |
| | | style="vertical-align: top" | | | | style="vertical-align: top" | |
| | === [[README_MITAB2.6_for_iRefIndex|Download]] === | | === [[README_MITAB2.6_for_iRefIndex|Download]] === |
| | + | Download version 20.0 of the iRefIndex in PSI-MITAB tab-delimited format. |
| | | | |
| − | Download version 14.0 of the iRefIndex in PSI-MITAB tab-delimited format.
| |
| − | |<imagemap>
| |
| − | Image:Accessories-text-editor-80x80.png
| |
| − | default [[iRefIndex_Release_Notes]]
| |
| − | desc none
| |
| − | </imagemap>
| |
| − | | style="vertical-align: top" |
| |
| − |
| |
| − | === [[iRefIndex Release Notes]] ===
| |
| | | | |
| − | View release notes and news for each release of iRefIndex.
| + | <!--More about iRefIndex row--> |
| | |- | | |- |
| | + | |
| | + | <!-- iRefIndex logo --> |
| | |<imagemap> | | |<imagemap> |
| − | Image:pubmed-logo.png|80x80px | + | Image:iRefIndex_logo.png|80x80px |
| − | default [[iRefIndex_Citations]] | + | default [[ iRefIndex more ]] |
| | desc none | | desc none |
| | </imagemap> | | </imagemap> |
| − | | style="vertical-align: top" colspan="3" |
| |
| − | === [[iRefIndex_Citations | Publications, citing, citations and further reading]] ===
| |
| | | | |
| − | iRefIndex related publications, references for source databases and works citing and using the iRefIndex. | + | <!-- iRefIndex more link and text --> |
| − | |-
| |
| − | |<imagemap>
| |
| − | Image:CytoscapeLogo.png|80x80px
| |
| − | default [[iRefScape]]
| |
| − | desc none
| |
| − | </imagemap>
| |
| | | style="vertical-align: top" | | | | style="vertical-align: top" | |
| − | === [[iRefScape|iRefScape]] ===
| |
| | | | |
| − | iRefScape is a plugin for [http://www.cytoscape.org/ Cytoscape] that exposes iRefIndex data as a navigable graphical network. '''Support for iRefScape is currently no available for release 14.'''
| + | === [[ iRefIndex more | More about iRefIndex ]] === |
| − | |<imagemap> | + | |
| − | Image:firefox.png|80x80px
| + | More ways to access iRefIndex, documentation, release notes, citations and references, technical details, mailing list, contact and license. |
| − | default [http://wodaklab.org/iRefWeb/]
| + | |
| − | desc none
| |
| − | </imagemap>
| |
| − | | style="vertical-align: top" |
| |
| | | | |
| − | === [http://wodaklab.org/iRefWeb/ 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. '''iRefWeb presently supports version 13 of iRefIndex'''. Join the iRefIndex Google groups mailing list if you want to be informed of changes.
| + | <!--More about Donaldson Research row--> |
| | |- | | |- |
| − | |<imagemap>
| |
| − | Image:R-logo.jpg|80x80px
| |
| − | default [[iRefR]]
| |
| − | desc none
| |
| − | </imagemap>
| |
| − | | style="vertical-align: top" |
| |
| | | | |
| − | === [[iRefR]] ===
| + | <!-- donaldson research logo --> |
| − | | |
| − | An R package providing access to iRefIndex data.
| |
| | |<imagemap> | | |<imagemap> |
| − | Image:Applications-internet-80x80.png | + | Image:donaldson_research_logo.png|80x80px |
| − | default [[README_PSICQUIC_web_services_for_iRefIndex]] | + | default [[ Donaldson Research ]] |
| | desc none | | desc none |
| | </imagemap> | | </imagemap> |
| − | | style="vertical-align: top" |
| |
| | | | |
| − | === [[PSICQUIC|Web services]] ===
| + | <!-- iRefIndex more link and text --> |
| − | New psicquic webservices are now available at psicquic.irefindex.org. See the [[PSICQUIC | Web Services for iRefIndex]] page for more. PSISCORE web services are still discontinued for the time being.
| |
| − | |-
| |
| − | |<imagemap>
| |
| − | Image:Youtube-256.png|80x80px
| |
| − | default [[iRefIndex_Videos]]
| |
| − | desc none
| |
| − | </imagemap>
| |
| | | style="vertical-align: top" | | | | style="vertical-align: top" | |
| | + | === [[ Donaldson Research | More about Donaldson Research ]] === |
| | | | |
| − | === [[iRefIndex Videos|iRefIndex videos]] ===
| + | Support for updates to and use of iRefIndex can be provided by Donaldson Research. |
| | | | |
| − | Video learning materials for iRefIndex, iRefScape and iRefWeb.
| |
| − | |<imagemap>
| |
| − | Image:Internet-mail-80x80.png
| |
| − | default [[iRefIndex#Contact and mailing list]]
| |
| − | desc none
| |
| − | </imagemap>
| |
| − | | style="vertical-align: top" |
| |
| − | === [[iRefIndex#Contact and mailing list|Contact information and mailing list]] ===
| |
| | | | |
| − | How to get in touch with the developers.
| + | <!--More about VIB row--> |
| | |- | | |- |
| | + | |
| | + | <!-- VIB logo --> |
| | |<imagemap> | | |<imagemap> |
| − | Image:Emblem-notice-80x80.png | + | Image:donaldson_research_logo.png|80x80px |
| − | default [[Sources_iRefIndex]] | + | default [[ Donaldson Research ]] |
| | desc none | | desc none |
| | </imagemap> | | </imagemap> |
| − | | style="vertical-align: top" |
| |
| − | === [[Sources_iRefIndex|Source data information]] ===
| |
| | | | |
| − | Details of all the different source databases that provide the foundation for iRefIndex.
| + | <!-- VIB more link and text --> |
| − | |<imagemap>
| |
| − | Image:X-office-spreadsheet-80x80.png
| |
| − | default [[Statistics_iRefIndex]]
| |
| − | desc none
| |
| − | </imagemap>
| |
| | | style="vertical-align: top" | | | | style="vertical-align: top" | |
| − | === [[Statistics_iRefIndex|Statistical information]] ===
| |
| | | | |
| − | Statistics for the current iRefIndex release.
| + | === [http://irefindex.vib.be More about the VIB Bioinformatics Core] === |
| − | |}
| |
| | | | |
| − | == Technical information on the iRefIndex database ==
| + | The iRefIndex site is now hosted at the VIB Bioinformatics Core including [http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS PSICQUIC webservices] that can be accessed [https://irefindex.vib.be/webservices here] using either SOAP or REST. |
| | | | |
| − | Build process: [[iRefIndex Manual]]
| + | |} |
| | | | |
| − | Feedback files: [[README iRefIndex Feedback]]
| |
| | | | |
| − | Mapping files: [[Protein identifier mapping]]
| |
| − |
| |
| − | Normalization of MI cv terms: [[Mapping of terms to MI term ids - iRefIndex]]
| |
| − |
| |
| − | Canonicalization: [[Canonicalization]]
| |
| − |
| |
| − | Disease Groups: [[DiG: Disease groups]]
| |
| − |
| |
| − | All iRefIndex pages and archived releases: [[iRefIndex#All_iRefIndex_Pages|see below]]
| |
| − |
| |
| − | License and disclaimer: [[iRefIndex#License_and_disclaimer|see below]]
| |
| | | | |
| | ---- | | ---- |
| | | | |
| − | == A reference index for protein interaction data == | + | == Contact == |
| | | | |
| − | iRefIndex provides an index of protein interactions available in a number of primary interaction databases including [http://bond.unleashedinformatics.com/ BIND], [http://www.thebiogrid.org/ BioGRID], [http://mips.gsf.de/genre/proj/corum/index.html CORUM], [http://dip.doe-mbi.ucla.edu/ DIP], [http://www.hprd.org/ HPRD], [http://www.ebi.ac.uk/intact/site/index.jsf IntAct], [http://mint.bio.uniroma2.it/mint/Welcome.do MINT], [http://mips.gsf.de/genre/proj/mpact MPact], [http://mips.gsf.de/proj/ppi/ MPPI] and [http://ophid.utoronto.ca/ 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.
| + | If you have comments, questions or would like to be added to a list receiving news of updates, please write to us at: |
| | | | |
| − | 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.
| + | VIB Bioinformatics core [mailto:bits@vib.be] or Ian Donaldson [mailto:ian@donaldsonresearch.com email me] |
| − | | |
| − | == Publications and further reading ==
| |
| − | | |
| − | iRefIndex related publications, references for source databases and works citing and using the iRefIndex are provided on the [[iRefIndex Citations]] page.
| |
| | | | |
| | ---- | | ---- |
| | | | |
| − | == Long term goals of the iRefIndex project ==
| + | [[Category:iRefIndex]] |
| | | | |
| − | 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.
| + | |<html> |
| | + | <form action="https://www.paypal.com/cgi-bin/webscr" method="post" target="_top"> |
| | + | <input type="hidden" name="cmd" value="_s-xclick"> |
| | + | <input type="hidden" name="hosted_button_id" value="EE635XFGX4E8L"> |
| | + | <input type="image" src="https://www.paypalobjects.com/en_US/NO/i/btn/btn_donateCC_LG.gif" border="0" name="submit" alt="PayPal - The safer, easier way to pay online!"> |
| | + | <img alt="" border="0" src="https://www.paypalobjects.com/en_US/i/scr/pixel.gif" width="1" height="1"> |
| | + | </form> |
| | + | </html> |
| | | | |
| − | :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.
| + | | style="vertical-align: top" | |
| − | | |
| − | ;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: MITAB tab-delimited text files, iRefWeb interface, iRefScape plugin for Cytoscape, PSICQUIC Web services, and an interface for the R programming language environment. See the links at the top of this page. For the license and disclaimer, [[iRefIndex#License_and_disclaimer | see below]].
| |
| − | | |
| − | == Credits and collaborations ==
| |
| − | | |
| − | '''Ian Donaldson''' presently maintains iRefIndex
| |
| | | | |
| − | iRefIndex was originally developed by '''Sabry Razick and Ian Donaldson''' at the Biotechnology Centre of Oslo, University of Oslo.
| |
| | | | |
| − | '''Paul Boddie''' rewrote the iRefIndex codebase in Bash, Python and PostgreSQL while at the Biotechnology Centre of Oslo, University of Oslo.
| + | === [[ Donations | Donations welcome ]] === |
| | | | |
| − | '''George Magklaras''' provided systems engineer support and [http://www.no.embnet.org/ EMBNet Norway] provided hardware support while iRefIndex was hosted at the University of Oslo.
| + | About iRefIndex costs and donating. |
| | | | |
| − | '''Antonio Mora''' developed [[iRefR|iRefR]].
| |
| − |
| |
| − | '''Katerina Michalickova''' developed [[DiG:_Disease_groups|Disease groups]].
| |
| − |
| |
| − | '''Brian Turner and Andrei Turinsky''' from the [http://wodaklab.org/ws/ Wodak group] at the Hospital for Sick Children in Toronto, Canada developed the [http://wodaklab.org/iRefWeb/ iRefWeb interface].
| |
| − |
| |
| − | <imagemap>
| |
| − | Image:IMEx_logo_webmedium.jpg|100x100px
| |
| − | default [http://www.psimex.org]
| |
| − | desc none
| |
| − | </imagemap>
| |
| − |
| |
| − | iRefIndex is a PSIMex partner: http://www.psimex.org
| |
| − |
| |
| − | <!--
| |
| − | === 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.
| |
| | | | |
| | --> | | --> |
| − | ----
| |
| − |
| |
| − | == License and disclaimer==
| |
| − |
| |
| − | Data released on the public FTP site is released under the [http://creativecommons.org/licenses/by/2.5/ Creative Commons Attribution 2.5 Generic (CC BY 2.5) license].
| |
| − |
| |
| − | <imagemap>
| |
| − | Image:By-100x35.png
| |
| − | default [http://creativecommons.org/licenses/by/2.5/]
| |
| − | desc none
| |
| − | </imagemap>
| |
| − |
| |
| − | 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.
| |
| − |
| |
| − | ----
| |
| − |
| |
| − | == Contact and mailing list ==
| |
| − |
| |
| − | Suggestions, requests and comments are welcome.
| |
| − |
| |
| − | <pre>ian@donaldsonresearch.com</pre>
| |
| − |
| |
| − | Full contact details are available at the [http://www.biotek.uio.no/english/research/groups/donaldson-group/ group home page].
| |
| − |
| |
| − | <imagemap>
| |
| − | Image:google-groups-logo.gif
| |
| − | default [http://groups.google.com/group/irefindex]
| |
| − | desc none
| |
| − | </imagemap>
| |
| − |
| |
| − | See the [http://groups.google.com/group/irefindex iRefIndex Google Group] for announcements and discussion.
| |
| − |
| |
| − | == All iRefIndex Pages ==
| |
| − |
| |
| − | Follow this link for a listing of all iRefIndex related pages (archived and current).
| |
| − | [[Category:iRefIndex]]
| |
