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. 2022 Apr 12:2022:baac026.
doi: 10.1093/database/baac026.

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

Philippe Le Mercier  1 , Jerven Bolleman  1 , Edouard de Castro  1 , Elisabeth Gasteiger  1 , Parit Bansal  1 , Andrea H Auchincloss  1 , Emmanuel Boutet  1 , Lionel Breuza  1 , Cristina Casals-Casas  1 , Anne Estreicher  1 , Marc Feuermann  1 , Damien Lieberherr  1 , Catherine Rivoire  1 , Ivo Pedruzzi  1 , Nicole Redaschi  1 , Alan Bridge  1
Affiliations

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

Philippe Le Mercier et al. Database (Oxford). .

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.

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Figures

Figure 1.
Figure 1.
Image of a generic cell from the Clade Eumetazoa; This cell illustrates all the cellular components found in any Eumetazoan, although in reality no cell carries all of them; All components are individual groups in the SVG file, which can be hidden or colored.
Figure 2.
Figure 2.
SwissBioPics page for budding yeast cell; The ‘Cell membrane’, selected on the sidebar list, is colored orange, with a tooltip showing a description of the organelle and links to the UniProt, AmiGO and QuickGO websites; The mouse is hovering on ‘Cell wall’ in the list, coloring this part blue.
Figure 3.
Figure 3.
UniProtKB entry AT8B2_ HUMAN (P98198) shows an embedded SwissBioPics image: The generic animal cell (Eumetazoa) is selected based on organism taxonomy; the cell membrane and endoplasmic reticulum are highlighted using annotations from the UniProt entry.
Figure 4.
Figure 4.
Displaying quantitative data in SwissBioPics using colors. The image shows the fold change (FC) of the RAD51-AS1 non-protein-coding transcript in the nucleus and mitochondrion (26).
See this image and copyright information in PMC

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