Welcome to iRefIndex
Proteomics Standard Initiative Common Query InterfaCe for iRefIndex

New iRefIndex release!

iRefIndex iRefIndex is a meta resource based on matching protein sequence data, providing access to a large collection of protein-protein interaction data aggregated from major primary public databases (including BIND, BAR, BioGRID, CORUM, DIP, InnateDB, IntAct, HPRD, HuRi, MATRIXDB, MPACT, MPPI and MPIDB, REACTOME, VIRUSHOST, UNIPROTPP, HPIDB, BHF-UCL, and QuickGO). This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. Hence, iRefIndex represents a unifying index that facilitates searching for these data whilst grouping together redundant interaction data and recording the methods used to perform this grouping. 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. This tool originally developed by Ian Donaldson is maintained by VIB Technologies.

Furthermore, the PSICQUIC web service of this new version has been setup and is hosted on a virtual server at University of Ghent. We anticipate to release more regular updates in the future.

More information on the current version 20 at the iRefIndex wiki page

Contact: technologies.software@vib.be

Scope of use of iRefIndex

Background: iRefIndex is a meta-resource that provides information about physical protein-protein interactions: proteins that interact physically with one another, detected by various experimental methods. It provides information on the proteins involved in the interaction, the methods used to detect the interaction, and the publications in which the interactions were reported. This information can be used by scientists to better understand the molecular mechanisms of cellular processes and to aid in the discovery of new therapeutic targets. Indeed, physical protein interactions contribute to nearly all cellular processes [1], and their disruption often causes disease [2,3]

iRefIndex can be used to:

1. Understand the molecular mechanisms of cellular processes.
2. Identify new drug targets and understand how drugs interact with their targets.
3. Help generate hypotheses for further experimentation.
4. Study protein-protein interactions and networks and help to understand the complexity of biological systems.
5. Provide a resource for functional annotation and data integration.
6. Identify potential new partners for a protein of interest.
7. Aid in the prediction of protein functions.
8. Help to identify and understand the role of disease-associated proteins.

Overall, iRefIndex is a valuable resource for life scientists to help them better understand the complex interactions and networks in living systems. Resources which use iRefIndex for their application:

HumanNet v3: an improved database of human gene networks for disease research (https://doi.org/10.1093/nar/gkab1048)
m6Acancer-Net: identification of m6A-mediated cancer driver genes from gene-site heterogeneous network (https://doi.org/10.1016/j.ymeth.2022.04.002)
BETA: a comprehensive benchmark for computational drug–target prediction (https://doi.org/10.1093/bib/bbac199)
XDeathDB: a visualization platform for cell death molecular interactions (https://www.nature.com/articles/s41419-021-04397-x)
FunCoup 5: functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity (https://doi.org/10.1016/j.jmb.2021.166835)
Genoppi: an open-source software for robust and standardized integration of proteomic and genetic data (https://rdcu.be/cP8gI) TargetMine:
TargetMine: a web-based platform that provides integrated access to various data resources related to drug target discovery and validation. Including information on proteins, pathways, drugs and small molecules, as well as their interactions. https://targetmine.mizuguchilab.org/bluegenes)

About iRefIndex

iRefIndex has first been developed by Ian Donaldson and his Team in Norway in 2008 [4] In 2010 it has been incorporated into the IrefWeb resource developed by the group of Shoshana Wodak (Hospital of Sick Children, and University of Toronoto) [5]. Since 2017 iRefIndex has moved to the VIB (Vlaams Institute of Biotechnology), where it is being further developed by and actively maintained in collaboration with Shoshana Wodak currently Visiting Group Leader at the VIB-VUB Center for structural Biology (https://wodaklab.sites.vib.be/en) [6]
Background: Interaction data for a given protein may be spread across multiple databases.  We set out to create a unifying index that would facilitate searching for these data and that would group together redundant interaction data while recording the methods used to perform this grouping.

Results: We present a method to generate a key for a protein interaction record and a key for each participant protein. These keys may be generated by anyone using only the primary sequence of the proteins, their taxonomy identifiers and the Secure Hash Algorithm. Two interaction records will have identical keys if they refer to the same set of identical protein sequences and taxonomy identifiers. We define records with identical keys as a redundant group. Our method required that we map protein database references found in interaction records to current protein sequence records. Operations performed during this mapping are described by a mapping score that may provide valuable feedback to source interaction databases on problematic references that are malformed, deprecated, ambiguous or unfound. Keys for protein participants allow for retrieval of interaction information independent of the protein references used in the original records.

Conclusion: We have applied our method to protein interaction records from BIND, BioGrid, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. The resulting interaction reference index is provided in PSI-MITAB 2.5 format at https://irefindex.vib.be/wiki. This index may form the basis of alternative redundant groupings based on gene identifiers or near sequence identity groupings."

[1]Alberts B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 1998;92(3):291-294.
[2]Barabasi AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet 2011;12(1):56-68.
[3] Ideker T, Sharan R. Protein networks in disease. Genome Res 2008;18(4):644-652.
[4] Razick, S., Magklaras, G., & Donaldson, I. M. (2008). iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics, 9(1), 405. https://doi.org/10.1186/1471-2105-9-405
[5] iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Turner B, Razick S, Turinsky AL, Vlasblom J, Crowdy EK, Cho E, Morrison K, Donaldson IM, Wodak SJ. Database (Oxford). 2010 Oct 12;2010:baq023. doi: 10.1093/database/baq023. PMID: 20940177]
[6]Navigating the Global Protein-Protein Interaction Landscape Using iRefWeb. Turinsky AL, Dupont S, Botzki A, Razick S, Turner B, Donaldson IM, Wodak SJ. Methods Mol Biol. 2021;2199:191-207. doi: 10.1007/978-1-0716-0892-0_12. PMID: 33125652]


"The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement."

del-Tro, N., Dumousseau, M., Orchard, S., Jimenez, R. C., Galeota, E., Launay, G., Hermjakob, H. (2013). A new reference implementation of the PSICQUIC web service. Nucleic Acids Research, 41(W1), W601-606. https://doi.org/10.1093/nar/gkt392

Access the WebService

The list of available services is available under https://irefindex.vib.be/webservices/