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Recommendations from the AIRR Common Repository Working Group

Authors: Sanchita Bhattacharya, Tania Bubela, Brian Corrie, David Klatzmann, Uri Laserson, Holly Longstaff, Tony Moody, Bjoern Peters, Adrian Thorogood, Yariv Wine, Corey Watson, Lindsay Cowell

v0.2.0 (draft) August 2016

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 discussion at the AIRR 2016 Community Meeting: Progress in Standards, Tools and a Common Repository for Adaptive Immune Receptor Repertoire Data held at the National Institutes of Health, Rockville, Maryland, USA from June 27-30, 2016.

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 facilitate data deposit and enable access and use, data should be made available under the least restrictive terms possible (see Recommendation 3). 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. 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).

Compliant AIRR Data Repositories

Recommendation 4: Raw-read sequence and quality-score data should be shared via deposition in the Sequence Read Archive (SRA) - http://www.ncbi.nlm.nih.gov/sra. The AIRR Working Groups should work with the SRA to customize metadata capture for AIRR data.

Recommendation 5: Dedicated AIRR repositories should be established for hosting processed repertoire-sequencing data and annotations. These repositories should link to the raw data in SRA (see Recommendation 4).

Recommendation 6: Compliant AIRR data repositories should state policies and practices that comply with Recommendations 1-3. 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.

Recommendation 7: 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 8: A compliant repository should adhere with the Digital Object Compliance Principles, under development as part of the NIH Data Commons Initiative (https://datascience.nih.gov/commons/ ). The principles are designed to ensure that digital objects are Findable, Accessible, Interoperable, and Reproducible (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 9: 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 10: 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 (http://science.sciencemag.org/content/350/6266/1312.full).

Recommendation 11: 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 12: 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 the raw data in the SRA and to the processed data and annotations in a compliant AIRR data repository.

Recommendation 13: AIRR sequencing studies should be registered in ImmPort. Links should be maintained to the raw data in the SRA and the processed data and annotations in a compliant AIRR data repository. 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 finalize these recommendations and the recommendations from the other Working Groups so that all recommendations may be approved by the AIRR community, through a new association or a poll of attendees of community meetings. Specifically, collaborative efforts with other Working Groups should focus on:

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

Next Step 2: The AIRR Community/Association 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/Association will need to seek funding to develop and maintain a central registry of compliant repositories.

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

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

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