Damien Lieberherr
A5070436721- Biomedical Text Mining and Ontologies
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Advanced Proteomics Techniques and Applications
- Scientific Computing and Data Management
- Machine Learning in Bioinformatics
- Computational Drug Discovery Methods
- Genomics, phytochemicals, and oxidative stress
- Microbial Metabolic Engineering and Bioproduction
- Plant-Microbe Interactions and Immunity
- Plant Disease Resistance and Genetics
- Genomics and Rare Diseases
- Cell Image Analysis Techniques
- Photosynthetic Processes and Mechanisms
- Research Data Management Practices
- Chromosomal and Genetic Variations
- Semantic Web and Ontologies
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Enzyme Production and Characterization
- Metabolism and Genetic Disorders
- Plant Pathogens and Resistance
- Enzyme Structure and Function
- Glycosylation and Glycoproteins Research
- Fungal Plant Pathogen Control
SIB Swiss Institute of Bioinformatics
2010-2025
European Bioinformatics Institute
2024
Stanford University
2023
University of Padua
2023
University College London
2023
Phoenix Bioinformatics
2023
University at Buffalo, State University of New York
2023
University of Southern California
2023
Nara Institute of Science and Technology
2003-2005
University of Fribourg
2003
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...
SummaryThe Swiss Institute of Bioinformatics (SIB), the European (EBI), and Protein Information Resource (PIR) form Universal (UniProt) consortium. Its main goal is to provide scientific community with a central resource for protein sequences functional information. The UniProt consortium maintains KnowledgeBase (UniProtKB) several supplementary databases including Reference Clusters (UniRef) Archive (UniParc). (1) UniProtKB comprehensive sequence knowledgebase that consists two sections:...
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 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...
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of International Genome Sequencing (IRGSP), manually curated annotation sequence, and other genomics information that could be useful for comprehensive understanding rice biology. Since last publication RAP-DB, IRGSP has been revised reassembled. In addition, a large number rice-expressed tags have released, functional resources produced worldwide. Thus, we thoroughly updated our by manual...
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...
We present here the annotation of complete genome rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions identified or inferred in 19,969 (70%) proteins, 131 possible npRNAs (including 58 antisense transcripts) found. Almost 5000 annotated protein-coding genes found to be disrupted insertional mutant lines, which will accelerate future experimental validation annotations....
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...
Abstract Mitogen-activated protein kinase (MAPK) cascades are activated in plants during responses to pathogens or pathogen-derived elicitors and mediate intracellular stress responses. Here, we show that a rice (Oryza sativa) MAPK, OsMAPK6, was posttranslationally cell culture by sphingolipid elicitor. Suppression of OsMAPK6 expression RNA interference resulted strong reduction pathogen-induced Phe ammonia-lyase mRNA, whereas the mRNA level another OsMAPK5a, highly increased. Silencing...
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...
The expression of two members the glutathione S-transferase (GST) multigene family was studied in Arabidopsis plants inoculated with an avirulent strain Pseudomonas syringae pv. tomato (Pst). Accumulation AtGSTF2 and AtGSTF6 transcripts started 4 2 h after inoculation, respectively, clearly preceded induction pathogenesis-related PR-1 gene. aim this work to find reason for faster GSTs compared classical salicylic acid (SA)-regulated PR-proteins. Expression studies Pst-inoculated SA-signaling...
Abstract 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, ID Mapping tool, along supporting data controlled vocabularies. Users can their favorite programming language generate example code snippets databases using documentation page...
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.
Abstract SwissBioPics (www.swissbiopics.org) is a freely available resource of interactive, high-resolution cell images designed for the visualization subcellular location data. provides describing types from all kingdoms life—from specialized muscle, neuronal and epithelial cells animals, to rods, cocci, clubs spirals prokaryotes. All in are drawn Scalable Vector Graphics (SVG), with each tagged unique identifier controlled vocabulary locations organelles UniProt...
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...
UniProt Knowledgebase (UniProtKB) is a publicly available database with access to vast amount of protein sequence and functional information. To widen the scope publications associated entry, has introduced computationally mapped additional bibliography section, which includes literature collected from external sources. In this article, we describe text mining system, eGenPub, selects articles that are 'about' specific proteins allows automatic identification for given entries. Focusing on...
The UniProt Knowledgebase UniProtKB is a comprehensive, high-quality, and freely accessible resource of protein sequences functional annotation that covers genomes proteomes from tens thousands taxa, including broad range plants microorganisms producing natural products medical, nutritional, agronomical interest. Here we describe work enhances the utility as support for both study their discovery. foundation this an improved representation product metabolism in using Rhea, expert-curated...