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1.
Nucleic Acids Res ; 52(D1): D107-D114, 2024 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-37992296

RESUMEN

Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell Expression Atlas (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene and protein expression and localisation in bulk and at single cell level. These resources aim to allow users to investigate their expression in normal tissue (baseline) or in response to perturbations such as disease or changes to genotype (differential) across multiple species. Users are invited to search for genes or metadata terms across species or biological conditions in a standardised consistent interface. Alongside these data, new features in Single Cell Expression Atlas allow users to query metadata through our new cell type wheel search. At the experiment level data can be explored through two types of dimensionality reduction plots, t-distributed Stochastic Neighbor Embedding (tSNE) and Uniform Manifold Approximation and Projection (UMAP), overlaid with either clustering or metadata information to assist users' understanding. Data are also visualised as marker gene heatmaps identifying genes that help confer cluster identity. For some data, additional visualisations are available as interactive cell level anatomograms and cell type gene expression heatmaps.


Asunto(s)
Bases de Datos Genéticas , Perfilación de la Expresión Génica , Proteómica , Genotipo , Metadatos , Análisis de la Célula Individual , Internet , Humanos , Animales
2.
Bioinformatics ; 38(11): 3141-3142, 2022 05 26.
Artículo en Inglés | MEDLINE | ID: mdl-35380605

RESUMEN

SUMMARY: To advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents. AVAILABILITY AND IMPLEMENTATION: Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Disciplinas de las Ciencias Biológicas , Metadatos , Semántica , Programas Informáticos
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