Parit Bansal
A5078746245- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Advanced Proteomics Techniques and Applications
- Machine Learning in Bioinformatics
- Scientific Computing and Data Management
- Research Data Management Practices
- Computational Drug Discovery Methods
- Semantic Web and Ontologies
- Cell Image Analysis Techniques
- Molecular Biology Techniques and Applications
- Gene expression and cancer classification
- Enzyme Structure and Function
- Genetics, Bioinformatics, and Biomedical Research
- Plant biochemistry and biosynthesis
- RNA and protein synthesis mechanisms
- Neural Networks and Applications
- Data Mining Algorithms and Applications
- AI in cancer detection
- Microbial Natural Products and Biosynthesis
- Genomics and Rare Diseases
- Natural Language Processing Techniques
SIB Swiss Institute of Bioinformatics
2015-2024
European Bioinformatics Institute
2024
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...
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...
Abstract Rhea (https://www.rhea-db.org) is an expert-curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI (Chemical Entities Biological Interest) (https://www.ebi.ac.uk/chebi). In this paper, we describe a number key developments in since our last report database issue Nucleic Acids Research 2019. These include improved reaction coverage Rhea, adoption as reference vocabulary for enzyme annotation UniProt UniProtKB (https://www.uniprot.org), development new...
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...
To provide high quality computationally tractable enzyme annotation in UniProtKB using Rhea, a comprehensive expert-curated knowledgebase of biochemical reactions which describes reaction participants the ChEBI (Chemical Entities Biological Interest) ontology.We replaced existing textual descriptions with their equivalents from is now standard for enzymatic UniProtKB. We developed improved search and query facilities UniProt website, REST API SPARQL endpoint that leverage chemical structure...
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...
Abstract The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/) is a federation bioinformatics research and service groups. international life science community in academia industry has been accessing the freely available databases provided by since its inception 1998. In this paper we present 11 which currently offer semantically enriched data accordance with FAIR principles (Findable, Accessible, Interoperable, Reusable), as well Personalized Health Network initiative (SPHN)...
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...
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 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 the ontology ChEBI (Chemical Entities Biological Interest). Results We replaced existing textual descriptions with their equivalents from is now standard for enzymatic UniProtKB. developed improved search and query facilities UniProt website, REST API, SPARQL endpoint that...
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...
Abstract Motivation There now exist thousands of molecular biology databases covering every aspect biological data. This database infrastructure takes significant effort and funding to develop maintain. The creators these need make strong justifications funders prove their impact or importance. are many publication metrics tools available such as Google Scholar measure citation AltMetrics multiple measures including social media coverage. Results In this article, we describe a series novel...