Final Micro B3 / OSD Data Policy

Final Micro B3 / OSD Data Policy

Authored by the OSD Data Policy Working Group with the OSD Consortium

OSD Data Policy Working Group

Dawn Field, Oxford University, OSD, WP2 Leader

Mesude Bicak, Oxford University, OSD Co-ordinator/Bioinformatician

Anna Klindworth, MPI Bremen, OSD Co-ordinator

Frank Oliver Glöckner, Jacobs University Bremen & MPI Bremen, Micro B3 Coordinator

Arianna Broggiato, BIOGOV, ABS (WP8)

Arul Scaria, BIOGOV, Data Policy (WP8)

Tom Dedeurwaerdere Univ Louvain WP8 Leader

Alban Ramette, AWI, Biostatistics (WP5 & WP6)

Linda-Amaral Zettler, Woods Hole, MicroB3 Scientific Advisory Role (ICOMM MIRADA LTER)

Petra ten Hoopen, EBI, Metadata & Standards (WP2 & WP4)

Michelle Barbier, CIESM, Med Co-ordinator (WP2, 4, 8 & 9)

Neil Davies, UC Berkeley, GOs Network, WAML, Pacific Region

Jack Gilbert, Argonne National Labs, EMP

Katie Barker, Smithsonian Institution, GGI Bio-Archiving

Status to date

This data policy covers the collection, dissemination, analysis and publication of OSD data.  It was developed over the past years of OSD pilot events. Within Micro B3, WP8 is responsible for the Micro B3 data policy.  The OSD policy is based on this policy and consultation with the OSD Consortium.  It was finalized at the Micro B3 General Assembly (GA) April 2014. It remains the responsibility of the OSD Data Policy working group to make sure the policy is fit for purpose and all are aware of it when submitting and using data of the OSD Consortium.  If you would like to join the group please contact osd-contact@microb3.eu.We welcome input from all OSD participants on shaping of the OSD data policy. Please send comments to osd-contact@microb3.eu.

Background

The OSD Data Policy was created by drawing on existing policies (See Biosharing: http://biosharing.org/policies) and current best practice in genomics and the needs of Micro B3 and the OSD community.  It was developed and will be maintained according to the “12 steps to a data policy” outlined in Field et al (2009) Science:

12 Step Path to a Data Policy:

http://blog.biosharing.org/2010/02/12-steps-to-creating-data-sharing.html

Tenets of Ocean Sampling Day (The policy applies to all in the OSD Consortium. It is a mandatory part of taking part in OSD)

The OSD data set is generated by the members of the OSD Consortium - to be part of the Consortium you must be formally registered and substantively contribute to the collaboration.

The OSD dataset will be a reference data set and should be as widely accessible and used to support downstream research as possible.

As OSD is one event (a one-off event) it should be easier to get all contributors (their official sites) to release the data publicly.

All OSD data must be standards compliant - must include metadata - this includes compliance with the Micro B3 standard, which includes the GSC’s MIxS standard.

All OSD genomic data must be tightly linked to environmental data - contextual information is a top priority.

Sequence data without deposition of accompanying metadata (minimum of lat, long, time, depth, temp, salinity according to OSD Handbook) will not be released after the June solstice 2014 event.  The OSD Consortium will work towards release of all data.

The OSD data policy covers the pilot events, the main OSD event and any subsequent events.

Data must be submitted to the public repositories (e.g. INSDC).  Micro B3 will make sure 2012-2015 data sets are submitted to the ENA/MG-Portal.

All data will be processed/stored in the Micro B3 infrastructure as it is built and the full data set will eventually be available through this infrastructure. Data can flow in many analysis pipelines/databases - we welcome its wider use

All samples must be collected legally (with appropriate permits) and individual collectors are responsible for making sure of this.  Specifically ABS/MTA/DTA agreements will be in place as required (bioarchiving at GGI requires OSD MTA, proof of relevant ABS and metadata)

The OSD Consortium

This data policy applies to everyone in the OSD Consortium (to date this means everyone who has constructively contributed to OSD sampling events).

Release of the data and metadata

At the 2013 EEB meeting of the Micro B3 project we agree on the importance of the OSD data set as a whole (the sum of participating sites) and the desire to support open sharing of the data.  The EEB agreed to work towards: ”immediate release of all OSD data as soon as sequenced and quality checked to the public”.  In this, sense “public” means beyond Micro B3 and OSD participants to the public at large.  To protect the rights of the consortium to publish the first global analysis of the data, the data will be released under Ft Lauderdale principles.  This is routinely used in large sequencing projects and promotes the use of the data by the wider community while safeguarding the scientific contributions of the data generators.  For example, a complete Neanderthal genome was released to the public prior to publication in 2013 under these principle  (see: http://www.eva.mpg.de/neandertal/index.html).

This statement will accompany all access to OSD sequence data.

Use of the sequence data

All data will be made freely available. However, we ask users to observe the Ft. Lauderdale principles, which entitles the data producers to make the first presentation and publish the first genome-wide analysis of the data.  The data can be used freely for studies of individual genes or other individual features of these sequences.

Collaborative Data Analysis

We hope that the OSD reference data set will be helpful in a variety of ways and we encourage those interested in analysis of the data to declare their interests and formally join the OSD Data Analysis working group.  Together, we are working towards “OSD reports” that will be generated following each event.  Ideally, each report will provide a high level overview of the event and, if multiple events are available, comparison and contextualization with past data.  Predictions about future events may also be included.  It is our vision that this type of transparent collaboration where interested parties declare how they would like to contribute to the data analysis,  will help maximize the efforts of the community and build the strongest possible biological interpretation of the data.

Publication

We expect the authorship of the global analysis of the OSD data set to belong to the OSD Consortium.  Authorship will be defined on a case-by-case basis for more specialist publications.

Evolution of this Policy

According to the “12 steps for policy development” process, this policy may evolve according to best practice.  As agreed at the May 2013 EEB meeting of Micro B3, changes to the policy will be done in consultation with the community.  Specifically, policy issues will be taken forward through the OSD Data Policy Working group who is responsible for building consensus on any issues or changes. Final authority for any changes and for upholding the policy will rest with the leadership of Micro B3

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