Delphine Baratin
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View article: The UniProt website API: facilitating programmatic access to protein knowledge
The UniProt website API: facilitating programmatic access to protein knowledge Open
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…
View article: UniProt: the Universal Protein Knowledgebase in 2025
UniProt: the Universal Protein Knowledgebase in 2025 Open
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication, we…
View article: Perspectives on tracking data reuse across biodata resources
Perspectives on tracking data reuse across biodata resources Open
Motivation Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much of this knowledge has been collated into molecula…
View article: The SIB Swiss Institute of Bioinformatics Semantic Web of data
The SIB Swiss Institute of Bioinformatics Semantic Web of data Open
The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/) is a federation of bioinformatics research and service groups. The international life science community in academia and industry has been accessing the freely available dat…
View article: MBDBMetrics: an online metrics tool to measure the impact of biological data resources
MBDBMetrics: an online metrics tool to measure the impact of biological data resources Open
Motivation There now exist thousands of molecular biology databases covering every aspect of biological data. This database infrastructure takes significant effort and funding to develop and maintain. The creators of these databases need t…
View article: Annotation of biologically relevant ligands in UniProtKB using ChEBI
Annotation of biologically relevant ligands in UniProtKB using ChEBI Open
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 supp…
View article: UniProt: the Universal Protein Knowledgebase in 2023
UniProt: the Universal Protein Knowledgebase in 2023 Open
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…
View article: Annotation of biologically relevant ligands in UniProtKB using ChEBI
Annotation of biologically relevant ligands in UniProtKB using ChEBI Open
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 supp…
View article: UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase Open
View article: UniProt: the universal protein knowledgebase in 2021
UniProt: the universal protein knowledgebase in 2021 Open
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…
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase Open
View article: HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes
HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes Open
Background Genome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of effort, increased costs, and suboptimal annotation quality. One way to address these issue…
View article: Enzyme annotation in UniProtKB using Rhea
Enzyme annotation in UniProtKB using Rhea Open
Motivation To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants using the ChEBI (Chemical E…
View article: FAIR adoption, assessment and challenges at UniProt
FAIR adoption, assessment and challenges at UniProt Open
View article: Enzyme annotation in UniProtKB using Rhea
Enzyme annotation in UniProtKB using Rhea Open
Motivation To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants using the ontology ChEBI (C…
View article: HAMAP rules as SPARQL A portable annotation pipeline for genomes and proteomes
HAMAP rules as SPARQL A portable annotation pipeline for genomes and proteomes Open
Motivation Genome and proteome annotation pipelines are generally custom built and therefore not easily reusable by other groups, which leads to duplication of effort, increased costs, and suboptimal results. One cost-effective way to incr…
View article: HAMAP as SPARQL: annotate all your proteins
HAMAP as SPARQL: annotate all your proteins Open
View article: PROSITE, a database for domain and site detection and annotation
PROSITE, a database for domain and site detection and annotation Open