1 Basic feature overview
2 New to ExPASy
3 Experienced ExPASy users
4 Updates and new releases

1 Basic feature overview

  1. A portal with several features and interfaces.
    • Several scientific categories: ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, evolution, population genetics, transcriptomics etc. The portal provides detailed information on resources from more than 20 different SIB groups all over Switzerland. Each resource is semantically annotated in cooperation with resource providers (i.e. SIB groups) and the SIB Web team. Annotations include scientific categories (proteomics, genomics, structural bioinformatics etc.), keywords, software types (web site, command line tool, library etc.) and others. External resources are also listed but there is no support from them by the ExPASy Team or SIB.
    • Visual Guidance interface addressed to newcomers of ExPASy. It allows you to discover resources based on visual aids such as graphical images and tag clouds. Additionally, this interface proposes alternative entry-points (views) for resources based on DNA, RNA, Protein, Cell, Organism, Population.
  2. Advanced search/query features
    The search feature allows to query databases and to discover resources on the portal:
    • Query databases (cross-resource search functionality): query a set of selected SIB resources for data/content (query types can include free text, UniProtID, UniProtAC, PDBID, GeneIDs etc.). A cross-resource search interface needs to be implemented by each resource that participates in the query.
    • Find resources, i.e. discover databases and/or software tools federated via the portal and provided by different SIB groups or external institutions.
  3. Monitoring of SIB resources
    Each SIB resource that is listed on the portal is periodically checked for availability (i.e. HTTP/FTP test requests are sent to the resource - extensible to more detailed tests). The status of each resource is indicated by a small green (OK) or red (not available) icon. Internally, this functionality is used by service providers and ExPASy operators to ensure a high availability of resources - automatic notifications are sent in case of certain resource failures.
  4. Several links to previous lists of ExPASy resources (proteomics tools, life science directory) are available.

2 New to ExPASy

If you are new to ExPASy, we suggest that you start with the Visual Guidance interface to explore what resources are available.

3 Experienced ExPASy users

Some questions and answers for experienced users of ExPASy.org are given below:

  • Where should I start?
    If you're used to ExPASy.org (i.e. if you knew the previous version before June 2011), you are mainly using resources in the domain of proteomics. Please look in the category "proteomics" for your resources.
  • What is the main difference between the previous (version before June 2011) and the current ExPASy?
    The previous version of ExPASy was a dedicated proteomics server. Now, ExPASy includes all scientific domains supported by SIB groups (genomics, transcriptomics etc.).
  • Where can I report problems?
    Any questions and feedback on ExPASy (incl. resources maintained by the SIB - indicated by red SIB logo) should be reported using the ExPASy helpdesk on the Support page.

4 Updates and new releases

Release in February 2013

The release focuses on some improvements with respect to the resource search feature and keywords:
  • Keywords can now have synonyms
  • Some keywords have been removed from certain resources.

Release in September 2012: External Resources are enabled

  • Several ExPASy users requested that "external" tools (i.e. resources not maintained by the SIB but listed on the page proteomics software tools) should be included in the "Find resources" search and in the proteomics category. This feature has now been enabled. Therefore, SIB and external resources are clearly distinguished by the following logos:
    • SIB resources
    • External resources - (No support from the ExPASy Team)

Update in April 2012

The update mainly focuses on improving the query feature and other minor visual improvements and technical changes. In detail:
  • Query all databases: ExPASy auto-detects the query type, i.e. interprets your input and guesses whether it is a UniProt, PDB, NCBI etc. identifier or free text. If it looks like a database identifier, a more stringent search is performed, and a link to a full text search is provided in case the detected query type does not correspond to the user's expectation.
  • Find resources (previously called "query Resources"): several improvements have been made to return more pertinent results. Just above the list of query results, a box has been introduced to provide query details, e.g. if the result set only shows highest scoring matches or if an approximate search was performed (based on fuzzy text match). In some cases, this may also include a link to include more results with less stringent matches (a button named "Show more results" will appear).
ExPASy new features

The poster gives an overview of ExPASy's features.