PSICQUIC and PSISCORE: accessing and scoring molecular interactions

By Bruno Aranda, H. Blankenburg, Samuel Kerrien, Fiona S. L. Brinkman, Arnaud Céol, Emilie Chautard, J. M. Dana, J De Las Rivas, M. Dumousseau, Eugenia Galeota and 30 more. 2011

292 citations recorded by the source corpus.

To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood. A plethora of resources now exist to capture molecular interaction data from the many laboratories generating…

Subfields: Computational Theory and Mathematics, Molecular Biology

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Citations in the corpus

ChEMBL: a large-scale bioactivity database for drug discovery (2011, methodology): “…interoperability of the ChEMBL data with molecular interaction and pathway data (e.g. for annotation of pathways with chemical tools), a subset of the database (compounds active in binding assays against protein targets) is available in PSI-MITAB 2.5 format (30) via PSICQUIC web services (31).”
InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation (2012, methodology): “PSICQUIC web services are RESTful (REpresentational State Transfer) but can also be accessed through SOAP (Simple Object Access Protocol).”
The BioGRID interaction database: 2015 update (2014, methodology): “Finally, we have also implemented support for the PSICQUIC API interface (87), which has resulted in more than 140 000 queries per month from a wide variety of users.”
PATRIC, the bacterial bioinformatics database and analysis resource (2013, methodology): “These data are obtained by mining the public repositories of interaction data found in the PSICQUIC (16) registry.”
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium (2012, methodology): “Recently, a standard interface for direct computational access to standards-compliant molecular interaction data resources, the PSI Common Query Interface (PSICQUIC) was developed 26 .”
The Reactome pathway knowledgebase (2013, methodology): “Reactome is open-source and open-data, and we have continuously supported the major open-data standards in the domain, including BioPAX levels 2 and 3 (24), PSI MITAB (18), Protégé (http://protege.stanford.edu), SBML-ML (25) and SBGN export format.”
MINT, the molecular interaction database: 2012 update (2011, background): “Proteomics Standards Initiative common query interface (PSICQUIC) (11) is a project aimed at standardizing the programmatic access to molecular interaction databases.”
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology (2015, background): “…pathway pages in Reactome (21–23) BindingDB also participates in the Protein Standard Interface Common Query Interface (PSICQUIC; www.ebi. ac.uk/Tools/webservices/psicquic/view/main.xhtml) (24), a web service which provides standardized access to multiple molecular interaction databases.”
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins (2016, background): “Integration efforts made in subdomain areas such as protein–protein interactions have already developed successful solutions (16, 17).”
The IntAct molecular interaction database in 2012 (2011, methodology): “Data is available using IntAct’s PSICQUIC service (8), in addition to being made searchable on the IntAct website.”
HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores (2012, methodology): “The live version of HIPPIE is monthly updated making use of the web query interface PSICQUIC [28], which allows us to automatically retrieve the newest interaction data from most of the manually curated source databases (BioGrid, IntAct, MINT, DIP and BIND) and integrate the new interactions and upd”
HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks (2016, background): “Standards and protocols have been developed that allow the exchange and aggregation of these data (17), facilitating the development of a number of databases that collect the information from different curated sources (2).”
Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences (2016, unknown): “The International Molecular Exchange consortium (IMEx) [93] produced a unique platform (Proteomics Standard Initiative Common QUery InterfaCe) through which PPI databases within the consortium can be queried simultaneously [89, 94].”
The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions (2020, methodology): “Automated retrieval of BioGRID data is also available through the widelyused PSICQUIC interface.(17) Individual users interested in interactions for specific genes or proteins can use the search interface at the top of the BioGRID main page.”
The ConsensusPathDB interaction database: 2013 update (2012, methodology): “To facilitate the exchange and integration of data from different resources, standard ﬁle formats such as PSI-MI (3) and BioPAX (4), and respective platforms for data exchange such as PSICQUIC (5) and Pathway Commons (6) have been developed.”