Services: data resources

A database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a graphical form. 

The European Genome-phenome Archive (EGA) allows users to explore datasets from numerous genotype experiments, including case-control, population and family studies, that are supplied by a range of data providers. 

The European Nucleotide Archive (ENA) contains all the nucleotide sequences in the public domain and consolidates data from EMBL-Bank, the European Trace Archive and the Sequence Read Archive.

Based on ICGC PanCancer infrastructure for organising and processing NGS data using workflow plugins including:  

• Workflow Plug-Ins - provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).
• Cloud/HPC - IT Infrastructure for de.NBI users based on ICGC and TCGA PanCancer technology
• OTP - "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing.
• Roddy - a framework for large scale NGS processing pipelines on Petabyte scale for the management of workflows in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project.

This catalogue lists available Translational Medicine datasets, coming from academic and industry research projects as well as from clinical cohorts and genome consortia. 

The Norwegian services for sensitive data, is a platform enabling collection, storage and analysis of sensitive research data in a secure environment.

The glycomic MS database and repository.

Universal Catalog Database for biological findings

UniLectin is a platform integrating information regarding non-enzymatic carbohydrate-binding proteins usually referred to as lectins with the prospect of building and refining a structural and functional classification of these proteins. It includes the reference Lectin3D a database of 3D structures curated from the PDB. Interactive resource for the exploration of lectins

UniProt produces and maintains automatic and manually curated annotation of all publicly available protein sequences and serves these to users through various interfaces. 

Curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, with experimentally validated functional motifs and cross-links to interacting regulatory proteins.

Collection of validation results for the entire Protein Data Bank.

VarAFT is a software designed to annotate and filter Human NGS data. This system was developed within the RD-Connect project and was instrumental for the creation of the RD-Connect Genome-Phenome platform. As a stand-alone java system, it ensures full data protection, critical for clinical use. VarAFT provides experiments’ quality, annotates, and allows the filtration of VCF files. Data from multiple samples can be combined to address different Mendelian Inherited Disorders, Population Genetics or Cancers. It contains unique variant priorization features including OMIM, HPO, Gene Ontology, pathways and predictions from UMD-Predictor and Human Splicing Finder in addition to classical annotations from dbNSFP . It is used by many research and clinical laboratories worldwide.

VEuPathDB provides access to diverse genomic and other large scale datasets related to eukaryotic pathogens and invertebrate disease vectors.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB) parasitic species (EuPathDB), fungi (FungiDB) and vector species (VectorBase)

A resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries. 

An open, collaborative platform dedicated to the curation of biological pathways