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Recommendations from the AIRR Community Common Repository Working Group

Working Group membership can be found on the Common Repository Working Group AIRR Communinty page.

Revisions:

  • v0.4.0 (Ratified at AIRR Community Meeting, December 2017)
  • v0.5.0 (revisions to use the phrase "AIRR Data Commons", August 2018)
  • v0.6.0 (Ratified at AIRR Community Meeting, May 2019)
  • v0.7.0 (Ratified at AIRR Community Meeting, December 2020)
  • v0.8.0 (Ratified at AIRR Community Meeting, May 2022)
  • v0.9.0 (To be ratified at AIRR Community Meeting, May 2024)

Background

The use of high-throughput sequencing for profiling B-cell and T-cell receptors has resulted in a rapid increase in data generation. It is timely, therefore, for the Adaptive Immune Receptor Repertoire (AIRR) Community to establish a clear set of community-accepted data and metadata standards; analytical tools; and policies and practices for infrastructure to support data deposit, curation, storage, and use. Such actions are in accordance with the policies of international funding bodies and publishers, which promote data deposition and sharing. At a minimum, data on which scientific publications are based should be made available immediately on publication. Data deposit in publicly accessible repositories ensures that published results can be validated. Such deposition also facilitates reuse of data for the generation of new hypotheses and new knowledge.

The AIRR Community (AIRR-C) Common Repository Working Group (CRWG) developed a set of recommendations that promote the deposit, sharing, and use of AIRR sequence data. These recommendations were refined following community discussions at the AIRR 2016 and 2017 Community Meetings and were approved through a vote by the AIRR Community at the AIRR Community Meeting in December 2017. The current version here is being submitted for ratification at the June 2024 AIRR Meeting.

There are four sets of recommendations:

  1. General principles for sharing of data related to AIRR sequencing studies (hereinafter AIRR Data);
  2. Outline of the characteristics of compliant repositories for data deposit, storage, and access;
  3. Description of the AIRR Data Commons - a distributed model for compliant repositories for data linked by a central registry; and
  4. Specific recommendations to existing repositories of related data types.

The concluding section addresses next steps for the AIRR CRWG and the AIRR Community more broadly.

Section 1: Statement of Principles - AIRR Data Sharing

Recommendation 1.1: Facilitate deposit, access, and use of data

To enable and facilitate data deposit and broad access and use, data should be made available under the least restrictive terms possible. The default data sharing policy should be to deposit data in a publicly accessible repository with no restrictions over deposit, access, storage, curation, and use.

Recommendation 1.2: No intellectual property restrictions

For data deposited in publicly accessible repositories, depositors of data and repositories should have no right to interfere with access to and use of the data by others, including through the assertion of any intellectual property rights.

Recommendation 1.3: Legal exceptions

Exceptions to open data sharing (Recommendation 1.1) should only be considered in circumstances that require compliance with local legal norms (e.g., privacy/health information) or Institutional Review Boards (e.g., respect for participant consent).

Recommendation 1.4: Exceptions for commercially valuable data

AIRR Data may be commercially valuable. In exceptional circumstances, where there is an intent to commercialize AIRR sequence data and/or associated materials, data generators may be prevented from publicly sharing those sequences/materials of potential value. In these cases, data generators are nevertheless encouraged to share the data using individually/institutionally negotiated legal instruments.

Section 2: AIRR Data Repositories

Recommendation 2.1: Establishment of dedicated AIRR data repositories

Dedicated repositories should be established for hosting processed repertoire-sequencing (AIRR-seq) data and annotations to facilitate data queries and cross-study meta-analyses. Annotated AIRR-seq data and relevant repertoire metadata should be deposited in AIRR-compliant repositories following the MiAIRR data standard. These repositories should link to the raw data deposited in INSDC repositories (see Recommendation 2.2).

Recommendation 2.2: Long-term storage of data at INSDC

In addition, for long-term storage, data and metadata should also be deposited in repositories of the International Nucleotide Sequence Database Collaboration (INSDC), per the recommendations published by the AIRR Community Minimal Standards Working Group [DOI:10.1038/ni.3873]. The AIRR Community Working Groups should work with INSDC and its individual repositories to customize metadata capture for AIRR sequence data.

Recommendation 2.3: Compliance of AIRR data repositories

To be considered compliant, AIRR data repositories must implement and adhere to policies and practices that comply with Recommendations 1.1-1.4. In addition, repositories should require submitters, during the data submission process, to attest that they have sought appropriate informed consent or other authorization for sharing, where necessary. AIRR data repositories will not be required to host data that have access restrictions, but they may choose to do so on an individual basis.

Recommendation 2.4: Development of operational compliance criteria

The AIRR Community Working Groups should collaboratively develop operational criteria for compliant repositories. At the operational level, a compliant repository should use a standard, open source, data serialization framework for ensuring interoperability, performance, maintainability, and evolution. Operational Criteria should include implementation of:

  1. A standardized set of queries that make AIRR-seq data findable and accessible (AIRR Data Commons API);
  2. Standardized data elements with exact (computable) specifications that make AIRR-seq data interoperable and reusable (AIRR Data Representation);
  3. A standardized data submission process (including standardized data and metadata formats) (MiAIRR);
  4. A system for assigning unique identifiers that ensures coordination among repositories/registries, for example, the system used by the OBO Foundry to coordinate ontology term identifiers across orthogonal ontologies.

Recommendation 2.5: FAIR Digital Objects

A compliant repository should ensure that digital objects are Findable, Accessible, Interoperable, and Reusable (FAIR) [DOI:10.1038/sdata.2016.18], adhere to the FAIR principles, and follow best practices in providing FAIR Digital Objects.

Recommendation 2.6: Compliance with applicable legal norms for data access

A compliant repository should adhere to applicable legal norms that govern data access and use. Repositories that host data whose access and use are limited by local regulations (e.g., privacy/health/genetic information) or institutional review/research ethics boards (e.g., participant consent) should enable controlled access and use of such data to the maximum extent permissible. Repositories should enable the findability of such protected data via non-protected associated metadata. Note that the securing of these data should not impede access to all non-protected data and associated metadata.

Section 3: AIRR Data Commons - A System of Distributed Repositories Supported by a Centralized Registry

Recommendation 3.1: AIRR Data Commons

The dedicated AIRR repositories (Recommendation 2.1) should comprise a system of multiple, distributed repositories supported by a centralized registry consistent with an intermediate distributed model as described in [DOI:10.1126/science.aaa7485]. Dedicated AIRR repositories that are techically integrated into the distributed system will be jointly referred to as the AIRR Data Commons (ADC).

Recommendation 3.2: Maintain a central registry of AIRR Data Commons repositories

In order to enable the ability to find and access data in the ADC, the AIRR Community should strive to maintain a registriy AIRR compliant repositories. This registry should provide a discovery mechanism for ADC repositories.

Section 4: Specific Recommendations for Common Data Types and Existing Repositories of Related Data Types

Recommendation 4.1: AIRR data with known epitopes

AIRR sequences for which epitopes are known should be deposited in recognized international resources for such data, such as the Immune Epitope Database (IEDB). Links should be maintained to associated data and metadata in AIRR Data Commons repositories (Recommendation 2.1) as well as INSDC repositories (Recommendation 2.2).

Recommendation 4.2: Other related data

AIRR sequencing studies that include data beyond the scope of the ADC should link to external repositories as appropriate. Related data sets in repositories such as Immune Epitope Database (IEDB) or other similar resources should be referenced where possible. Links should be maintained to associated data and metadata in AIRR Data Commons repositories (Recommendation 2.1) as well as INSDC repositories (Recommendation 2.2).

Next Steps for CRWG, Other Working Groups, and the AIRR Community

Next Step: The AIRR Community will need to work with repositories to establish an accreditation system for compliance with AIRR-C standards.

Next Step: The AIRR Community will work on establishing an appropriate system for the citation/attribution of the repository and/or the data.

Next Step: The AIRR Community will need to seek funding to develop and maintain a central registry of AIRR Data Commons repositories.

Next Step: The AIRR Community will need to seek funding to develop and maintain the AIRR Data Commons.

Next Step: The AIRR Community will need to work with funders and publishers to establish mechanisms for compliance with these recommendations.

Next Step: The AIRR CRWG will continue to work collaboratively with the other Working Groups to maintain and extend:

  1. The AIRR Data Standards including their computable specifications; and
  2. A standardized data submission process and associated submission formats.