SARS-CoV-2 Contextual Data Specification - Collection template and associated materials for SARS-CoV-2 metadata
The Public Health Alliance for Genomic Epidemiology (PHA4GE) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatic tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics.
In the face of the current SARS-CoV-2 pandemic, PHA4GE has identified a clear and present need for a fit-for-purpose, open source SARS-CoV-2 contextual data standard. As such, we have developed a SARS-CoV-2 contextual data specification based on harmonizable, publicly available, community standards.
Public health genomics contextual data includes sample metadata, lab/clinical/epidemiological data, and analysis methods information. Contextual data enables the interpretation of the sequence data, informs decision making for public health responses, and facilitates scientific understanding of infectious disease. Structured and consistent contextual data can also be more easily processed, aggregated, and reused by both humans and computers for different types of analyses.
The SARS-CoV-2 contextual data specification includes a metadata collection template, reference guides, controlled vocabulary, and mapping to existing standards. We also provide a suite of protocols for submitting sequence data and contextual data to public repositories, enabling global interoperability of the data. The specification and all of the supporting materials are freely available and detailed below.
It contains the following items (tabs in the spreadsheet):
- a template for populating the complete set of contextual data;
The collection template contains "required" (colour-coded yellow), "strongly recommended" (colour-coded purple) and "optional" (colour-coded white) fields.
- guidance for populating the template;
The reference guide aims to facilitate the use of the collection template. It contains field definitions, further guidance/instructions, and examples of structured data.
- ontology-mapped controlled vocabulary for the picklists.
Lists of controlled vocabulary, agreed upon by PHA4GE, are provided here for populating the template.
Due to JSON format limitation, it deviates slightly from the collection template where the "required" (colour-coded yellow) fields are set as required and both the "strongly recommended" (colour-coded purple) and "optional" (colour-coded white) fields are both set as optional.
A Standard Operating Procedure (SOP) containing instructions for using the collection template. This SOP provides users with step-by-step instructions for populating the template, looking up standardized terms, and how best to structure sample descriptions. Also included are a number of ethical, practical, and privacy considerations for data sharing. The SOP is available in protocols.io under the DOI dx.doi.org/10.17504/protocols.io.btpznmp6.
WHO recommended contextual data mapping to PHA4GE fields
PHA4GE fields are mapped to corresponding contextual data elements recommended by the World Health Organization (World Health Organization. Guidance for surveillance of SARS-CoV-2 variants: interim guidance. WHO/2019-nCoV/surveillance/variants2021.1).
PHA4GE to sequence repository field mappings
A mapping file indicating which PHA4GE fields correspond to which fields within the different repository submission forms is provided to facilitate data transformations for submissions. Field mappings to the following repositories are available in the document:
- GISAID
- ENA
- NCBI
Submission protocols are available for the following data repositories:
The entire collection of submission protocols is available as a workflow at protocols.io under the DOI dx.doi.org/10.17504/protocols.io.bsypnfvn. This workflow includes the following individual protocols:
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PHA4GE contextual metadata SOP This SOP provides users with step-by-step instructions for populating the collection template. The SOP is available in protocols.io under the DOI dx.doi.org/10.17504/protocols.io.btpznmp6
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Overview of NCBI's submission process and the metadata required Provides an overview of the submission process and includes a brief training video. The protocol is available at protocols.io under the DOI dx.doi.org/10.17504/protocols.io.bsbpnamn.
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SARS-CoV-2 NCBI submission protocol: SRA, BioSample, and BioProject Step-by-step instructions for establishing a new NCBI laboratory submission account, creating and linking a new BioProject to an existing umbrella effort, and submitting raw sequence data with assocated metadata to SRA and BioSample. The protocol is available at protocols.io under the DOI dx.doi.org/10.17504/protocols.io.bsypnfvn.
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SARS-CoV-2 NCBI consensus submission protocol: GenBank Step-by-step instructions for submitting SARS-CoV-2 consensus sequencing to NCBI GenBank and linking to existing BioProject, BioSamples, and raw data. The protocol is available at protocols.io under the DOI dx.doi.org/10.17504/protocols.io.bid7ka9n.
The entire collection os submission protocols is available as a workflow at protocols.io under the DOI dx.doi.org/10.17504/protocols.io.buqnnvve.
Three separate protocols are included:
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SOP for populating EBI submission templates The protocol is available at protocols.io under the DOI dx.doi.org/10.17504/protocols.io.bh5dj826.
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SARS-CoV-2 EBI submission protocol: ENA, BioSample, and BioProject The protocol is available at protocols.io under the DOI dx.doi.org/10.17504/protocols.io.bhwdj7a6.
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SARS-CoV2 EBI assembly submission protocol The protocol is available at protocols.io under the DOI dx.doi.org/10.17504/protocols.io.bhwqj7dw.
This protocol provides the steps needed to establish a new GISAID submission environment for your laboratory. Once established, this protocol covers genome submission sample metadata to GISAID. The protocol is available in protocols.io under the DOI dx.doi.org/10.17504/protocols.io.bumknu4w.
The JSON is produced automatically from the csv version of the template using the the script available from SARS-CoV-2-Data-Spec-JSON repository.
Table 1 Terms for SARS-CoV-2 submission template according to the PHA4GE contextual data collection specification in PHA4GE SARS-CoV-2 Standardised Terms
| Column | Description |
|---|---|
| Interface Label | Column headers in the submission template |
| Required/Optional | Type of requirement according to PHA4GE's template specification. Limited to the values "Optional", "Recommended" and "Required". |
| Definition | Short description for the expected interface label value. |
| Ontology | Ontology ID for the label |
| Value Type | Expected interface label's value type. Expected values: "String", "Int", "Float", "Bioproject_ID", "Biosample_ID", "SRA_ID", "Genbank_ID", "GISAID_ID", "Email", "Date" and "Integer_or_Range". |
| Example | Example for the expected interface label value. |
| Guidance | Detailed description for the expected interface label value. |
For more information and/or assistance, contact datastructures@pha4ge.org or the issue page of this repository.
Emma J Griffiths, Ruth E Timme, Catarina Inês Mendes, Andrew J Page, Nabil-Fareed Alikhan, Dan Fornika, Finlay Maguire, Josefina Campos, Daniel Park, Idowu B Olawoye, Paul E Oluniyi, Dominique Anderson, Alan Christoffels, Anders Gonçalves da Silva, Rhiannon Cameron, Damion Dooley, Lee S Katz, Allison Black, Ilene Karsch-Mizrachi, Tanya Barrett, Anjanette Johnston, Thomas R Connor, Samuel M Nicholls, Adam A Witney, Gregory H Tyson, Simon H Tausch, Amogelang R Raphenya, Brian Alcock, David M Aanensen, Emma Hodcroft, William W L Hsiao, Ana Tereza R Vasconcelos, Duncan R MacCannell, on behalf of the Public Health Alliance for Genomic Epidemiology (PHA4GE) consortium, Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package, GigaScience, Volume 11, 2022, giac003, https://doi.org/10.1093/gigascience/giac003