Services: Data Resources

The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers).

A comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales: local gene order, karyotypes, matrix plots, etc.  Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus.  

User interface to data from high-throughput sequencing studies of fungal communities across terrestrial biomes. Includes sequencing data, sample locations, sample metadata.

Glyco@Expasy centralizes web-based glycoinformatics resources developed within an international network of glycoscientists. The philosophy is that it should be {glycoscientist AND protein scientist}–friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. Glyco@Expasy was designed with glycoscientists to meet the growing needs of the community for glycoinformatics.

GlyConnect is a platform integrating several sources of information to characterise the molecular actors of glycosylation, mainly glycoproteins and N- and O-linked glycans. The purpose of GlyConnect is to bring out in a single resource the relationships between glycans, the proteins that carry them, the enzymes that synthesise or degrade them and the proteins that bind them.

GnpIS is an interoperable Information System for plant and pest genomics. It is a powerful multispecies centralized information system with seven linked relational databases. 

The UniProt  GO annotation program (GOA) aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB).

The NHGRI-EBI GWAS Catalog is a quality-controlled, manually curated, literature-derived collection of all published genome-wide association studies.
 

Providing a centralized compilation of summary level findings from genetic association studies, both large and small

A specialized and medically-oriented database of published variations observed within the internal ribosome entry site (IRES) variants in hepatitis C virus.

Human Endogenous RetroViruses Database.

The HLA Ligand Atlas is a comprehensive collection of tissue and HLA allele specific HLA ligands that are naturally presented. The data was generated in standardized mass spectrometry experiments and analyzed using our reproducible computational analysis workflow. (Data analysed with the OpenMS MHCquant workflow) 

Database of human mitochondrial genomes from primary INSDC databases, personal submissions and application of MtoolBox to NGS data.

Human transmembrane proteome database

Database with millions of high-resolution images.

A population-based database that collects all the cases with malignancies in Hungary by reports of oncology care hospitals. Registration is mandatory. The Registry is regulated by the order of the Hungarian Government and maintained by the  National Institute of Oncology.

Integrated Database of Small Molecules.
Aggregating many different sources of information about small molecules into a single, logically coherent and semantically interconnected information source.

An integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species. 

IntAct provides a freely available, open source database system and analysis tools for molecular interaction data.

IntOGen collects and analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes.

InterPro classifies proteins into families and predicts the presence of important domains and sites.

Integrated Proteogenomics DataBases an open source database that provides integrated annotations, predictions and a six-frame translation for one respective genome sequence in an easily usable format, both as a search DB (FASTA format) with informative identifiers and a GFF file that integrates all annotations and identifiers.

The Italian COVID-19 Data Portal provides information, guidelines, tools and services to support researchers in creating and sharing research data on COVID-19.

ITSoneDB is a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences.

A Galaxy-based workbench providing established tools (e.g BioMaS, Mothur and qiime2) targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-throughput sequencing.

A curated database of drug targets, prescription medicines and experimental drugs.

An open access database of manually curated, non-redundant transcription factor (TF) binding profiles

Species focused genome data resource for sea lice, provides a genome browser, access to high-throughput data and LIMS.

Provides access to lipid nomenclature, databases, tools, protocols, standards, tutorials, meetings, publications, and other resources and serving the international lipid research community.