The Proteomes webpage has been redesigned to enable users to view full details of their proteome(s) of interest in a single table view (Figure 2). et al InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Since we started the pilot in release 2019_08 we have seen a continuing increase in user submissions. Garcia L., Bolleman J., Gehant S., Redaschi N., Martin M., Consortium UniProt, Karsch-Mizrachi I., Takagi T., Cochrane GInternational Nucleotide Sequence Database Collaboration. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (. . Information extracted from an entry describing Hepatitis C viral protein (UniProtKB:{"type":"entrez-protein","attrs":{"text":"P27958","term_id":"130461","term_text":"P27958"}}P27958) highlighting annotation added at the processed mature chain level, describing the p21 core protein. UniProtKB/TrEMBL contains high-quality computationally analysed records enriched with automatic annotation and classification. These unreviewed records are enriched with functional annotation by systems using the protein classification tool InterPro (24), which classifies sequences at superfamily, family and subfamily levels, and predicts the occurrence of functional domains and important sites. UniProt provides an up-to-date, comprehensive body of protein information. Bacillus subtilis proteomes viewed on the Proteomes webpage with BUSCO and CPD scores. spectral libraries search tools). The CPTAC data Portal: a resource for cancer proteomics research. 22 894 ARBA rules were used to annotate 87 325 890 proteins in release 2020_04, increasing the combined coverage of the rule-based annotation systems from 35% to 49% in UniProtKB/TrEMBL. . The UniProt databases exist to support biological and biomedical research by providing a complete compendium of all known protein sequence data linked to a summary of the experimentally verified, or computationally predicted, functional information about that protein. National Library of Medicine UniProt also provides the new format PEFF (PSI Extended FASTA Format) proposed by the HUPO-PSI (Human Proteome Organization-Proteomics Standard Initiative) for sequence databases (39) to be used by sequence search engines and other associated tools (e.g. Using WormBase ParaSite: an integrated platform for exploring helminth genomic data. (iii) After submission and review the publication and information are displayed in the relevant UniProtKB entry with attribution to submitter (red box) in a future public release. We have also reviewed and updated our data licencing policies. The evaluation of experimental data published in the scientific literature, and summarizing key points of biological relevance in the appropriate reviewed UniProtKB/Swiss-Prot record, is fundamental to the operation of the UniProt database. We have adapted our data model to capture machine-readable functional annotations for specific isoforms and polyprotein cleavage products, and now provide such knowledge for >5000 protein sequence entries. The redundant proteome sequences are available through UniParc to researchers and stable proteome identifiers (of the form UPXXXXXXXXX, where Xs are integers) are maintained for each redundant proteome to ensure findability. Accessibility The information is filed in different subsections. Clinically relevant sources of variation (e.g. Contributors are asked to supply their ORCID (https://orcid.org/), a researcher personal ID, which is used to both validate that the submission is genuine and to give credit to the submitter for their work (Figure 5). To enable researchers to evaluate proteome completeness and expected gene content, we have adopted the BUSCO (Benchmarking Universal Single-Copy Orthologs) scoring method for vertebrate, arthropod, fungal, and prokaryotic organisms on the Proteomes portal, in addition to providing details of species and the protein count. To enable researchers to evaluate proteome completeness and expected gene content, we have adopted the BUSCO (Benchmarking Universal Single-Copy Orthologs) scoring method for vertebrate, arthropod, fungal, and prokaryotic organisms on the Proteomes portal, in addition to providing details of species and the protein count. 8600 Rockville Pike As the number of completely sequenced genomes continues to increase, huge efforts are being made in the research community to understand as much as possible about the proteins encoded by these genomes. The ever-increasing amount of genomic data arising from current sequencing projects means that the proportion of unreviewed records in UniProtKB/TrEMBL describing largely predicted proteins represents by far the largest, and most rapidly growing, section of UniProtKB. The UniProt publication has been prepared by Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H. Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan Da Silva, Paul Denny, Tunca Dogan, ThankGod Ebenezer, Jun Fan, Leyla Garcia Castro, Penelope Garmiri, George Georghiou, Leonardo Gonzales, Emma Hatton-Ellis, Abdulrahman Hussein, Alexandr Ignatchenko, Giuseppe Insana, Rizwan Ishtiaq, Petteri Jokinen, Vishal Joshi, Dushyanth Jyothi, Antonia Lock, Rodrigo Lopez, Aurelien Luciani, Jie Luo, Yvonne Lussi, Alistair MacDougall, Fabio Madeira, Mahdi Mahmoudy, Manuela Menchi, Alok Mishra, Katie Moulang, Andrew Nightingale, Carla Susana Oliveira, Sangya Pundir, Guoying Qi, Shriya Raj, Daniel Rice, Milagros Rodriguez Lopez, Rabie Saidi, Joseph Sampson, Tony Sawford, Elena Speretta, Edward Turner, Nidhi Tyagi, Preethi Vasudev, Vladimir Volynkin, Kate Warner, Xavier Watkins, Rossana Zaru, and Hermann Zellner at the EMBL- European Bioinformatics Institute; Alan Bridge, Sylvain Poux, Nicole Redaschi, Lucila Aimo, Ghislaine Argoud-Puy, Andrea Auchincloss, Kristian Axelsen, Parit Bansal, Delphine Baratin, Marie-Claude Blatter, Jerven Bolleman, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Edouard de Castro, Kamal Chikh Echioukh, Elisabeth Coudert, Beatrice Cuche, Mikael Doche, Dolnide Dornevil, Anne Estreicher, Maria Livia Famiglietti, Marc Feuermann, Elisabeth Gasteiger, Sebastien Gehant, Vivienne Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Nevila Hyka-Nouspikel, Florence Jungo, Guillaume Keller, Arnaud Kerhornou, Vicente Lara, Philippe Le Mercier, Damien Lieberherr, Thierry Lombardot, Xavier Martin, Patrick Masson, Anne Morgat, Teresa Batista Neto, Salvo Paesano, Ivo Pedruzzi, Sandrine Pilbout, Lucille Pourcel, Monica Pozzato, Manuela Pruess, Catherine Rivoire, Christian Sigrist, Karin Sonesson, Andre Stutz, Shyamala Sundaram, Michael Tognolli, and Laure Verbregue at the SIB Swiss Institute of Bioinformatics; Cathy H. Wu, Cecilia N. Arighi, Leslie Arminski, Chuming Chen, Yongxing Chen, John S. Garavelli, Hongzhan Huang, Kati Laiho, Peter McGarvey, Darren A. Natale, Karen Ross, C. R. Vinayaka, Qinghua Wang, Yuqi Wang, Lai-Su Yeh, and Jian Zhang at the Protein Information Resource. Antonazzo G., Urbano J.M., Marygold S.J., Millburn G.H., Brown N.H.. Building a pipeline to solicit expert knowledge from the community to aid gene summary curation. Growth in the number of entries in the UniProt databases over the last decade. We follow a user-centered design process, conducting regular workshops, user testing, surveys and user research activities involving many users worldwide with varied research backgrounds and use cases. This system is freely available for groups to use for in-house protein annotation projects (26) or to contribute their own rules in the URML (UniProt Rule Markup Language) format which may be reused for the annotation of UniProtKB entries. Vallenet D., Calteau A., Dubois M., Amours P., Bazin A., Beuvin M., Burlot L., Bussell X., Fouteau S., Gautreau G. et al. including isoforms) that map to the genome. UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. Expert curation of those proteins biochemically characterized remains a key focus of our activities, to both inform on these well-studied entities and also to act as template entries for information transfer to proteins in related species. UniProt users have always actively engaged with us and provide important feedback to the resource. MacDougall A., Volynkin V., Saidi R., Poggioli D., Zellner H., Hatton-Ellis E., Joshi V., ODonovan C., Orchard S., Auchincloss A.H. et al. Sequence feature predictions are currently excluded from annotation by ARBA. An official website of the United States government. Thank you for submitting a comment on this article. This enables us to leverage the scientific community as a resource for enhancing our curated content, emulating a model already adopted by a number of model organism databases, such as WormBase (40), PomBase (41) and FlyBase (42). 22 894 ARBA rules were used to annotate 87 325 890 proteins in release 2020_04, increasing the combined coverage of the rule-based annotation systems from 35% to 49% in UniProtKB/TrEMBL. UniProtKB/Swiss-Prot - SIB Swiss Institute of Bioinformatics | Expasy Pan Q., Shai O., Lee L.J., Frey B.J., Blencowe B.J. UniProt additionally integrates and visualizes unique and non-unique peptides identified by mass spectrometry proteomic data deposited through the ProteomeXchange Consortium (31) (e.g. The UniProt Knowledgebase (UniProtKB), the centrepiece of the UniProt Consortiums activities, is an expertly and richly curated protein database, consisting of two sections called UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. Bacillus subtilis proteomes viewed on the Proteomes webpage with BUSCO and CPD scores. The redundant proteome sequences are available through UniParc to researchers and stable proteome identifiers (of the form UPXXXXXXXXX, where Xs are integers) are maintained for each redundant proteome to ensure findability. To further ensure our data is both human-readable and also computationally-tractable and continues to adhere to the FAIR principles (2), we are working to standardize the representation of all existing UniProt data on the functional impact of human variation. Functional positional annotations from the UniProt human reference proteome are now being mapped to the corresponding genomic coordinates on the GRCh38 version of the human genome for each release of UniProt. These are now part of the Nightingale visualization web component library (https://ebi-webcomponents.github.io/nightingale/#/) and are publicly available as lightweight, flexible, and modular components that can be more easily extended with new features, modified and implemented by users in their own resources (Figure 6B). and transmitted securely. ABLNCPP: Attention Mechanism-Based Bidirectional Long Short-Term Memory for Noncoding RNA Coding Potential Prediction. Users can also search using Rhea identifiers as well as identifiers, names, synonyms and chemical structures (encoded as InChIKeys) from ChEBI. We also display the results of the Complete Proteome Detector (CPD), an in-house algorithm, which statistically evaluates the completeness and quality of each proteome by directly comparing it to those of a group of at least three closely taxonomically related species. As of release 2020_04 there have been 674 submissions relating to 424 publications and 557 entries, from 149 unique users (https://community.uniprot.org/bbsub/STATS.html). National Eye Institute, National Human Genome Research Institute, National Heart, Lung, and Blood Institute, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of General Medical Sciences, National Cancer Institute, National Institute On Aging, and National Institute of Mental Health of the National Institutes of Health [U24HG007822]; National Human Genome Research Institute [U41HG002273]; National Institute of General Medical Sciences [R01GM080646, P20GM103446] (the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health);Biotechnology and Biological Sciences Research Council [BB/T010541/1]; British Heart Foundation [RG/13/5/30112]; Open Targets; Swiss Federal Government through the State Secretariat for Education, Research and Innovation SERI; European Molecular Biology Laboratory core funds. This gives our production team the time required to complete data import, proteome redundancy removal, data checking, integration of external data . UniProt release 2022_05. Functional positional annotations from the UniProt human reference proteome are now being mapped to the corresponding genomic coordinates on the GRCh38 version of the human genome for each release of UniProt. The UniProt Knowledgebase (UniProtKB), the centrepiece of the UniProt Consortium's activities, is an expertly and richly curated protein database, consisting of two sections called UniProtKB/Swiss-Prot and UniProtKB/TrEMBL.