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Recommendations from the AIRR Common Repository Working Group

Working Group Members: Meredith Ashby, Felix Breden, Syed Ahmad Chan Bukhari, Tania Bubela, Scott Christley, Brian Corrie, David Klatzmann, Uri Laserson, Bjoern Peters, Adrian Thorogood, Yariv Wine

Working Group Co-Chairs: Lindsay Cowell, Corey Watson

v0.4.0 (draft) December 2017

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 international funder and journal policies that promote data deposition and data sharing – at a minimum, data on which scientific publications are based should be made available immediately on publication. Data deposit in publicly accessible databases ensures that published results may be validated. Such deposition also facilitates reuse of data for the generation of new hypotheses and new knowledge.

The AIRR 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 (http://airr.irmacs.sfu.ca/meetings).

The first three sets of recommendations: (1) state the general principles for sharing of AIRR sequence data [hereinafter data]; (2) outline the characteristics of compliant repositories for data deposit, storage and access; and (3) describe a distributed model for compliant repositories for AIRR data, linked by a central registry. The fourth set of recommendations are specific to existing repositories of related data types. The concluding section addresses next steps for the AIRR CRWG and the AIRR community more broadly.

Statement of Principles -- AIRR Data Sharing

Recommendation 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 public domain database with no restrictions over deposit, access, storage, curation, and use.

Recommendation 2: No intellectual property restrictions. For data deposited in public domain databases/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 3: Legal exceptions. Exceptions to open data sharing (Recommendation 1) should only be considered in rare circumstances that require compliance with local laws (e.g., privacy/health information) and Institutional Review Boards (e.g., respect for participant consent).

Recommendation 4: Commercially valuable AIRR sequence data. AIRR sequence 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.

Compliant AIRR Data Repositories

Recommendation 5: For long-term storage, data and metadata should be deposited in databases of the International Nucleotide Sequence Database Collaboration (INSDC), per the recommendations established by the AIRR Minimal Standards Working Group. The AIRR Working Groups should work with INSDC and its individual databases to customize metadata capture for AIRR data.

Recommendation 6: Dedicated AIRR repositories should be established for hosting processed repertoire-sequencing data and annotations to facilitate data queries and cross-study meta-analyses. These repositories should link to the raw data deposited in INSDC databases (see Recommendation 5).

Recommendation 7: Compliant AIRR data repositories should state policies and practices that comply with Recommendations 1-4. In addition, compliant 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 8: The AIRR 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 (e.g., Apache Avro, Thrift, and Protocol Buffers – the CRWG currently recommends Thrift). Operational Criteria should include implementation of:

  1. standardized data elements with exact (computable) specifications;
  2. a standardized data submission process (including standardized data and metadata formats);
  3. a standardized set of queries;
  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 9: A compliant repository should adhere to the Digital Object Compliance Principles, under development as part of the NIH DataCommons Initiative (PMC4792175). The principles are designed to ensure that digital objects are Findable, Accessible, Interoperable, and Reusable (FAIR). Currently, the most basic level of Digital Object Compliance expects digital objects to have:

  1. Unique digital object identifiers;
  2. A minimal set of searchable metadata;
  3. Physical availability through a cloud-based Commons provider;
  4. Clear access rules and controls; and
  5. An entry (with metadata) in one or more indices.

Recommendation 10: Hosting PII or PHI. For repositories that choose to host personally identifiable information (PII) or protected health information (PHI), the securing of these data should not impede access to the repertoire sequencing data and its associated, non-identifiable, non-protected metadata.

System of Distributed Repositories Supported by a Centralized Registry

Recommendation 11: The dedicated AIRR repositories (Recommendation 5) should comprise a system of multiple, distributed repositories supported by a centralized registry consistent with an intermediate distributed model as described in http://science.sciencemag.org/content/350/6266/1312.full.

Recommendation 12: Maintain a central registry of compliant repositories. The registry may implement an interface that supports cross-repository queries for a standard set of queries.

Specific Recommendations for Common Datatypes and Existing Repositories of Related Data Types

Recommendation 13: AIRR sequences for which epitopes are known should be deposited in the Immune Epitope Database (IEDB) - http://www.iedb.org/. Links should be maintained to associated data and metadata in INSDC databases (Recommendation 5) and a compliant AIRR data repository (Recommendation 6).

Recommendation 14: AIRR sequencing studies that fall within the scope of ImmPort should be registered there. Links should be maintained to associated data and metadata in INSDC databases (Recommendation 5) and a compliant AIRR data repository (Recommendation 6). Links within ImmPort should also be maintained to other data types generated within the same study.

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

Next Step 1: The AIRR CRWG should work collaboratively with the other Working Groups to advance development of:

  1. customized metadata for submission of AIRR sequencing data to INSDC databases,
  2. standardized queries to be supported by the distributed repositories,
  3. data elements with computable specifications,
  4. a standardized data submission process and associated submission formats, and
  5. more detailed specifications for recommended technologies for repository implementation.

Next Step 2: The AIRR Community will need to work with repositories to establish an accreditation system for compliant repositories. This should include an appropriate system for the citation/attribution of the repository and/or the data.

Next Step 3: The AIRR Community will need to seek funding to develop and maintain a central registry of compliant repositories.

Next Step 4: The AIRR Community will need to seek funding to develop and maintain dedicated repositories for AIRR data.

Next Step 5: The AIRR Community will need to work with funders and journals to establish mechanisms for compliance with these recommendations.

Next Step 6: The AIRR Community should work to develop consistent consent documents that are compliant with best practices for the broad sharing of AIRR data.