Overview
Stop database hopping
visynData is a foundational discovery knowledge base and ETL pipeline that integrates public data from a wide range of biological and drug data sources information available with published data from landmark disease studies.
80+ public data sources
Object storage
Relational DB
FTP
Your data
Object storage
Relational DB
FTP
Powerful + flexible ETL pipeline
Harmonised biological database
Harmonised biological database
Your proprietary data
Gene
Variant
Expression
Protein
+ Much more
visynData is a powerful complement to Aevidence and Ordino
Ordino
Aevidence
GraphQL access
80+ public data sources
Object storage
Relational DB
FTP
Your data
Object storage
Relational DB
FTP
Powerful + flexible ETL pipeline
Harmonised biological database
Harmonised biological database
Your proprietary data
Gene
Variant
Expression
Protein
+ Much more
visynData is a powerful complement to Aevidence and Ordino
Ordino
Aevidence
GraphQL access
visynData is a unified biological knowledge platform that interconnects 80+ carefully curated drug discovery and genomics datasets—from ChEMBL and DrugCentral to TCGA, OpenTargets, and GWAS Catalog—so researchers can answer complex questions through a single GraphQL API, not spreadsheets and database hopping.
Accelerate target prioritization, compound profiling, and disease translation without the integration headache.
Licensed data
In-house data
Public data
Core knowledge base
Comprises data from more than 80 bioinformatics and disease-specific resources.
Powerful ETL
Enhance visynData with your in-house experimental data, using our easy to use visynPlugin system (with support from our bioinformatics experts).
Tailored experience
Our team of data visualization and bioinformatics experts is happy to work with you to create a custom visynData that perfectly supports your research focus.
Data sources
Inside visynData
Take a closer look at the vast array of biological intelligence included in the current version of visynData, which includes data from the Universal Protein knowledgebase (UniProt), Genotype-Tissue Expression Portal (GTEx), ChEMBL, and Reactome as well as cancer research-specific resources, such as the cBioPortal for Cancer Genomics, Cancer Dependency Map Project (DepMap), and The Cancer Genome Atlas (TCGA).
TitleCategoryDescriptionLink
AACR Project GENIECancer GenomicsGENIE(Genomics Evidence Neoplasia Information Exchange) is a large-scale, international data-sharing initiative focused on cancer genomics. It was launched by the American Association for Cancer Research (AACR) with the goal of accelerating precision medicine for cancer.Link
depmapCancer GenomicsDepMap (The Cancer Dependency Map) is a research initiative and database that identifies essential genes for cancer cell survival. By targeting these genes in various cancer cell lines. To represent the diversity of human cancer, DepMap builds on the original Cancer Cell Line Encyclopedia (CCLE) project and more than 2000 cell line models have been collected.Link
cBioPortalCancer GenomicscBioPortal is a web-based tool for exploring cancer genomics data, it provides access to large-scale cancer datasets, allowing researchers and clinicians to explore genetic mutations, alterations, and clinical outcomes across different cancer types.Link
TCGACancer GenomicsTCGA (The Cancer Genome Atlas) is a comprehensive project that provides detailed genomic, epigenomic, transcriptomic, and clinical data on various types of cancer.Link
Systematic analysis of protein turnover in primary cells (Paper)Chemical Biologydata from the Systematic analysis of protein turnover in primary cells paperLink
miRWalkChemical BiologymiRWalk is a comprehensive database that provides information on microRNA (miRNA) target predictions. It offers data on the potential binding sites of miRNAs on genes across the entire genome. miRWalk integrates both predicted and experimentally validated miRNA-target interactions, covering a wide range of species.Link
NA (Paper)Chemical Biologydata from paper: 'Reimagining high-throughput profiling of reactive cysteines for cell-based screening of large electrophile libraries'Link
FDA - UNIIClinicalFDA - UNII (Unique Ingredient Identifier) is a system developed by the U.S. Food and Drug Administration (FDA) to assign unique, non-proprietary identifiers to substances used in pharmaceuticals, biologics, food, and cosmetics.Link
Protac-DBDrug/CompoundProtac-DB is a specialized database focused on PROTACs (PROteolysis-TArgeting Chimeras). PROTACs are a novel class of therapeutic agents designed to target and degrade specific proteins within cells by harnessing the cell's own ubiquitin-proteasome system. Protac-DB provides comprehensive information on PROTACs, including their structures, target proteins, mechanisms of action, and related research.Link
ChEMBLDrug/CompoundChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.Link
ChEBIDrug/CompoundChEBI (Chemical Entities of Biological Interest) is a dictionary of small molecular entities used to standardize chemical nomenclature by offering a consistent way to describe and reference chemical entities.Link
DrugbankDrug/CompoundDrugBank is a comprehensive database that provides detailed information on drugs and drug targetsLink
FDA - Adverse Event Reporting SystemDrug/CompoundThe FDA Adverse Event Reporting System (FAERS) is a database that contains information on adverse event and medication error reports submitted to FDA, designed to support the FDA's post-marketing safety surveillance program for drug and therapeutic biologic products.Link
UbiNetDrug/CompoundUbiNet 2.0 (Database of E3-Substrate Interactions) is a knowledge repository that provides updated, validated, and abundant E3-substrate interactions, detailed classification of human E3 ligases, and visualization tools to investigate ubiquitination network.Link
DrugcentralDrug/CompoundDrugCentral is an online drug information resource that provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.Link
The Human Protein AtlasExpressionThe Human Protein Atlas is a comprehensive resource that provides detailed information on the expression, localization, and function of proteins in human tissues and cells.Link
GTExPortalExpressionThe Genotype Tissue Expression (GTEx) is a comprehensive resource of WGS, RNA-Seq and QTL data from 54 non-diseased tissue sites across nearly 1000 individuals to study human gene expression and regulation, and its relationship to genetic variation across multiple diverse tissues and individuals.Link
Ensembl – GeneGeneEnsembl is a comprehensive genome database that provides detailed information about genes and their associated genomic features across a wide range of species, including humans.Link
BorealisGeneBorealis, the Canadian Dataverse Repository is a platform that provides access to research data across various disciplines. Hosted by Scholars Portal, we use Borealis as a source for conservation scores.Link
GencodeGeneGencode is a resource for comprehensive and accurate annotations of human and mouse genomes.Link
NCBI - GeneGeneNCBI gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.Link
NCBI - OrthologsGeneNCBI's Eukaryotic Genome Annotation pipeline identifies ortholog gene groups for the NCBI Gene dataset using a combination of protein sequence similarity and local synteny information.Link
HomoloGeneGeneAn automated system of the NCBI for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic speciesLink
EBI – HGNCGeneEBI – HGNC (HUGO Gene Nomenclature Committee) is an organization that provides a standardized and unique naming system for human genes.Link
Pig RNA atlasGeneThe Pig RNA Atlas presents the genome-wide expression of all 22342 protein-coding genes in 98 pig tissues.Link
BiomartGeneBioMart is a data management system provide an easy-to-use web-based tool that allows researchers to query, filter, and retrieve biological data from multiple databases in a unified and efficient manner. we use BioMart as a source for gene and protein identifiers mapping.Link
MyGeneGeneMyGene is a web-based resource that provides a simple-to-use interface for accessing gene annotation data.Link
GeneRIFGeneGeneRIF (Gene Reference Into Function) is a database that provides concise summaries of the functions of genes, based on information from scientific publications.Link
EBI – GWAS CatalogGeneThe EBI – GWAS Catalog is a public database that compiles results from genome-wide association studies (GWAS). These studies investigate the associations between genetic variants and traits or diseases.Link
OMIMGeneticsOMIM (Online Mendelian Inheritance in Man) is a comprehensive, online database that catalogs human genes and genetic disorders. It contains information on all known mendelian disorders and over 16,000 genes.Link
JASPARGeneticsJASPAR is a database of curated, non-redundant transcription factor (TF) binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups.Link
ClinVarGeneticsClinVar is a public database that aggregates information about the clinical significance of genetic variants.Link
OpenTargetsGeneticsOpenTargets is a platform that use human genetics and genomics data for systematic drug target identification and prioritisation. It combines information from multiple sources, including genomics, transcriptomics, proteomics, and clinical data, to evaluate the relationship between genes, diseases, and potential therapeutic interventions.Link
dbSNPGeneticsdbSNP (Database of Single Nucleotide Polymorphisms) contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.Link
MonarchInteractionMonarch is a knowledge platform focused on integrating and analyzing data related to genotype-phenotype relationships across various species, including humans.Link
AlphaMissenseInteractionAlphaMissense is an adaptation of AlphaFold fine-tuned on human and primate variant population frequency databases to predict missense variant pathogenicity.Link
BioGRIDInteractionBioGRID (Biological General Repository for Interaction Datasets) is an public database that collects and curates data on protein and genetic interactions across various organisms.Link
IntActInteractionIntAct is a public database managed by the European Bioinformatics Institute (EBI) and provides information on molecular interactions, primarily focusing on protein-protein interactions and supporting a wide range of interaction types, including direct physical interactions and indirect associations.Link
STRINGInteractionSTRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a comprehensive database and web resource that provides information on known and predicted protein-protein interactions. It integrates data from various sources, including experimental studies, computational predictions, and literature, to offer a detailed view of protein interactions within biological systems.Link
Complex PortalInteractionComplex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms. The majority of complexes are made up of proteins but may also include nucleic acids or small molecules.Link
PDBe ChemLigandsPDBe Chem provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components.Link
ReactomePathwayReactome database provides information about biological pathways and processes. It offers curated data on the interactions and reactions involving proteins, genes, and small molecules within various cellular pathways.Link
GSEA - MSigDBPathwayMSigDB (Molecular Signatures Database) is a curated collection of gene sets that represent various biological states or processes, such as signaling pathways, gene ontologies, and gene expression signatures. These gene sets are used as input for GSEA to explore and interpret large-scale gene expression data.Link
GeneontologyPathwayGene Ontology (GO) is a framework for classifying and describing the functions of genes across different species. It provides a standardized vocabulary for annotating genes in terms of biological process, molecular function, and cellular component.Link
ScannetProteinScannet provides information about the likelihood or confidence that a specific amino acid residue within a protein is involved in a protein-protein interaction (PPI).Link
SWISS-MODELProteinThe SWISS-MODEL Repository is a database of annotated 3D protein models generated by automated homology modelling for relevant model organisms and experimental structure information for all sequences in UniProtKB.Link
PDBbind-CNProteinPDBbind is a comprehensive collection of experimentally measured binding affinity data for all biomolecular complexes deposited in the Protein Data Bank (PDB). It provides an essential linkage between the energetic and structural information of those complexes.Link
Protein Half Life (Paper)Proteindata from paper: ‘Proteome-wide mapping of short-lived proteins in human cells’Link
Uniprot - TremblProteinUniProt (Universal Protein Resource) is a comprehensive and highly curated database of protein sequence, functional annotations and protein variants information. It serves as a central repository for protein data.Link
CompartmentsProteinCompartments is a database that provides detailed information about the subcellular localization of proteins (e.g., nucleus, cytoplasm, mitochondria). It integrates data from various sources, including experimental data, predictions, and high-throughput studies.Link
SIFTSProteinStructure Integration with Function, Taxonomy and Sequence (SIFTS) is a project in the PDBe-KB resource for residue-level mapping between UniProt and PDB entries. SIFTS also provides annotation from the IntEnz, GO, InterPro, Pfam, CATH, SCOP, PubMed, Ensembl and Homologene resources.Link
Uniprot - Swiss-ProtProteinUniProt (Universal Protein Resource) is a comprehensive and highly curated database of protein sequence, functional annotations and protein variants information. It serves as a central repository for protein data.Link
Expasy - ENZYMEProteinENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.Link
InterProProteinInterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. InterPro uses predictive models, known as signatures, provided by several databases.Link
Uniprot - Subcellular locationProteinUniprot - Subcellular location subsection provides information on the location and the topology of the mature protein in the cell.Link
CHESS IsoformsProtein StructureThe Comprehensive Human Expressed SequenceS (CHESS) database is a catalogue of genes derived from GTEx. In a follow up study the authors used AlphaFold to predict non-canonical isoform structures.Link
SAbDabProtein/AntibodySAbDab database containing all the antibody structures available in the PDB, annotated and presented in a consistent fashion.Link
Human Phenotype Ontology (HPO)TerminologyThe Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms.Link
NCBI TaxonomyTerminologyThe NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.Link
Orphanet/ORDOTerminologyOrphanet provides a comprehensive resource for rare diseases including nosology, gene-disease relationships, external connections and an ontology (ORDO).Link
EFOTerminologyThe Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog.Link
NCI ThesaurusTerminologyThe NCI Thesaurus (NCIt) is a comprehensive biomedical terminology that provides a structured vocabulary for cancer research and clinical care.Link
OncotreeTerminologyOncoTree is a comprehensive, community-led cancer classification system that adapts to the evolving demands of precision oncology.Link
Cell OntologyTerminologyCell Ontology provides a standardized vocabulary for describing cell types and their relationships across different biological contexts.Link
MeSHTerminologyMedical Subject Headings (MeSH) is a comprehensive vocabulary used for indexing, cataloging, and searching biomedical and health-related information including terms for diseases, chemicals, drugs, procedures, and other health-related conceptsLink
MondoTerminologyThe Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. it standardizes the classification and naming of diseases across different medical and biological databases.Link
Disease OntologyTerminologyThe Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease conceptsLink
UBERONTerminologyUberon is an anatomical ontology that represents body parts, organs and tissues in a variety of animal species, with a focus on vertebrates.Link
CellosaurusTerminologyCellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research. It includes information such as their origin, characteristics and genetic informationLink
UMLSTerminologyUMLS (Unified Medical Language System) is a comprehensive framework and set of resources developed by the U.S. National Library of Medicine (NLM) to facilitate the integration and interoperability of biomedical information.Link
Mouse Genome Informatics (MGI)TerminologyThe Mouse Genome Informatics (MGI) database MGD serves as a primary resource for a spectrum of genetic, genomic and biological data supporting the use of the mouse as a model for understanding human biology and disease.Link
72 of 72 sources