SwissBioPics—an interactive library of cell images for the visualization of subcellular location data

Abstract SwissBioPics (www.swissbiopics.org) is a freely available resource of interactive, high-resolution cell images designed for the visualization of subcellular location data. SwissBioPics provides images describing cell types from all kingdoms of life—from the specialized muscle, neuronal and epithelial cells of animals, to the rods, cocci, clubs and spirals of prokaryotes. All cell images in SwissBioPics are drawn in Scalable Vector Graphics (SVG), with each subcellular location tagged with a unique identifier from the controlled vocabulary of subcellular locations and organelles of UniProt (https://www.uniprot.org/locations/). Users can search and explore SwissBioPics cell images through our website, which provides a platform for users to learn more about how cells are organized. A web component allows developers to embed SwissBioPics images in their own websites, using the associated JavaScript and a styling template, and to highlight subcellular locations and organelles by simply providing the web component with the appropriate identifier(s) from the UniProt-controlled vocabulary or the ‘Cellular Component’ branch of the Gene Ontology (www.geneontology.org), as well as an organism identifier from the National Center for Biotechnology Information taxonomy (https://www.ncbi.nlm.nih.gov/taxonomy). The UniProt website now uses SwissBioPics to visualize the subcellular locations and organelles where proteins function. SwissBioPics is freely available for anyone to use under a Creative Commons Attribution 4.0 International (CC BY 4.0) license. Database URL www.swissbiopics.org

[1]  Anushya Muruganujan,et al.  The Gene Ontology resource: enriching a GOld mine , 2020, Nucleic Acids Res..

[2]  Peter B. McGarvey,et al.  UniProt: the universal protein knowledgebase in 2021 , 2020, Nucleic Acids Res..

[3]  Phani Garapati,et al.  FlyBase: updates to the Drosophila melanogaster knowledge base , 2020, Nucleic Acids Res..

[4]  T. Lithgow,et al.  Formation and function of bacterial organelles , 2020, Nature Reviews Microbiology.

[5]  Anne Morgat,et al.  UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase , 2020, Bioinformatics.

[6]  Melinda R. Dwinell,et al.  The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform , 2019, Nucleic Acids Res..

[7]  Kimberly Van Auken,et al.  WormBase: a modern Model Organism Information Resource , 2019, Nucleic Acids Res..

[8]  Shila Ghazanfar,et al.  The human body at cellular resolution: the NIH Human Biomolecular Atlas Program , 2019, Nature.

[9]  Howard Y. Chang,et al.  Atlas of Subcellular RNA Localization Revealed by APEX-Seq , 2018, Cell.

[10]  Henning Hermjakob,et al.  Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes , 2018, Nucleic Acids Res..

[11]  Jürg Bähler,et al.  PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information , 2018, Nucleic Acids Res..

[12]  Edith D. Wong,et al.  Saccharomyces genome database informs human biology , 2017, Nucleic Acids Res..

[13]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[14]  The RNAcentral Consortium.  RNAcentral: a comprehensive database of non-coding RNA sequences , 2016, Nucleic Acids Res..

[15]  Martin Ringwald,et al.  Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research. , 2017, Methods in molecular biology.

[16]  Suzanna Lewis,et al.  Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes , 2016, Database J. Biol. Databases Curation.

[17]  Erik Schultes,et al.  The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.

[18]  Christoph Steinbeck,et al.  ChEBI in 2016: Improved services and an expanding collection of metabolites , 2015, Nucleic Acids Res..

[19]  G. von Heijne,et al.  Tissue-based map of the human proteome , 2015, Science.

[20]  W. Martin,et al.  Endosymbiotic theory for organelle origins. , 2014, Current opinion in microbiology.

[21]  Christian Stolte,et al.  COMPARTMENTS: unification and visualization of protein subcellular localization evidence , 2014, Database J. Biol. Databases Curation.

[22]  B. Lang,et al.  Mitochondrial Evolution , 1999 .

[23]  B. Hall,et al.  Human cell type diversity, evolution, development, and classification with special reference to cells derived from the neural crest , 2006, Biological reviews of the Cambridge Philosophical Society.

[24]  H. Gest.  The Remarkable Vision of Robert Hooke (1635-1703): First Observer of the Microbial World , 2005, Perspectives in biology and medicine.

[25]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.