Chantal Hulo
A5000732341- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Bacteriophages and microbial interactions
- Advanced Proteomics Techniques and Applications
- RNA and protein synthesis mechanisms
- Genomics and Rare Diseases
- Scientific Computing and Data Management
- Hepatitis C virus research
- Machine Learning in Bioinformatics
- HIV Research and Treatment
- Animal Virus Infections Studies
- Research Data Management Practices
- Virus-based gene therapy research
- HIV/AIDS drug development and treatment
- Semantic Web and Ontologies
- Computational Drug Discovery Methods
- Natural Language Processing Techniques
- Microbial Community Ecology and Physiology
- Hepatitis B Virus Studies
- Gene expression and cancer classification
- Genetics, Bioinformatics, and Biomedical Research
- Enzyme Structure and Function
- FinTech, Crowdfunding, Digital Finance
- Data Mining Algorithms and Applications
SIB Swiss Institute of Bioinformatics
2012-2025
European Bioinformatics Institute
2024
University of Padua
2023
University of Southern California
2023
University College London
2023
Stanford University
2023
Phoenix Bioinformatics
2023
University at Buffalo, State University of New York
2023
University of Geneva
2014-2017
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this article, we describe significant updates that have made over last two years resource. number in UniProtKB has risen approximately 190 million, despite continued work reduce sequence redundancy at proteome level. We adopted new methods assessing completeness quality. continue extract detailed annotations from...
Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this publication we describe enhancements made our data processing pipeline website adapt an ever-increasing information content. number in UniProtKB has risen over 227 million are working towards including reference proteome for each taxonomic group. We continue extract detailed annotations from literature...
The primary mission of Universal Protein Resource (UniProt) is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references querying interfaces freely accessible the scientific community. UniProt produced Consortium which consists groups from European Bioinformatics Institute (EBI), Swiss (SIB) Information (PIR). comprised four major components, each optimized for...
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over past year, GOC has implemented several processes to increase quantity, quality and specificity GO annotations. First, number manual, literature-based annotations grown at an increasing rate. Second, as result new 'phylogenetic annotation' process, manually reviewed, homology-based...
The molecular diversity of viruses complicates the interpretation viral genomic and proteomic data. To make sense gene functions, investigators must be familiar with virus host range, replication cycle virion structure. Our aim is to provide a comprehensive resource bridging together textbook knowledge sequences. ViralZone web ( www.expasy.org/viralzone/ ) provides fact sheets on all known families/genera easy access sequence A selection reference strains (RefStrain) annotated standards...
The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 proteins in more than 360,000 taxa, this has increased 2-fold last 2 years benefited wealth checks improve correctness consistency as well now greater information content enabled format developments. Detailed, manual obtained...
Abstract 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 Biological Interest), to better support efforts study and predict functionally interactions between protein sequences structures small molecule ligands. Results We structured data model cognate ligand site annotations performed a complete reannotation all stable unique identifiers from...
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set protein sequences annotated functional information. In this publication, we describe ongoing changes our production pipeline limit available in UniProtKB high-quality, non-redundant reference proteomes. We continue manually curate scientific literature add latest data use machine learning techniques. also encourage community curation...
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. number GO annotations products has increased due to curation efforts among Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. ontologies continue expand improve as result targeted ontology development, introduction computable logical definitions...
The hepatitis C virus (HCV) genome shows remarkable sequence variability, leading to the classification of at least six major genotypes, numerous subtypes and a myriad quasispecies within given host. A database allowing researchers investigate genetic structural variability all available HCV sequences is an essential tool for studies on molecular virology pathogenesis as well drug design vaccine development. We describe here European Hepatitis Virus Database (euHCVdb,...
Abstract Motivation The number of protein records in the UniProt Knowledgebase (UniProtKB: https://www.uniprot.org) continues to grow rapidly as a result genome sequencing and prediction protein-coding genes. Providing functional annotation for these proteins presents significant continuing challenge. Results In response this challenge, has developed method annotation, known UniRule, based on expertly curated rules, which integrates related systems (RuleBase, HAMAP, PIRSR, PIRNR) by members...
ViralZone (http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host–virus interactions. The information divided into viral fact sheets describe shape, molecular biology epidemiology for each genus, with links the corresponding annotated proteomes of UniProtKB. Each genus page contains detailed illustrations, text PubMed references. This new update provides linked view through 133 ontology...
Abstract ViralZone (http://viralzone.expasy.org) is a knowledge repository for viruses that links biological and databases. It contains data on virion structure, genome, proteome, replication cycle host-virus interactions. The new update provides better access to the through contextual popups higher resolution images in Scalable Vector Graphics (SVG) format. These are designed be dynamic interactive with human give users data. In addition, coronavirus-specific resource regularly updated...
The Gene Ontology project is a collaborative effort to provide descriptions of gene products in consistent and computable language, species-independent manner. designed be applicable all organisms but up now has been largely under-utilized for prokaryotes viruses, part because lack appropriate ontology terms.
UniProt continues to support the ongoing process of making scientific data FAIR. Here we contribute this with a FAIRness assessment our UniProtKB dataset followed by critical reflection on challenges and future directions adoption validation FAIR principles metrics.
Our growing knowledge of viruses reveals how these pathogens manage to evade innate host defenses. A global scheme emerges in which many usurp key cellular defense mechanisms and often inhibit the same components antiviral signaling. To accurately describe processes, we have generated a comprehensive dictionary for eukaryotic host-virus interactions. This controlled vocabulary has been detailed 57 ViralZone resource web pages contain description all molecular processes. In order annotate...
Abstract Background Genome and proteome annotation pipelines are generally custom built not easily reusable by other groups. This leads to duplication of effort, increased costs, suboptimal quality. One way address these issues is encourage the adoption standards technological solutions that enable sharing biological knowledge tools for genome annotation. Results Here we demonstrate one approach generate portable users can run without recourse software. proof concept uses our own rule-based...
The Human Immunodeficiency Virus (HIV) is one of the pathogens that cause greatest global concern, with approximately 35 million people currently infected HIV. Extensive HIV research has been performed, generating a large amount and host genomic data. However, no effective vaccine protects from infection available still spreading at an alarming rate, despite antiretroviral (ARV) treatment. In order to develop therapies, we need expand our knowledge interaction between proteins. contrast...
UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established collaboration to improve data sharing. One of major steps in this effort was 'Dicty annotation marathon', week-long exercise with 30 annotators aimed at achieving increase number D. discoideum proteins represented UniProtKB/Swiss-Prot. The marathon led over 1000 Concomitantly, there were large updates dictyBase concerning gene symbols, names models. This...
Viruses are genetically diverse, infect a wide range of tissues and host cells follow unique processes for replicating themselves. All these were investigated indexed in ViralZone knowledge base. To facilitate standardizing data, simple ontology viral life-cycle terms was developed to provide common vocabulary annotating data sets. New terminology address replication cycle processes, existing modified adapted. The virus is classically described by schematic pictures. Using this ontology, it...
Bacterial viruses, also called bacteriophages, display a great genetic diversity and utilize unique processes for infecting reproducing within host cell. All these were investigated indexed in the ViralZone knowledge base. To facilitate standardizing data, simple ontology of viral life-cycle terms was developed to provide common vocabulary annotating data sets. New terminology address replication cycle processes, existing modified adapted. Classically, is described by schematic pictures....