Full table of tools and resources
| Tool or resource | Description | Related pages | Registry |
|---|---|---|---|
| ArrayExpress | A repository of array based genomics data | ArrayExpress BioStudies Expression Atlas Omics Discovery Index | Tool info Standards/Databases Training Publication |
| Beacon v2 | API framework and data model for cross-cohort searching. | How to add to and edit... GA4GH Beacon | Standards/Databases Publication |
| BioImage Archive | The BioImage Archive is a free, publicly available online resource which stores and distributes biological images. It accepts submissions of data from any imaging modality, as long as the data are either associated with a peer-reviewed publication, or of value beyond a single experiment. | BioStudies | Standards/Databases Publication |
| BioSamples | BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. | BioSample | Tool info Standards/Databases Training Publication |
| BioStudies | A database hosting datasets from biological studies. Useful for storing or accessing data that is not compliant for mainstream repositories. | BioStudies | Tool info Standards/Databases Training Publication |
| cBioPortal | Interactive exploratory analysis tool for exploring large cancer genomics datasets | cBioPortal | Tool info Standards/Databases Publication |
| China National Genomics Data Center - National Genomics Data Center (CNCB-NGDC) | China's national initative to build platforms and infrastructure to support life science researchers in academia and industry | BioProject BioSample | Publication |
| Data Repository Service (DRS) | GA4GH standard API for accessing and retrieving data files | GA4GH | |
| Data Use Ontology (DUO) | GA4GH standard ontology for describing access and use restrictions on datasets | GA4GH | Publication |
| Database of Genotypes and Phenotypes (dbGAP) | The database of Genotypes and Phenotypes (dbGaP) archives and distributes data from studies investigating the interaction of genotype and phenotype in Humans | dbGAP Omics Discovery Index | Tool info Standards/Databases Training Publication |
| DNA Data Bank of Japan (DDBJ) | Japan-based Nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. | BioSample Repositories | Tool info Publication |
| DUOS | DUOS is a multi-sided data sharing platform bringing together researchers submitting and requesting data, and data access committees and institutional officials overseeing the use of the data. | Data Access Committee ... | Standards/Databases |
| Electron Microscopy Public Image Archive (EMPIAR) | EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw images underpinning 3D cryo-EM maps and tomograms | BioStudies | Standards/Databases Publication |
| EMBL-EBI's data submission wizard | EMBL-EBI's wizard for finding the right EMBL-EBI repository for your data. | Repositories | |
| European Nucleotide Archive (ENA) | A record of sequence information scaling from raw sequcning reads to assemblies and functional annotation | Repositories | Tool info Standards/Databases Training Publication |
| Experimental Factor Ontology (EFO) | The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI. | EGA | Standards/Databases Publication |
| Expression Atlas | Expression Atlas is an open science resource that gives users a powerful way to find information about gene and protein expression across species. Data is analysed with standardised best-practice pipelines and displayed in an interactive format. | Expression Atlas | Standards/Databases Training Publication |
| FigShare | Data publishing platform | Other repositories | Standards/Databases Training |
| Gen3 | An open source data platform with customisable data dictionary to enable data harmonisation, discovery, sharing and analysis. | ||
| GenBank | A database of genetic sequence information. GenBank may also refer to the data format used for storing information around genetic sequence data. | Repositories | Tool info Standards/Databases Training |
| Gene Expression Omnibus (GEO) | A repository of MIAME-compliant genomics data from arrays and high-throughput sequencing | Gene Expression Omnibus Omics Discovery Index | Publication |
| Genome Expression Archive (GEA) | Functional genomics archive run by DDBJ in Japan | Publication | |
| Genome Sequence Archive for Human (GSA Human) | GSA Human is a China-based controlled-access repository for sensitive human data | GSA Human | Publication |
| htsget | GA4GH standard protocol for securely streaming genomic data | GA4GH | Publication |
| International Nucleotide Sequence Database Collaboration (INSDC) | A collaborative database of genetic sequence datasets from DDBJ, EMBL-EBI and NCBI | BioProject | Tool info |
| iProX | Integrated proteome resources centre to accelerate worldwide data sharing in proteomics. | Publication | |
| Japan Proteome Standard Repository (jPOSTrepo) | A public repository for storing and sharing mass spectrometry-based Proteome data. | Publication | |
| Japanese Genome-Phenotype Archive (JGA) | A controlled access data repository for human data managed by the DDBJ. | JGA Omics Discovery Index | Publication |
| Mass Spectrometry Interactive Virtual Environment (MassIVE) | A community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. | ||
| Metabobank | Repository for metabolomics data from mass spectrometry, NMR and imaging run by DDBJ | ||
| Metabolights | MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. | Publication | |
| National Center for Biotechnology Information (NCBI) | Online database hosting a vast amount of biotechnological information including nucleic acids, proteins, genomes and publications. | BioSample dbGAP | |
| Nextflow | Nextflow is a framework for data analysis workflow execution | Tool info Publication | |
| OmicsDI | Omics Discovery Index (OmicsDI) provides a knowledge discovery framework across heterogeneous omics data (genomics, proteomics, transcriptomics and metabolomics) | Omics Discovery Index | Tool info Standards/Databases Training Publication |
| OMOP-CDM | OMOP is a common data model for the harmonisation for of observational health data. | Standards/Databases | |
| Passports | GA4GH open standard to encode data access permissions of users | GA4GH | Publication |
| Pedigree | A GA4GH standard to allow for computable exchange of family health history and representation of larger, more complex families | ||
| Phenopackets | GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. | GA4GH EGA | Publication |
| Proteomics Identifications Archive (PRIDE) | A centralized, standards compliant, public data repository for mass spectrometry proteomics data | Publication | |
| REMS | REMS (Resource Entitlement Management System), developed by CSC, is a tool that can be used to manage researchers‚ access rights to datasets. | Data Access Committee ... | Tool info Training |
| The European Genome-phenome Archive (EGA) | EGA is a service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects | BioSample EGA Omics Discovery Index Repositories | Tool info Standards/Databases Training Publication |
| Variant Representation (VRS) | GA4GH standard for representing genomic variants | GA4GH | Publication |
| Workflow Execution Service (WES) | GA4GH standard protocol for sending workflows to compute | GA4GH | |
| Zenodo | Generalist research data repository built and developed by OpenAIRE and CERN | Other repositories | Standards/Databases Training |
Editor
Australian BioCommons / University of Melbourne