Inspired by the efforts of scientists around the world and the game-changing efforts of projects like the Creative Commons, the Wikipedia Foundation, and the Free Software movement, we hope to engage the larger community in an open and fruitful discussion on issues concerning the use and reuse of scientific data, including the balance of openness and how to make ends meet in an increasingly competitive environment.
If you would like to join our efforts to highlight the use and reuse of data in the sciences, please feel free to contact us on our tracker, create a pull request against our repository, or join our forum.
We are not lawyers and this is not legal advice: all institutions and groups have their own perspectives and counsel. We are a group of scientists, engineers, librarians, and specialists that are concerned about the use and reuse of increasingly interconnected, derived, and reprocessed data. We want to make sure that data-driven scientific endeavors can work with one another in meaningful ways without undue legal concerns.
The (Re)usable Data Project is meant provide a resource that looks at some of the issues around the reuse of scientific data and open a conversation about how to deal with them.
We also want to actively work with the community in considering our criteria and in making sure that our information about scientific data resources is up-to-date and correct. If you have any questions, concerns, or see any problems, please open a ticket on our GitHub tracker.
The initial driving concern of this project is the use
and reuse of biological and biomedical data. However,
this is a general problem in the scientific community
and needs to be addressed directly.
For each resource, using our criteria, we attempt to objectively assign zero to five stars for how well we believe a resource's data may build upon, edited, modified, and redistributed.
If you see any problems with our determinations or would like to make corrections or clarifications, please open a ticket for us on our issue tracker.
This is a short overview of the criteria that we use when evaluating a resource's data license for use and reuse. We have attempted to balance many needs (credit, mutability, commercialization, redistribution, etc.) and focused on trying to objectively see how licenses can interact across resources.
|Name||Tags||Grade||Description||License Info||License Issues|
|Name||Tags||Grade||Description||License Info||License Issues|
|Alliance of Genome Resources (AGR) 🔗||biology, MOD, functional annotation, disease-gene association||∅||The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.||unknown 🔗|
|BGee (data) 🔗||biomedical, x-species, expression data||★||Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data).||unknown|
|BGee (ontology) 🔗||biomedical, expression data, ontology||★ ★ ★ ★||Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced from multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data).||copyleft 🔗|
|BioGRID 🔗||biology, cross-species, protein-protein interaction||★ ★ ★ ★ ★||BioGRID is an interaction repository with data compiled through comprehensive curation efforts. Our current index is version 3.4.155 and searches 63,959 publications for 1,507,991 protein and genetic interactions, 27,785 chemical associations and 38,559 post translational modifications from major model organism species. All data are freely provided via our search index and available for download in standardized formats.||permissive 🔗|
|BRENDA Tissue Ontology 🔗||biology, ontology, enzyme sources||★ ★ ★ ★ ½||A structured controlled vocabulary for the source of an enzyme. It comprises terms of tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.||permissive 🔗|
|ChEMBL 🔗||biology, biochemical, bioactive drug-like small molecules||★ ★ ★||ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).||copyleft 🔗|
|Clinical Interpretation of Variants in Cancer (CIViC) 🔗||biomedical, human, cancer, precision medicine, variants, variant disease associations||★ ★ ★ ★ ★||CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. Our goal is to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations.||permissive 🔗|
|ClinVar 🔗||biomedical, human, disease-gene association, variant-disease association, variant definitions||★ ★ ★ ★||ClinVar archives and aggregates information about relationships among variation and human health. ClinVar collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about the submitter, and other supporting data.||public domain 🔗|
|Comparative Toxicogenomics Database (CTD) 🔗||biology, x-species, disease-gene association||★ ★ ½||CTD promotes understanding about the effects of environmental chemicals on human health by integrating data from curated scientific literature to describe chemical interactions with genes and proteins, and associations between diseases and chemicals, and diseases and genes/proteins.||restrictive 🔗|
|dbGaP (public) 🔗||biology, human, genotype-phenotype||∅||The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans. Provides authorized access to protected and raw data (e.g., Genotype-Tissue Expression (GTEx) project).||unknown 🔗|
|DECIPHER 🔗||biology, human, gene, genotype, rare disease, phenotype, variant, submicroscopic chromosomal imbalance, rare sequence variants||★||DECIPHER is used by the clinical community to share and compare phenotypic and genotypic data. The DECIPHER database contains data from 24848 patients who have given consent for broad data-sharing; DECIPHER also supports more limited sharing via consortia.||closed pool 🔗|
|dictyBase 🔗||biology, MOD, genotype-phenotype association, disease-model association, gene expression||★||dictyBase is a database that provides a centralized source of Dictyostelium information for Dictyostelium researchers and Non-Dictyostelium researchers. This includes tutorials, dictyNews, techniques, the Stock Center, genomic and molecular information, colleague infromation, Dictyostelium literature, and much more.||unknown 🔗|
|DrugBank 🔗||pharmacology, drug, bioinformatics, cheminformatics, drugs, drug-protein interactions, targets, pathways||★ ★ ★ ★||The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information.||restrictive 🔗|
|DrugCentral 🔗||phamacology, drug-target interaction, chemical structure of drugs, drug, diseaase||★ ★ ★ ★||DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. We monitor FDA, EMA, and PMDA for new drug approval on regular basis to ensure currency of the resource.||copyleft 🔗|
|Dryad Digital Repository 🔗||general, any||★ ★ ★ ★ ½||DataDryad.org is a curated general-purpose repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Dryad has integrated data submission for a growing list of journals; submission of data from other publications is also welcome.||permissive 🔗|
|ENCODE 🔗||biology, genomic resource, genomic elements||★ ★ ★ ★ ½||The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active.||permissive 🔗|
|Fantom5 🔗||biology, human, gene expression||★ ★ ★ ★ ★||We are complex multicellular organisms composed of ~400 distinct cell types. This diversity of cell types allow us to see, think, hear, fight infections etc. yet all of this is encoded in the same genome. The difference between all these cells is what parts of the genome they use – for instance, neurons use different genes than muscle cells, and therefore they work very differently. In FANTOM5, we have systematically investigated exactly what are the sets of genes used in virtually all cell types across the human body, and the genomic regions which determine where the genes are read from. We aim to use this information to build transcriptional regulatory models for every primary cell type that makes up a human.||permissive 🔗|
|FlyBase 🔗||biology, MOD, genotype-phenotype association||★ ★ ½||FlyBase is the model organism database providing integrated genetic, genomic, phenomic, and biological data for Drosophila melanogaster.||copyright 🔗|
|Genomic Data Commons (GDC) 🔗||biology, human, cancer genome, variants, mRNA and miRNA sequence data||★||The NCI\'s Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine.||unknown|
|Genome Aggregation Database (gnomAD) 🔗||biology, human, exome sequencing data, genome sequencing data, disease-specific genetic studies, population genetic studies||★ ★ ★ ★ ½||The Genome Aggregation Database (gnomAD), is a coalition of investigators seeking to aggregate and harmonize exome and genome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. In its first release, which contained exclusively exome data, it was known as the Exome Aggregation Consortium (ExAC).||copyleft 🔗|
|Gene Ontology (annotations) 🔗||biology, x-species, gene annotation, gene association, biological process, molecular function, cellular component||★ ★ ★ ★ ★||The mission of the GO Consortium is to develop an up-to-date, comprehensive, computational model of biological systems, from the molecular level to larger pathways, cellular and organism-level systems.||permissive 🔗|
|Gene Ontology (ontology) 🔗||biology, x-species, ontology, biological process, molecular function, cellular component||★ ★ ★ ★ ★||The mission of the GO Consortium is to develop an up-to-date, comprehensive, computational model of biological systems, from the molecular level to larger pathways, cellular and organism-level systems.||permissive 🔗|
|GTEx 🔗||biology, human, gene expression||★ ★ ½||The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. This project will collect and analyze multiple human tissues from donors who are also densely genotyped, to assess genetic variation within their genomes. By analyzing global RNA expression within individual tissues and treating the expression levels of genes as quantitative traits, variations in gene expression that are highly correlated with genetic variation can be identified as expression quantitative trait loci, or eQTLs.||permissive 🔗|
|Human Phenotype Ontology (HPO) 🔗||biology, human, disease-phenotype association||★ ★ ½||A curated database of human hereditary syndromes from OMIM, Orphanet, and DECIPHER mapped to classes of the human phenotype ontology. Various meta-attributes such as frequency, references and negations are associated with each annotation. These are presently limited to rare mendelian diseases.||restrictive 🔗|
|International Mouse Phenotyping Consortium (IMPC) 🔗||biology, mouse, genotype-phenotype association||★||The International Mouse Phenotyping Consortium (IMPC) is generating a knockout mouse strain for every protein coding gene by using the embryonic stem cell resource generated by the International Knockout Mouse Consortium (IKMC). Systematic broad-based phenotyping is performed by each IMPC center using standardized procedures found within the International Mouse Phenotyping Resource of Standardised Screens (IMPReSS) resource. Gene-to-phenotype associations are made by a versioned statistical analysis.||copyright|
|Kyoto Encyclopedia of Genes and Genomes (KEGG), FTP 🔗||biology, genomic resource, gene-pathway association, disease-gene association, orthology||★ ★||KEGG is an integrated database resource consisting of the seventeen main databases including systems, genomic, chemical, and health information.||restrictive 🔗|
|Mouse Genome Informatics (MGI) 🔗||biology, MOD, genotype-phenotype association, disease-model association, gene expression||★ ★ ★ ★||MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.||permissive 🔗|
|Monarch Initiative 🔗||biology, x-species, gene, genotype, disease, phenotype, variant, disease-phenotype associations, genotype-phenotype associations||★ ★||Integrate, align, and re-distribute cross-species gene, genotype, variant, disease, and phenotype data. Provide a portal for exploration of phenotype-based similarity. Facilitate identification of animal models of human disease through phenotypic similarity. Enable quantitative comparison of cross-species phenotypes. Develop embeddable widgets for data exploration. Influence genotype and phenotype reporting standards. Improve ontologies to better curate genotype-phenotype data.||permissive 🔗|
|Mouse Phenome Database (MPD) 🔗||biology, MOD, genotype (strain)-phenotype association||★ ★ ★ ★ ½||The Mouse Phenome Database is a collaborative standardized collection of measured data on laboratory mouse strains, and includes: baseline phenotype data sets; studies of drug, diet, disease and aging effect; protocols, projects, and publications; and SNP, variation and gene expression studies. MPD collects data for classical inbred strains, other fixed-genotype strains, derived lines and populations that are openly acquirable (strain panel examples). Strains can be from JAX-Mice or from any other vendor that\'s a recognized breeding source.||permissive 🔗|
|MSigDB 🔗||biology, gene sets||★ ★ ★ ★ ½||The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software.||permissive 🔗|
|MyGene.info 🔗||biology, genomic resource, gene definition||★ ★||MyGene.info provides simple-to-use REST web services to query/retrieve gene annotation data.||restrictive 🔗|
|MyVariant.info 🔗||biology, genomic resource, variants, variant annotation||★ ★||MyVariant.info provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources.||restrictive 🔗|
|National Center for Biotechnology Information (Gene) 🔗||biology, genomic resource, gene definition, taxon definition, gene-publication association||★ ½||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.||unknown 🔗|
|neXtProt 🔗||biology, human, protein-related data, protein functional data, protein-protein interaction, sub-cellular location||★ ★ ★||Developed by the SIB Swiss Institute of Bioinformatics neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.||restrictive 🔗|
|Online Mendelian Inheritance in Animals (OMIA) 🔗||biology, veterinary x-species, gene-disease association||★ ★ ★||Online Mendelian Inheritance in Animals (OMIA) is a catalogue/compendium of inherited disorders, other (single-locus) traits, and genes in 215 (non-model) animal species.||copyright 🔗|
|Mendelian Inheritance in Man (OMIM) 🔗||biomedical, human, disease-phenotype association, gene-disease association, variant-disease association||½||OMIM is a comprehensive, authoritative compendium of human genes and genetic phenotypes with full-text, referenced overviews that contains information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype.||restrictive 🔗|
|OncoKB 🔗||biology, human, variants, cancer genes, gene expression||★ ★ ★ ½||OncoKB is a precision oncology knowledge base and contains information about the effects and treatment implications of specific cancer gene alterations. It is developed and maintained by the Knowledge Systems group in the Marie Josée and Henry R. Kravis Center for Molecular Oncology at Memorial Sloan Kettering Cancer Center (MSK), in partnership with Quest Diagnostics.||restrictive 🔗|
|Orphanet portal for rare diseases and orphan drugs 🔗||biomedical, human, disease-gene association, disease-phenotype association, disease classification, ontology||★ ★ ★||Orphanet provides reference information on rare diseases and orphan drugs to help improve the diagnosis, care and treatment of patients with rare diseases.||unknown 🔗|
|Orphanet portal for rare diseases and orphan drugs (open access subset) 🔗||biomedical, human, disease-gene association, disease-phenotype association, disease classification, ontology||★ ★ ★||Orphanet provides reference information on rare diseases and orphan drugs to help improve the diagnosis, care and treatment of patients with rare diseases.||restrictive 🔗|
|Protein ANalysis THrough Evolutionary Relationships Classification System (PANTHER) 🔗||biology, genomic resource, orthology||★ ★ ★||The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System was designed to classify proteins (and their genes) according to evolutionary family/subfamily, molecular function, biological process, and pathway. The PANTHER Classifications are the result of human curation as well as sophisticated bioinformatics algorithms.||copyright|
|Pfam 🔗||biology, protein familys, protein family alignments, HMMs||★ ★ ★ ★ ★||The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).||permissive 🔗|
|Pharos 🔗||biology, disease, targets, ligands||★||copyleft 🔗|
|PomBase 🔗||biology, MOD, genotype-phenotype association, disease-model association, gene expression||★||PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets.||unknown 🔗|
|Reactome 🔗||biology, pathway, pathway data||★ ★ ★ ★ ½||Reactome is a free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education.||permissive 🔗|
|Rat Genome Database (RGD) 🔗||biology, MOD, genotype-phenotype association, disease-model association, gene expression||★ ★ ★ ★||The Rat Genome Database (RGD) was established in 1999 and is the premier site for genetic, genomic, phenotype, and disease data generated from rat research. In addition, it provides easy access to corresponding human and mouse data for cross-species comparisons.||permissive 🔗|
|Rhea 🔗||biology, biochemical, enzymes, metabolic networks, reactions||★ ★ ★ ★ ★||Rhea is an expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models. Rhea uses the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to precisely describe reactions participants and their chemical structures. All reactions are balanced for mass and charge and are linked to source literature, metabolic resources and other functional vocabularies such as the enzyme classification of the NC-IUBMB.||permissive 🔗|
|Saccharomyces Genome Database (SGD) 🔗||biology, MOD, genotype-phenotype association, disease-model association, gene expression||★ ★ ★ ★||The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.||permissive 🔗|
|STRING 🔗||biology, cross-species, protein-protein interaction, protein families||★ ★ ★ ★ ★||STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases.||permissive 🔗|
|The Arabidopsis Information Resource (TAIR, public) 🔗||biology, MOD, sequence, gene structure, gene expression, functional annotation||★ ★ ★ ★ ★||The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana.||permissive 🔗|
|UniProt 🔗||biology, sequence, protein sequence, protein function||★ ★ ★||The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Includes: UniProtKB, UniRef, UniParc, and Proteomes.||restrictive 🔗|
|WormBase 🔗||biology, model organism genome sequences||★||WormBase is an international consortium dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.||unknown 🔗|
|Zebrafish Information Network (ZFIN) 🔗||biology, model organism database||★ ★||The Zebrafish Information Resource is the community database resource for the laboratory use of zebrafish which develops and supports integrated zebrafish genetic, genomic and developmental information, maintains the definitive reference data sets of zebrafish research information toward facilitation of the use of zebrafish as a model for human biology.||restrictive 🔗|
All copyrightable materials on this site are ©
2017 the (Re)usable Data
Project under the
ReusableData.org is funded by the National Center for Advancing Translational Sciences (NCATS) OT3 TR002019 as part of the Biomedical Data Translator project.
The (Re)usable Data Project would like to acknowledge the assistance of many more people than can be listed here. Please visit the about page for the full list.