Xavier Watkins

The UniProt website API: facilitating programmatic access to protein knowledge

Shadab Ahmad, Leonardo Jose da Costa Gonzales, Emily Bowler-Barnett, Daniel L Rice et autres

The UniProt REST API is a freely available, open-access resource that powers the UniProt.org website and gives users flexible programmatic interaction with protein knowledge data. It provides access to UniProtKB, UniRef, UniParc, Proteomes, GeneCentric, ARBA, UniRule, and the ID Mapping tool, along …

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The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants

Luca Stefanucci, Janine Collins, Matthew C. Sims, Inigo Barrio‐Hernandez et autres

Rare genetic diseases affect millions, and identifying causal DNA variants is essential for patient care. Therefore, it is imperative to estimate the effect of each independent variant and improve their pathogenicity classification. Our study of 140 214 unrelated UK Biobank (UKB) participants …

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Nightingale: Web components for protein feature visualization

Gustavo A Salazar, Aurélien Luciani, Xavier Watkins, Swaathi Kandasaamy et autres

Motivation: The visualization of biological data is a fundamental technique that enables researchers to understand and explain biology. Some of these visualizations have become iconic, for instance: tree views for taxonomy, cartoon rendering of 3D protein structures, or tracks to represent features …

gb (code pays fourni par la source)

Nightingale: web components for protein feature visualization

Gustavo A Salazar, Aurélien Luciani, Xavier Watkins, Swaathi Kandasaamy et autres

Motivation: The visualization of biological data is a fundamental technique that enables researchers to understand and explain biology. Some of these visualizations have become iconic, for instance: tree views for taxonomy, cartoon rendering of 3D protein structures or tracks to represent features …

gb (code pays fourni par la source)

Annotation of biologically relevant ligands in UniProtKB using ChEBI

Elisabeth Coudert, Sébastien Géhant, Edouard de Castro, Delphine Baratin et autres

MOTIVATION: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support efforts to study and predict functionally relevant interactions between protein sequences …

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UniProt: the Universal Protein Knowledgebase in 2023

Alex Bateman, María Martin, Sandra Orchard, Michele Magrane et autres

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data processing pipeline and to our website to …

The IntAct database: efficient access to fine-grained molecular interaction data

Noemí del‐Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal et autres

The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the …

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UniProt: the universal protein knowledgebase in 2021

Alex Bateman, María Martin, Sandra Orchard, Michele Magrane et autres

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to …

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase

Alistair MacDougall, Vladimir Volynkin, Rabie Saidi, Diego Poggioli et autres

MOTIVATION: The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result of genome sequencing and the prediction of protein-coding genes. Providing functional annotation for these proteins presents a significant and continuing challenge. RESULTS: In …

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FAIR adoption, assessment and challenges at UniProt

Jerven Bolleman, Sébastien Géhant, Nicole Redaschi, María Martin et autres

UniProt continues to support the ongoing process of making scientific data FAIR. Here we contribute to this process with a FAIRness assessment of our UniProtKB dataset followed by a critical reflection on the challenges and future directions of the adoption and validation …

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UniProtKB and Alzheimer’s Disease: Linking molecular defects to disease phenotype

Yvonne Lussi, Lionel Breuza, Cristina Casals Casas, George P. Georghiou et autres

Alzheimer’s disease (AD) is a progressive, neurodegenerative disease and the most common form of dementia in elderly people. Linkage analysis was the first milestone in unravelling the mutations in APP, PSEN1 and PSEN2 that cause early-onset AD. The development of next-generation sequencing …

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Designing an intuitive web application for drug discovery scientists

Nikiforos Karamanis, Denise Carvalho‐Silva, Jennifer A. Cham, Luca Fumis et autres

Abstract Although a scientific web application that is intuitive can help scientists utilize data more easily and advance their research, there is little guidance on how to design such an application in the academic literature. We discuss how we designed an intuitive …

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