iRefIndex: A consolidated protein interaction database with provenance

By Sabry Razick, G. Magklaras, Ian M. Donaldson. BMC Bioinformatics, 2008

594 citations recorded by the source corpus.

BackgroundInteraction 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.ResultsWe 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.ConclusionWe 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 http://irefindex.uio.no. This index may form the basis of alternative redundant groupings based on gene identifiers or near sequence identity groupings.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a4379a159ff5a4540dd81f00b3a3fd1adc44e399

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

The BioGRID Interaction Database: 2011 update (2010, methodology): “BioGRID data are also available through partner model organism databases (MODs) including SGD (8), FlyBase (21), TAIR (10) and GeneDB (9), through external resources such as NCBI Entrez-Gene, DroID (22) and GermOnline (23), and through meta-databases such as STRING (24), iRefIndex (25) and Pathway C”
MINT, the molecular interaction database: 2009 update (2009, background): “Nevertheless no single database covers the entire interaction information reported in the literature and, to achieve the largest possible coverage, users or online resources are forced to combine data downloaded from diﬀerent databases with diﬀerent data models and ontologies (1–4).”
Pathway and Network Analysis of Cancer Genomes (2015, unknown): “These methods begin with a list of mutated or otherwise altered genes, and one or more databases of gene or protein interactions, such as those compiled by iRefIndex 35 , BioGRID 36 , IntAct 37 , STRING 38 , or GeneMANIA 39 ( Supplementary Table 2 ).”
The BioGRID interaction database: 2017 update (2016, background): “This feature enables external resources such as NCBI (29), Uniprot (28) and others (23– 25, 27, 30, 31 , 39 , 74– 76”
Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping (2011, methodology): “While there are already several interaction databases implementing the PSICQUIC interface [43-50], Bio::Homology:: InterologWalk currently relies on EBI IntAct [36] as its source of experimental interactions.”
GeneMANIA Prediction Server 2013 Update (2013, methodology): “Our network data come from six main sources: IRefIndex (23) and BioGRID (24) for physical (i.e., protein) interactions and genetic interactions; Gene Expression Omnibus (GEO) for co-expression networks (25); InterPro, via Ensembl, for protein domains (26); I2D for networks of interologs of physical ”
The BioGRID interaction database: 2015 update (2014, background): “…also accessible to the individual researcher indirectly through a number of other biological databases including NCBI Entrez-Gene (48), Uniprot (49), DroID (80), GermOnline (81), FlyBase (42), TAIR (73), SGD (41), PomBase (43), STRING (47), iRefIndex (82), GeneMania (83) and Pathway Commons (50).”
The BioGRID interaction database: 2013 update (2012, background): “5) and tabular (tab, tab2 and mitab) formats and are also available through NCBI Entrez-Gene (32), DroID (38) and GermOnline (39), through several major MODs such as FlyBase (26), TAIR (15), SGD (13) and PomBase (14), and through meta-databases such as STRING (40), iRefIndex (41) and Pathway Commons”