SIB Swiss Institute of Bioinformatics | Expasy e.g. If a resource provides a web service interface, detailed functionality tests can be done. One goal of the new ExPASy portal is to serve as entry point to all scientific databases and tools provided by the SIB, and we revisited the original focus on proteomics accordingly; federated portal rather than a single server. Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland. Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users Authors Sverine Duvaud 1 , Chiara Gabella 1 , Frdrique Lisacek 2 3 , Heinz Stockinger 1 , Vassilios Ioannidis 1 , Christine Durinx 1 Affiliations 1 SIB Swiss Institute of Bioinformatics, Quartier Sorge - Btiment Amphiple, CH-1015 Lausanne, Switzerland. As on-line bioinformatics usage spread and diversified, portals offering single access points were created (1,2) and later on, structured catalogues were proposed (3,4). A query feature is directly accessible from the page header (cf. to explore SIB resources according to various criteria, (iv) a detailed view of each resource providing the user with more information, and a You might also be interested in section allowing to broaden the scope to other SIB resources. Yet, professionals usually tend to wrongly assume that end-users share the same view and behave in a similar way in a given situation. An official website of the United States government. At the end of the iterative phase, the outcome that led to the final wireframe version (Figure 7) was the following: Overall, the users liked the unified search box and confirmed their unawareness of the regular search in the old implementation. Those terms are shown in the box Browse these keywords in Expasy. What information should the detailed views contain? This approach, widely used in other fields such as marketing, e-commerce, and design of mobile applications, is still scarcely explored in bioinformatics. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure . Provide a single search bar for all types of search, with all types of result on a joint page. UniProtKB family classification and annotation, Relationships between protein sequences and motifs, Portal to venom protein UniProtKB/Swiss-Prot entries. To update the pre-existing data, we started by removing decommissioned resources as well as non-SIB resources. Not only did this lead to very few users accessing the platform through mobile devices (around 6%), it also penalised indexing by the major search engines. This website is free and open to all users and there is no login requirement. This functionality, already introduced in the previous version of ExPASy (6), has been revised with the help of the respective web service providers. We also want to thank all the people who contributed to the design, implementation and operation of this new version of Expasy. Lastly, we would like to warmly thank the users who participated in the user testing sessions and those who have been faithful for decades. We also evaluated a series of well-established portals in the world of life sciences, the so-called competitors. It reflects the categories defined to filter the resources (see definition below). Provide an administration interface to add/update/delete resources, open to resource providers and administrators only. Bhagat J., Tanoh F., Nzuobontane E., Laurent T., Orlowski J., Roos M., Wolstencroft K., Aleksejevs S., Stevens R., Pettifer S.et al BioCatalogue: A universal catalogue of web services for the life sciences. Project strategy definition, 2. SIB Swiss Institute of Bioinformatics, Quartier Sorge - Btiment Amphiple, CH-1015 Lausanne, Switzerland. The portal is implemented using the web framework CakePHP (. (PDF) Expasy, the Swiss Bioinformatics Resource Portal - ResearchGate If desired, PeptideMass can return the mass of peptides known to carry post-translational . Appendix A1 for the full list of resources) from more than 20 different SIB groups. The bottom of the page [3] lists the suggestions of resources that share at least one term of the Topic type with ViralZone. Bienert S., Waterhouse A., DeBeer T.A.P., Tauriello G., Studer G., Bordoli L., Schwede T. Pavelin K., Cham J.A., deMatos P., Brooksbank C., Cameron G., Steinbeck C. Karamanis N., Pignatelli M., Carvalho-Silva D., Rowland F., Cham J.A., Dunham I. Posada-Cspedes S., Seifert D., Topolsky I., Jablonski K.P., Metzner K., Beerenwinkel N. Hulo C., DeCastro E., Masson P., Bougueleret L., Bairoch A., Xenarios I., LeMercier P. Liechti R., Gleizes A., Kuznetsov D., Bougueleret L., LeMercier P., Bairoch A., Xenarios I. Noll N.B., Aksamentov I., Druelle V., Badenhorst A., Ronzani B., Jefferies G., Albert J., Neher R.A. Pagni M., Ioannidis V., Cerutti L., Zahn-Zabal M., Jongeneel C.V., Hau J., Martin O., Kuznetsov D., Falquet L. Sigrist C.J.A., DeCastro E., Cerutti L., Cuche B.A., Hulo N., Bridge A., Bougueleret L., Xenarios I. Hadfield J., Megill C., Bell S.M., Huddleston J., Potter B., Callender C., Sagulenko P., Bedford T., Neher R.A. Alocci D., Mariethoz J., Gastaldello A., Gasteiger E., Karlsson N.G., Kolarich D., Packer N.H., Lisacek F. Ison J., Kala M., Jonassen I., Bolser D., Uludag M., McWilliam H., Malone J., Lopez R., Pettifer S., Rice P. Lamprecht A.L., Margaria T., Steffen B. Oxford University Press is a department of the University of Oxford. All the resource-specific information is stored in a relational database back-end and queried using Elastic Search (https://www.elastic.co/elasticsearch/, (20)), with fuzzy search or approximate string- matching search enabled. In the past 27 years, the portal has evolved. The mapping result was then sent to the resource providers along with additional information such as the long and short descriptions, the contact email or the URL. Examples of user-types (personas) and their use cases. Careers, Unable to load your collection due to an error. Project strategy definition, 2. PeptideMass [] cleaves a protein sequence from the UniProt Knowledgebase (Swiss-Prot and TrEMBL) or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. Chiara Gabella, Figure 1. EDAM applicability to searching, categorising and automatic handling of resources has been validated by implementations in eSysbio (https://nels.bioinfo.no/), Bio-jETI (29) and EMBOSS (30), demonstrating its relevance to resource catalogues. We have now turned it into a bioinformatics resource portal that serves not only the field of proteomics but also other domains of life sciences. the contents by NLM or the National Institutes of Health. Documentation. Bhagat J., Tanoh F., Nzuobontane E., Laurent T., Orlowski J., Roos M., Wolstencroft K., Aleksejevs S., Stevens R., Pettifer S. et al. UniProt - Wikipedia official website and that any information you provide is encrypted The added value of Expasy lies in the classification of the resources by category. By clicking on one of the EDAM terms in this box, the user can retrieve all resources that perform the same task. In this context, hundreds of cutting-edge resources are developed and made available to the life science community. Appel RD, Bairoch A, Hochstrasser DF. We have also used the opportunity to critically review the resources on the previous ExPASy server, update them and phase out some of them. Involving resource providers in the continuous content update of Expasy is crucial for ensuring accurate and relevant information. With this approach, the new version focuses specifically on resources developed by or in collaboration with SIB groups, in contrast with previous editions. We are particularly grateful to the SIB-cofounders Ron Appel and Amos Bairoch who created the first version of ExPASy almost three decades ago. The new version of Expasy aims to create a satisfactory user experience. However, old URLs will remain available for some time and are automatically redirected to new URLs. Since then, an increase of 15% in the number of daily users, compared to the same period last year, is observed. In software development, agile refers to discovering requirements and developing solutions through a high level of engagement of cross-functional teams, enabling early delivery and continuous improvement. It was established that testing a wireframe on no more than five users is sufficient to identify the major usability issues (6585%) (32). The redesign process started in 2019. Provide an administration interface to add/update/delete resources, open to resource providers and administrators only. Final product. ), (iii) different types of filters (categories, resource type, etc.) This project has furthermore received funding from ELIXIR and the European Union's Horizon 2020 research and innovation programme under grant agreement number 101003551. Thank you for submitting a comment on this article. sharing sensitive information, make sure youre on a federal Overall, the following information describes each resource: Detailed view of a resource (ViralZone). For instance, the search can even include resources that might not yet be known to the user but still be useful. Ocean Shores, WA Map & Directions - MapQuest The neXtProt knowledgebase in 2020: Data, tools and usability improvements. Our user-centric approach was successfully applied in all phases of development and will remain our strategy in future implementations. Links are provided to >70 databases, a user manual and other documents. National Library of Medicine To reflect the different scientific directions of the SIBs groups, the following scientific categories are currently available: proteomics, genomics, structural bioinformatics, systems biology, phylogeny/evolution, population genetics, transcriptomics, biophysics, imaging and drug design. HHS Vulnerability Disclosure, Help It was redesigned several times and the penultimate version was released in 2011, when it became the ExPASy SIB Bioinformatics Resource Portal, a catalogue of bioinformatics resources (6). Creating personas helps software developers to (i) assess the extent of different needs and expectations, and (ii) optimize the user experience (31). Bethesda, MD 20894, Web Policies It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. Process of development of Expasy. Ison J., Kala M., Jonassen I., Bolser D., Uludag M., McWilliam H., Malone J., Lopez R., Pettifer S., Rice P.. EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats, Bio-jETI: a framework for semantics-based service composition, EMBOSS: the European Molecular Biology Open Software Suite, Applying User Experience (UX) methodologies to science: the example of the BioSODA user interface, A Mathematical model of the finding of usability problems, Conference on Human Factors in Computing Systems - Proceedings, A literature review of the anchoring effect, http://creativecommons.org/licenses/by/4.0/, https://gs.statcounter.com/platform-market-share/desktop-mobile-tablet/worldwide, Docking of small ligands into protein active sites, Orthology inference among complete genomes, Ortholog evolutionary and functional annotations, Protein-protein interaction networks and enrichment analysis. Artimo P., Jonnalagedda M., Arnold K., Baratin D., Csardi G., DeCastro E., Duvaud S., Flegel V., Fortier A., Gasteiger E. et al. ExPASy: SIB bioinformatics resource portal - Oxford Academic Consequently, we regularly monitor all resources on the portal and provide the possibility to notify the resource providers in case of availability issues. Through Expasy ( https://www.expasy.org ), the Swiss Bioinformatics Resource Portal, the scientific community worldwide, freely accesses more than 160 SIB resources supporting a wide range of life science and biomedical research areas. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. Funding for open access charge:SIB Swiss Institute of Bioinformatics. Whenever needed, the user interfaces have been adapted. Through Expasy (https://www.expasy.org), the Swiss Bioinformatics Resource Portal, the scientific community worldwide, freely accesses more than 160 SIB resources supporting a wide range of life science and biomedical research areas. These featured links are updated every week and draws from the list of all SIB resources available via the portal. Furthermore, the workshop aimed to ease the adoption of the future version of Expasy, which is crucial for the long-term revision of resource descriptions, and more generally to sustainable content quality. In addition to an optimised interface that meets users' needs and expectations, the new version of Expasy provides an up-to-date and accurate description of high-quality resources based on a standardised ontology, allowing to connect functionally-related resources. ExPASy: the proteomics server for in-depth protein knowledge and Created in 1993, Expasy, the SIB bioinformatics resource portal, is now available as a new release, after a major overhaul. Databases accessible via the cross-resource search functionality. Liechti R., Gleizes A., Kuznetsov D., Bougueleret L., LeMercier P., Bairoch A., Xenarios I.. OpenFluDB, a database for human and animal influenza virus. Each resource is maintained independently but many of them still follow a common release cycle or database update schedule. A close look at the user behaviour flows revealed the low level of navigation between resources. If a search term is found (for instance UniProtKB), it is highlighted for the specific resource(s). The illustration of Expasy's redesign through a user-centric approach: all the elements that contributed to the process (icons) and the main strengths (stars) of the new implementation. Three personas were created: a bioinformatician, a junior, and a senior biologist (Supplementary File S3 represents the personas and illustrates to what extend the outcome of the study supports the features of each persona). We have added an attractive visual interface that is addressed to new users even if they have little experience with the provided domains and technologies; and. Received 2011 Dec 16; Revised 2012 Apr 10; Accepted 2012 Apr 17. SIB Swiss Institute of Bioinformatics, Quartier Sorge - Btiment Amphiple, CH-1015 Lausanne, Switzerland. The first wireframe of the Expasy project. Figure Figure33 shows a detailed view of ViralZone, a web resource for all virus genera and families. Its content is a long-term commitment of the resource provider community to describe each resource accurately and in a standardised manner. An official website of the United States government. Expasy, the Swiss Bioinformatics Resource Portal, as designed by its Here are some examples of exercises proposed to the users: At the end of the iterative phase, the outcome that led to the final wireframe version (Figure (Figure7)7) was the following: The final version of the iteratively refined wireframe as validated by the end-users. The study of the old ExPASy usage figures were based on Google Analytics spanning the year 2018. The https:// ensures that you are connecting to the Bethesda, MD 20894, Web Policies Genes, Proteins, & Sequence Analysis - Bioinformatics - Research Guides In the remainder of this article, we will present details of the new features as well as some hints for experienced users of the previous ExPASy version. A bounce is when the user opens a single page on a website and exits without triggering any other action. Entry point for the visual guidance interfaceincludes categories to be selected. http://creativecommons.org/licenses/by-nc/3.0, http://wiki.isb-sib.ch/web-team/Sib-resource_query-interface. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. In the old ExPASy, in-house keywords were used to describe each resource main features. Resources are linked one-to-the-other through ontology-based terms. By clicking on the number of hits, the user is redirected to the query results in the respective databases. Although most databases offer their own search functionality, the simultaneous query of a set of databases from a single hub is a convenient option. The details of this benchmarking can be found in Supplementary File S2. Expasy is an essential tool for a large variety of users, from beginners interested in discovering bioinformatics, to advanced scientists looking for specific biological answers. The resource providers were granted access to the Expasy administration interface and provided with a video tutorial. SIB Swiss Institute of Bioinformatics | Expasy With this procedure, along with the yearly update reminder sent to resource providers, we have optimised access to up-to-date and reliable data. Resources listed as cards and sorted randomly in the main section of the page. Since then, an increase of 15% in the number of daily users, compared to the same period last year, is observed. Additionally, a networked organisation of resource descriptions was implemented, to broaden the scope of the initial search and explore the diversity of the SIB resources. Galway Bay Irish Pub. All resources are listed as cards with the resource's name, a short description, type (database and/or tool) and categories. The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss) creates, maintains and disseminates a portfolio of reliable and state-of-the-art bioinformatics services and resources for the storage, analysis and interpretation of biological data. What information should the cards contain?

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