Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Jul;41(Web Server issue):W601-6.
doi: 10.1093/nar/gkt392. Epub 2013 May 13.

A new reference implementation of the PSICQUIC web service

Noemi del-Toro  1 , Marine Dumousseau, Sandra Orchard, Rafael C Jimenez, Eugenia Galeota, Guillaume Launay, Johannes Goll, Karin Breuer, Keiichiro Ono, Lukasz Salwinski, Henning Hermjakob
Affiliations

A new reference implementation of the PSICQUIC web service

Noemi del-Toro et al. Nucleic Acids Res. 2013 Jul.

Abstract

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 (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml).

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Structure of the URL to fetch data from PSICQUIC service.
Figure 2.
Figure 2.
Dataflow followed by the reference implementation from its origin in the molecular-interaction databases to the end user through PSICQUIC.
Figure 3.
Figure 3.
PSICQUIC View is a client for PSICQUIC services in which by formulating only one query fetches all the relevant molecular interactions available in the registered services. After the search, the user can choose from studying the results in more detail, viewing the interaction network, downloading or clustering the results.
Figure 4.
Figure 4.
Structure of the URL to fetch data from PSICQUIC registry.
See this image and copyright information in PMC

References

    1. Orchard S, Kersey P, Hermjakob H, Apweiler R. The HUPO proteomics standards initiative meeting: towards common standards for exchanging proteomics data. Comp. Funct. Genomics. 2003;4:16–19. - PMC - PubMed
    1. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, et al. The HUPO PSI's molecular interaction format–a community standard for the representation of protein interaction data. Nat. Biotechnol. 2004;22:177–183. - PubMed
    1. Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, et al. The minimum information required for reporting a molecular interaction experiment (MIMIx) Nat. Biotechnol. 2007;25:894–898. - PubMed
    1. Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H. Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition. Proteomics. 2007;7(Suppl. 1):28–34. - PubMed
    1. Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, et al. Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat. Methods. 2012;9:345–350. - PMC - PubMed

Publication types