Table 2.
FAIR indicators
| Core FAIR principle | FAIR principle | FAIR indicator |
|---|---|---|
| Findable | F1. (meta)data are assigned a globally unique and persistent identifier | Each GWAS is assigned a unique identifier that can be resolved externally through IDENTIFIERS.org e.g., GCST no. |
| F2. data are described with rich metadata (defined by R1 below) | Each GWAS is described by the metadata elements listed in “Proposed metadata standard reporting elements”a | |
| F3. metadata clearly and explicitly include the identifier of the data it describes | Metadata include the accession ID and are linked to the GWAS SumStats they describe | |
| F4. (meta)data are registered or indexed in a searchable resource | GWAS is searchable in the GWAS Catalog by accession ID, trait, publication, author, or locus (variant, gene, cytogenetic, or chr:bp-bp region) | |
| Accessible | A1. (meta)data are retrievable by their identifier using a standardized communications protocol | Metadata can be easily viewed on the GWAS Catalog web interface, with a specific page for each GWAS, accessible through a stable URL, which includes the accession ID, with a download link for the SumStats Metadata that can be retrieved from the GWAS Catalog’s REST API (https://www.ebi.ac.uk/gwas/docs/api) using the accession ID |
| A1.1 the protocol is open, free, and universally implementable | The GWAS Catalog (https://www.ebi.ac.uk/gwas/) website and datasets are freely accessible to all | |
| A1.2 the protocol allows for an authentication and authorization procedure, where necessary | Not applicable | |
| A2. metadata are accessible, even when the data are no longer available | Metadata will remain accessible via the accession ID, even if the SumStats are no longer available. Archived versions of GWAS Catalog metadata are available | |
| Interoperable | I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation | Metadata are accessible from the GWAS Catalog REST API (https://www.ebi.ac.uk/gwas/docs/api) using JSON formats |
| I2: (Meta)data use vocabularies that follow the FAIR principles | Traits are represented using Experimental Factor Ontology22 terms, ancestry information is represented using the GWAS Catalog’s standardized ancestry framework,23 and all variants (dbSNP accession ID), genes (HGNC symbols), and chromosome locations (Genome Reference Consortium genome assembly GRCh38) use accepted standards, vocabularies, and naming conventions | |
| I3. (meta)data include qualified references to other (meta)data | Links are provided to relevant external data, e.g., Europe PMC, and to relevant GWAS Catalog data, e.g., the trait and publication pages | |
| Reusable | R1. (meta)data are richly described with a plurality of accurate and relevant attributes | Each GWAS is described by the metadata elements listed in “Proposed metadata standard reporting elements”a |
| R1.1. (meta)data are released with a clear and accessible data usage license | All GWAS Catalog data are made available through EMBL-EBI’s standard terms of use (https://www.ebi.ac.uk/about/terms-of-use/), and submitted summary statistics are additionally made available under the terms of CC0 (https://creativecommons.org/publicdomain/zero/1.0/) | |
| R1.2. (meta)data are associated with detailed provenance | Each GWAS is linked to a source publication that can be accessed by either a digital object identifier (DOI) or ID (PMID) | |
| R1.3. (meta)data meet domain relevant community standards | Metadata and SumStats are made available using the standards agreed to in this workshopa |
Our recommended FAIR indicators for GWAS SumStats. We list each core FAIR principle and the associated indicators and provide examples of how they are implemented in the GWAS Catalog.
a
This indicator is not currently met in full by the GWAS Catalog. The data standards agreed to in this workshop require extensions or modifications to GWAS Catalog data content or formats, which we plan to implement soon.