The URLs for SWISS-PROT on the WWW are: http://www.expasy.ch/sprot and http://www. As a consequence, users typically ran the default search (cross-resource search in 77% of cases, according to the server logs). 8600 Rockville Pike Tel: +44 1223 494 457; Fax: +44 1223 494 468; Email: datasubs@ebi.ac.uk (for submission), or datalib@ebi. The new version of Expasy was released in October 2020. Secondly, the website was not responsive, that is, not optimized for mobile devices (Figure 5B). In SWISS-PROT two classes of data can be distinguished: the core data and the annotation. 46(W1), W296-W303 (2018). In reality, the development of high scientific quality resources used to their full potential and performing adequately, must include end-users in the design process from the very beginning. Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, 1211 Geneva 4, Switzerland and Such an endeavor is only a very preliminary step in the understanding of human biological processes. Project strategy definition, 2. High-quality protein knowledge resource: Swiss-Prot and TrEMBL Brief. SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc. Interactive access to SWISS-PROT and TrEMBL The most efficient and user-friendly way to browse interactively in SWISS-PROT or TrEMBL is to use the World-Wide Web (WWW) molecular biology server ExPASy (9). Expert Protein Analysis System: Expasy | PDF | Biostatistics - Scribd In particular, we thank the participants of the workshop in 2019 and the internal groups at SIB (Core-IT, LTTO and Communications and Scientific Events departments). For SWISS-PROT entries) and those databases that share some example, from the home page of SWISS-PROT and TrEMBL, identifier with SWISS-PROT (e.g. In the old ExPASy, in-house keywords were used to describe each resource main features. The law of diminishing returns (33) applies. The new version of Expasy aims to create a satisfactory user experience. SwissProt 20 Years - SwissProt20 and ISMB protein annoitation European Union's Horizon 2020 research and innovation programme under In User Experience (UX), the preliminary phase is essential for making informed decisions. Swiss-Prot is supplemented by TrEMBL which contains computer-annotated entries for all sequences not yet integrated in Swiss-Prot. This contributed to identifying the added-value of Expasy. Examples can be found in Table 3. ch/txt/userman.txt ) follows as closely as possible that of the EMBL Nucleotide Sequence Database. It is a high quality annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions. The final version of the iteratively refined wireframe as validated by the end-users. SWISS-PROT is available at: http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/. The field of bioinformatics evolves rapidly, therefore, through a card-sorting exercise, the categories and sub-categories were updated, as shown in Table 4. UniProt is anELIXIR Core Data Resource and a Global Core Biodata Resource. Provide filters to narrow down the number of resources. We have selected a number of organisms that are the target of genome sequencing and/or mapping projects and for which we intend: (ii) to provide a higher level of annotation; (iii) to provide cross-references to specialised database(s) that contain, among other data, some genetic information about the genes that code for these proteins; and. Full name: Description: SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases. A wireframe is a visual guide that represents the skeleton of a website. Swiss-Shop requests can be submitted at http://www.expasy. The first wireframe consisted of (i) a single search bar, performing the two types of search in parallel (regular and cross-resource search) with no prior selection from a drop-down list, (ii) a homepage showing all resources listed as small cards, with a short description and additional information (website, contact, type, etc. Secondary structure. Five users were recruited either through a mailing campaign across the authors of scientific articles citing Expasy or in person at various scientific meetings. SWISS-PROT protein sequence data bank and its supplement TrEMBL - new features and functionality. This illustrates how we took advantage of the familiarity factor. As a result, they form a network of seamlessly connected resources (more details below). In a few months the combined efforts of a number of sequencing centers and companies will produce a first draft of the human genome sequence. Process of development of Expasy. In SWISS-PROT, annotation is mainly found in the comment lines (CC), in the feature table (FT) and in the keyword lines (KW). UniProtKB/Swiss-Prot Protein knowledgebase Evolution biology Database Software tool Nextstrain Impact of pathogen genome data on science and . 3:275-284 (2002) Apweiler R. Functional information in Swiss-Prot: the basis for large-scale characterisation of protein sequences Brief. More specifically, the audience unanimously confirmed the following prerequisites: A unique search box performing the two search types (regular and cross-resource search). Since then, an increase of 15% in the number of daily users, compared to the same period last year, is observed. We believe that the systematic recourse both to publications other than those reporting the core data and to subject referees represents a unique and beneficial feature of SWISS-PROT. Abstract More sensitive, rapid and affordable diagnostic tools for pulmonary tuberculosis (PTB) are urgently needed. The outcome of our evaluation is summarised in Table 3. We initiated a process to convert the data into mixed case. Received 1999 Oct 12; Accepted 1999 Oct 13. 1. In the past 27 years, the portal has evolved. It consists of: UniProtKB/Swiss-Prot (expert-curated records) and UniProtKB/TrEMBL (computationally annotated records). Eleven people (developers, business analysts, product owner, SEO expert, user interface designer, graphic designer, system administrators) participated in the implementation phase, and the new Expasy went live on 15 October 2020. and Hochstrasser,D.F. Cross-references are provided in the form of pointers to information related to SWISS-PROT entries and found in data collections other than SWISS-PROT. Are you a journalist? lDDT, QS-Score, oligo-GDTTS, RMSD and DockQ are made In this context, hundreds of cutting-edge resources are developed and made available to the life science community. Accessibility Inclusion in an NLM database does not imply endorsement of, or agreement with, Provide a single search bar (for cross-resource and regular searches). nih.gov/Taxonomy/. The SWISS-PROT knowledgebase ( 3, 4) ( http://www.expasy.org/sprot/) is a curated protein sequence database, which strives to provide high quality annotations (such as the description of the function of a protein, its domain structure, post-translational modifications and variants), a minimal level of redundancy and a high level of integration w. Work on the Search Engine Optimization to increase the number of newcomers via organic searches. The list of resources that share at least one EDAM term of the Topic type is indicated in the You might also be interested in section, which allows the user to explore SIB resources (see Figure 3, bottom, for details). In this landscape, the ExPASy portal pioneered. 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. SWISS-PROT is an annotated protein sequence database established in 1986 and maintained collaboratively, since 1987, by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library [now the EMBL Outstation-The European Bioinformatics Institute (EBI) ()].The SWISS-PROT protein sequence data bank consists of sequence entries. 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. Identification of potential Akt activators: a ligand and structure-based computational approach. 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. See http://www.expasy/sprot/sp_docu.html for a list of all the documents that are currently available. SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc), a minimal level of redundancy and a high level of integration with other databases. Involving resource providers in the continuous content update of Expasy is crucial for ensuring accurate and relevant information. In SWISS-PROT we try as much as possible to merge all these data so as to minimise the redundancy of the database. The SWISS-PROT database distinguishes itself from other protein sequence databases by three distinct criteria: (i) annotations, (ii) minimal redundancy and (iii) integration with other databases. . The institute contributes to keeping Switzerland at the forefront of innovation by fostering progress in biological research and enhancing health. sharing sensitive information, make sure youre on a federal The creation of additional rules will be one of the priorities for TrEMBL over the next year. This is an example of an assumption we could validate. Expasy - Wikipedia Thank you for submitting a comment on this article. Table 1 illustrates three examples of typical users of the portal (so-called personas, see below) and their corresponding use-cases. The organisms currently selected are: Arabidopsis thaliana (mouse-ear cress), Bacillus subtilis, Caenorhabditis elegans (worm), Candida albicans, Dictyostelium discoideum (slime mold), Drosophila melanogaster (fruit fly), Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Homo sapiens (human), Methanococcus jannaschii, Mus musculus (mouse), Mycobacterium tuberculosis, Mycoplasma genitalium, Saccharomyces cerevisiae (budding yeast), Salmonella typhimurium, Schizosaccharomyces pombe (fission yeast), Sulfolobus solfataricus and Synechocystis sp. Detailed view of a resource (ViralZone). It now includes 19 SIB databases, such as ENZYME (21), MyHits (22), STRING(10), UniProtKB (23), ViralZone, PROSITE (24) and SWISS-MODEL Repository (see Table 2). Data stored in SWISS-PROT used to be represented exclusively in upper case. SwissVar - A portal to Swiss-Prot diseases and variants. upd_seq.dat Contains the entries for which the sequence data has been updated since the last release. Nucleic Acids Res. In October 1999 a cumulative total of 60 million connections was attained. We will also review and complete the annotation of the human sequences currently in SWISS-PROT. Figure 3 shows a detailed view of ViralZone, a web resource for all virus genera and families. Poux S., Arighi C.N., Magrane M., Bateman A., Wei C.-H., Lu Z., Boutet E., Bye-A-Jee H., Famiglietti M.L., Roechert B. et al. Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. Expasy was improved to maintain access to SIBs high-quality scientific resources and to offer up-to-date and accurate information on each of them, with a more efficient and easier-to-use search engine. The two grey boxes display the EDAM (28) terms related to Operations [1] and Topics, Data and Formats [2]. ebi.ac.uk/sprot, 882/5566 Technical section. Cook C.E., Lopez R., Stroe O., Cochrane G., Brooksbank C., Birney E., Apweiler R. Ison J., Ienasescu H., Chmura P., Rydza E., Menager H., Kala M., Schwammle V., Gruning B., Beard N., Lopez R. et al. . The new version of Expasy was intended as an evolving web application with a growing number of high-quality interconnected resources that forms a solid ground on which the life science community can stand. For example calcium binding regions, ATP-binding sites, zinc fingers, homeoboxes, SH2 and SH3 domains, etc. (1999), Fleischmann W., Moeller,S., Gateau,A. Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna Richardson, Gustavo A Salazar, Lowri Williams, Peer Bork, Alan Bridge, Julian Gough, Daniel H Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A Natale, Marco Necci, Christine A Orengo, Arun P Pandurangan, Catherine Rivoire, Christian J A Sigrist, Ian Sillitoe, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Cathy H Wu, Alex Bateman, Robert D Finn. NextProt - Exploring the universe of human proteins. accessible via the Expasy web server, The group also participates in the development and maintenance of many of the protein analysis tools listed on Expasy, the Swiss Bioinformatics Resource Portal. PMC. Selection of search type (cross-resource or regular) from a dropdown menu. We followed a UCD approach for the redesign, anticipating that optimised user interfaces and efficient organisation of information are more conducive to scientific discoveries. We will use the current information as the ground basis for what we call the Human Proteomics Initiative (HPI). . Usually, a wireframe is iteratively enhanced at each user test to produce an optimised prototype used by developers for implementation. How to monitor revision and long-term update of resource description? 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). Four-phased redesign process (preliminary phase, elaboration phase, iterative phase, implementation phase) and 3. Benchmarking is an efficient way to analyse user interfaces and community standards. Swiss-Prot group - Expasy . In case no result is returned (e.g. A wireframe is employed in user tests, allowing for early feedback on products. ExPASy is the main host for the following databases that are partially or completely developed at the SIB in Geneva: 1) The SWISS-PROT knowledgebase (http://www. Annotation of all known human polymorphisms at the protein sequence level. FindPept, a tool to identify unmatched masses in peptide mass It contains hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants. In this article, we describe the latest version of Expasy together with its redesign process that relied on rules of User-Centred Design (UCD). Although most databases offer their own search functionality, the simultaneous query of a set of databases from a single hub is a convenient option. (81.022%), Europe Many sequence databases contain, for a given protein sequence, separate entries which correspond to different literature reports. SIB Swiss Institute of Bioinformatics gratefully acknowledges the State Secretariat for Education, Research and Innovation SERI. The new user interface is the result of in-depth work with users to meet their needs and expectations. Some of these files have been available for a long time (the user manual, release notes, the various indices for authors, citations, keywords, etc. These files are available on the EBI and ExPASy servers, whose Internet addresses are listed above. A total of 154 resources were re-evaluated before the new Expasy implementation went live. The EBI and SIB also offer a range of search services (see http://www2.ebi.ac.uk/ or http://www.expasy.ch/tools/ ) to run SmithWaterman, FASTA and BLAST sequence similarity searches against SWISS-PROT + TrEMBL. A filter panel is proposed on the left side of the page. The most efficient and user-friendly way to browse interactively in SWISS-PROT or TrEMBL is to use the WWW molecular biology server ExPASy (6) as well as the one developed by the EBI. We also describe the Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT. Introduction to SWISS-MODEL Repository (SMR) The SWISS-MODEL Repository (SMR) is a database of 3D protein structure models generated by the SWISS-MODEL homology modelling pipeline. Currently, SWISS-PROT is linked to 31 different databases and has consolidated its role as the major focal point of bio-molecular databases interconnectivity. Tel: +44 1223 494 444; Fax: +44 1223 494 468; Email: datalib@ebi.ac.uk, From a computer linked to the Internet you can obtain SWISS-PROT and TrEMBL using anonymous FTP (File Transfer Protocol) from the following servers: ftp.expasy.ch and ftp.ebi.ac.uk. When a user, for example, types virus in the search bar, this results in a list of virus-related databases and software tools, such as V-pipe (16), ViralZone (17), OpenFlu (18) or COVID-19 Scenarios (19). Use an established ontology to describe the resources. It is harnessing the power of deep learning to accelerate literature triage and information extraction, thus delivering the most accurate and informative evidence to users in a timely manner. Expasy result page: the two types of search results are visually separated. . available with the Structure Assessment service. Rhea - An expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models. to all life science researchers worldwide. Thirty years of slug control using the parasitic nematode Phasmarhabditis hermaphrodita and beyond. Schwede, T. QMEANDisCo - distance constraints applied on model (iv) to provide specific indices or documents. SWISS-PROT + TrEMBL is distributed on CD-ROM by the EBI (2). Bioinform. Its address is: Complete and up to date mirror sites of ExPASy are available in Australia, Canada and Taiwan: http://expasy.proteome.org.au/ (at Australian Proteome Analysis Facility, Sydney), http://expasy.cbr.nrc.ca/ (at Canadian Bioinformatics Resource, Halifax), http://expasy.nhri.org.tw/ (at National Health Research Institutes, Taipei). The resource providers were granted access to the Expasy administration interface and provided with a video tutorial. PROSITE This should lead to a drastic increase in coverage by automatic annotation. For TrEMBL, a file containing all the new entries since the last full release (trembl_new.dat) is updated every week. Figure 2 shows the result page obtained with COVID-19 as input in the search box. It also takes into account post-translational modifications derived from the annotation of the SWISS-PROT database or supplied by the user, and chemical modifications of peptides. (PDF) THE SWISS-PROT PROTEIN SEQUENCE DATABASE USER MANUAL - ResearchGate To update the pre-existing data, we started by removing decommissioned resources as well as non-SIB resources. 2:9-18 (2001) Gasteiger E, Jung E, Bairoch A. Swiss-Prot: connecting biomolecular knowledge via a protein database Curr. 45, D313-D319 How do we manually annotate a UniProtKB entry. It depicts the layout of the user interface elements and their interactions. Proteins, once synthesized on the ribosomes, are subject to a multitude of modification steps. SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc. Databases, software tools and on-line services are essential resources in the daily work of most life scientists. In which tissue is this gene expressed in human? Expasy would not exist without the resource providers: we take this opportunity to thank them for their immense effort in developing, maintaining and revising the resources. ), a minimal level of redundancy and high level of integration with other databases. With this in mind, the redesign of Expasy was carried out through four developmental phases that are described below (see Figure 4 for an illustration of the process). SWISS-PROT accession numbers have been assigned to these entries. In the future, the SIB community will strive to provide more resources to Expasy users while ensuring that pre-existing information remains up to date. The details of this benchmarking can be found in Supplementary File S2. (PDF) Uniprotkb/Swiss-prot - ResearchGate Another factor of complexity to take into account is the amount of polymorphism at the protein sequence level. Even when all potential coding regions have been predicted, the user community will have at its disposition the sequences of between 80 000 and 100 000 naked proteins. Guex, N., Peitsch, M.C., Schwede, T. Automated comparative Sequence entries are composed of different line types, each with their own format. Overall, we observed a bounce rate of 50% which is considered as good. Recent developments of the database include: cross-references to additional databases; a variety of new documentation files and improvements to TrEMBL, a computer annotated supplement to SWISS-PROT. UniProtKB is produced by the UniProt consortium. For all aspects of the HPI projects, we would appreciate the help and collaboration of the scientific community. 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. protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A Electrophoresis 30, S162-S173 (2009). Originating from the computer industry, UCD is emerging in science, as its value has been acknowledged (14,15). Involve the resource providers in the description of resources and the continuous revision of information. To obtain this information we use, in addition to the publications reporting new sequence data, review articles to periodically update the annotations of families or groups of proteins. (Top) Cross-resource search result; with the number of hits found in each of the 19 databases; 2. It contains hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants. Further information on this new system is available from http://www.expasy.ch/announce/. Repository Help | SWISS-MODEL - Expasy 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. In the course of the next 9 months (up to April 2000) the human protein sequences that are not yet in SWISS-PROT will be fully annotated. or from the program DeepView (Swiss Pdb-Viewer). To contribute to the standardization of the taxonomies used in molecular sequence databases we have switched to the NCBI taxonomy, which is used by the DDBJ/EMBL/GenBank nucleotide sequence databases. The data file (sequences and annotations) requires 185 Mb of disk storage space. For standardisation purposes the format of SWISS-PROT (see http://www.expasy. The first pitfall to overcome is the detection of all coding regions on the genomic sequence. Focus on the group's mission. MTC2.1 Cartridge. Swiss-Prot-Related Conventions for the ExPASy Tools Unless otherwise stated, the ExPASy tools use Swiss-Prot annotations to process polypeptides to their mature forms before using them for calculations or protein identi-fication procedures. ac.uk (for enquiries).