ExPASy: SIB bioinformatics resource portal - PubMed (original) (raw)

. 2012 Jul;40(Web Server issue):W597-603.

doi: 10.1093/nar/gks400. Epub 2012 May 31.

Manohar Jonnalagedda, Konstantin Arnold, Delphine Baratin, Gabor Csardi, Edouard de Castro, Séverine Duvaud, Volker Flegel, Arnaud Fortier, Elisabeth Gasteiger, Aurélien Grosdidier, Céline Hernandez, Vassilios Ioannidis, Dmitry Kuznetsov, Robin Liechti, Sébastien Moretti, Khaled Mostaguir, Nicole Redaschi, Grégoire Rossier, Ioannis Xenarios, Heinz Stockinger

Affiliations

ExPASy: SIB bioinformatics resource portal

Panu Artimo et al. Nucleic Acids Res. 2012 Jul.

Abstract

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

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Figures

Figure 1.

Figure 1.

ExPASy homepage.

Figure 2.

Figure 2.

Detailed information describing a resource.

Figure 3.

Figure 3.

Overview of resources that can be queried via the cross-resource search interface (A) (Query all databases). If a resource implements the cross-resource search interface (B) (indicated by the red box named ‘Query interface’ and the arrow leading to the resource), ExPASy will query the resource directly. Other resources that do not implement this specific interface (even if they have other query features), are not included in ExPASy’s parallel query.

Figure 4.

Figure 4.

Entry point for the visual guidance interface—includes categories to be selected.

Figure 5.

Figure 5.

Tag cloud in the visual guidance interface.

Figure 6.

Figure 6.

Monitoring information for a specific resource on the portal. This information is available if one clicks on the resources status sign displayed on the top right in Figure 2.

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References

    1. Appel RD, Bairoch A, Hochstrasser DF. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem. Sci. 1994;19:258–260. - PubMed
    1. Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003;31:3784–3788. - PMC - PubMed
    1. Pettifer,S., Ison,J., Kalas,M., Thorne,D., McDermott,P., Jonassen,I., Liaquat,A., Fernández,J.M., Rodriguez,J.M., INB-Partners et al. (2010) The EMBRACE web service collection. Nucleic Acids Res., 38, W719–W723. - PMC - PubMed

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