1 DATA MANAGEMENT PLAN

**Project** 1  **Number:** 817998

**Project Acronym:** GENE-SWitCH

**Project title:** The regulatory GENomE of SWine and CHicken: functional
annotation during development

**Author** : Peter Harrison EMBL-EBI **Version** : 1.1

**Disclaimer**

The information in this document is provided as is and no guarantee or
warranty is given that the information is fit for any particular purpose. The
user thereof uses the information at its sole risk and liability.

**History of changes**  
  
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**VERSION**

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**PUBLICATION DATE**

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**CHANGES**

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**1.0**

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06.12.2019

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Initial version from WP3

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**1.1**

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23.12.2019

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Minor revisions from consortium comments

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#  1\. Data Summary

The GENE-SWitCH project aims to deliver to the livestock community two
functionally mapped monogastric genomes, for chicken and pig. These functional
maps and associated data collections will enable immediate translation into
the pig and poultry sectors for developments in sustainable production. For
example, within the project the datasets will be employed to evaluate the
effect of maternal diet on the epigenome of pig foetuses. A key aspect of the
generated datasets will be the extensive associated rich and controlled
metadata, information that is key for the development of phenome to genome
resources. The project will utilise existing pig and chicken datasets from the
FAANG collection and wider community from the public archives as test datasets
for the development of its openly developed bioinformatic pipelines and to
enrich its new functional maps; it will also use the existing reference
genomes from the community as a starting point for its own improved mapped
genomes. The tissue samples for sequencing are being collected for pig from
the INRA experimental unit GenESI in Lusignan, France and chicken samples from
the UK National Avian Research Facility (www.narf.ac.uk). In total the project
will generate data from 14 different assays, including both the core FAANG
assays and additionally DNA methylation, Hi-C and Whole Genome Sequencing
(Table 1). The Data Management Plan will be periodically updated throughout
the project to reflect changes in the data produced by the project and any
changes in storage and release. A future update will include the sizes of the
datasets produced by the project.

Table 1. The number of GENE-SWitCH assays and samples across developmental
stages.

All processed data generated in the project will be shared using standard
bioinformatic data file formats (i.e. FASTQ, FASTA, SAM/BAM, GFF/GTF, BED, and
VCF). The project will make extensive use of open access existing legacy
datasets and of additional datasets generated during the lifetime of the
project identified and accessed from EMBL-EBI public archives. Overall the
project contributes to the global FAANG coordinated effort with i) the
deliverance of high quality functional genome maps for the pig and the
chicken, ii) demonstrable impact of these new data resources on developments
in the breeding industry, and iii) the production of cutting edge
bioinformatic pipelines and experimental techniques that will be of wide
benefit to the scientific research community and breeding industries.

#  2\. FAIR data

##  2\. 1. Making data findable, including provisions for metadata

The proposed data deposition of GENE-SWitCH data through FAANG to the EMBL-EBI
public archives will ensure the generated data is highly discoverable. GENE-
SWitCH utilises the FAANG metadata standards  (
_https://data.faang.org/ruleset/samples#standard_ )  . All data submissions
will be validated through the FAANG validation and submission tools, that are
in fact being updated as part of the GENE-

SWitCH project and are accessible at (
_https://data.faang.org/validation/samples_

). The deposition in the public archives gives every data file a unique
accession. These accessions are globally recognised by the comparable archives
at the National Center for Biotechnology Information

(NCBI;  _https://www.ncbi.nlm.nih.gov/_ )  and DNA Databank of Japan (DDBJ;
_https://www.ddbj.nig.ac.jp/index-e.html)/_ )  . Different assay files are
linked through the inclusion of the BioSamples identifier in all data
submissions so that all of the datasets generated on each sample can be easily
grouped and accessed from downstream presentation resources. GENE-SWitCH will
conform with the FAANG record naming conventions. The FAANG data portal
utilises ElasticSearch to ensure that all ontology validated metadata fields
are keyword searchable using its predictive simultaneous search across
samples, reads and analyses (  _https://data.faang.org/search_ )  . It will be
possible to search for GENE-SWitCH data as part of an all search or pre-limit
the search specifically to only return GENESWitCH project data results. The
data portal utilises the rich ontology supported metadata to provide filters
that allow a user to explore the GENE-SWitCH data based on species,
technology, breeds, sex, material, organism part, cell type, assay type,
archive, and sequencing instrument. All software will be appropriately
versioned using an agreed versioning structure from its coding standards
document of work package 2\.

###  2.2. Making data openly accessible

All samples and `omics data will be deposited in the EMBL-EBI public archives
that includes BioSamples, the European Nucleotide Archive, the European
Variation Archive, PRIDE and BioImage archive. These are widely recognised and
approved repositories for the long-term storage of biological data and the
deposition routes are established with the FAANG Data Coordination Centre
(DCC), that itself is based within the Molecular Archives cluster at EMBL-EBI.
Apart from the reserved right of first publication stipulation set out in the
FAANG Data Sharing statement (  _https://www.faang.org/data-shareprinciple_ )
, there are no restrictions on use of the data, no data access committee is
required and apart from anonymous usage analytics no tracking of individual
data use will be made. The following data sharing statement is available both
via the websites and Application Programmatic Interfaces (machine readable) of
the public archives and FAANG data portal.

_**"** This study is part of the FAANG project, promoting rapid prepublication
of data to support the research community. These data are released under Fort
Lauderdale principles, as confirmed in the Toronto Statement (Toronto
International Data Release Workshop. Birney et al. 2009. Pre-publication data
sharing. Nature 461:168-170). Any use of this dataset must abide by the FAANG
data sharing principles. Data producers reserve the right to make the first
publication of a global analysis of this data. If you are unsure if you are
allowed to publish on this dataset, please contact the FAANG Consortium
(faang@iastate.edu) to enquire. The full guidelines can be found at _ _
_http://www.faang.org/data-share-principle_ .  **"** _

The EMBL-EBI public archives are fully aware and accepting of incoming FAANG
data including the data of the GENE-SWitCH project. Whilst the FAANG metadata
is fully machine readable and the license is available to both web and
programmatic users, further improvements will be investigated to further
improve the machine readability, in collaboration with the requirements of the
other H2020 SFS30 projects. The FAANG DCC will investigate specific license
API endpoints, html embedding of license links and license structure
formatting to improve machine-based access, a key component of FAIR
compliance.

The submission model for GENE-SWitCH will make the data available for direct
download from both the FAANG data portal that utilises the underlying public
archives infrastructure and from the public archives themselves. This provides
by default a range of data access methods including web browser download, FTP,
Aspera, Globus and API access to give flexibility to data consumers. All of
these download options are open source and the archives have extensive
documentation on the various data access options. The FAANG data portal
collates the files from the various underlying archives to a single access
point. The FAANG API provides programmatic users with the access FTP addresses
to make a secondary call to download the data files themselves.

All GENE-SWitCH software will be publicly developed on the FAANG GitHub
repository, so that the development process is open to community input and
available pre-publication. All of the GENESWitCH repositories will be given
the prefix ‘proj-gs-‘ within the FAANG GitHub repository  (
_https://github.com/FAANG_ )  . GENE-SWitCH will ensure that in the FAANG data
portal the bioinformatic pipeline that was used to generate the analysis file
is linked from the analysis file results page. This ensures that the analysis
file, the raw data that generated it, the protocols and the bioinformatic
pipelines are all downloadable from the same location. The software will
include complete documentation, nextflow workflow management and be
containerised in Docker. No specific tools are required to access the data
from the data portals or the FAANG data portal, as they will use standard
accepted file formats of the public archives. The FAANG data portal will
provide a GENE-SWitCH project slice that will allow the data portal and
programmatic access interface to provide a bulk download of all GENE-SWitCH
data at once, this will be available at  _http://data.faang.org/projects/gene-
switch_ .

###  2.3. Making data interoperable

GENE-SWitCH data will be submitted through the FAANG DCC that will ensure the
data is interoperable with other FAANG datasets and highly reusable by the
wider livestock community. To ensure interoperability with all other FAANG
datasets, including the other three H2020 SFS30 projects, GENESWitCH will
employ the latest version of the FAANG metadata standards (and utilise all
future updates

to these standards), currently version 3.8 (
_https://github.com/FAANG/dccmetadata/tree/master/rulesets_ )  , and in a more
readable form at  _https://data.faang.org/ruleset/samples#standard_ .  It will
ensure its compliance with these standards by running all data through the
FAANG validation software prior to submission to the public archives. GENE-
SWitCH will develop coding standards to ensure that all pipelines developed by
the consortium are easily utilised, they will be containerised to ease
installation and reuse. For its pipelines it will utilise open software
applications, that will be implemented with a nextflow workflow manager and
containerised using Docker to ensure consistent reuse across the project and
by downstream users.

To ensure interdisciplinary interoperability GENE-SWitCH will utilise the
recommended ontologies of the FAANG metadata standards as set by the FAANG
Metadata and Data Sharing Committee. A specific action of the project will be
through the coordination of the FAANG DCC to improve the coverage and quality
of ontologies for use in livestock metadata recording, and the consortium will
publish a manuscript on the state of the art and usage of ontologies. Wherever
an ontology is not possible we will employ controlled lists to prevent
erroneous metadata recording. The ontologies that will be utilised in the
project will be:

OBI https://www.ebi.ac.uk/ols/ontologies/obi

NCBI Taxonomy https://www.ebi.ac.uk/ols/ontologies/ncbitaxon

EFO https://www.ebi.ac.uk/ols/ontologies/efo

LBO https://www.ebi.ac.uk/ols/ontologies/lbo

PATO https://www.ebi.ac.uk/ols/ontologies/pato

VT https://www.ebi.ac.uk/ols/ontologies/vt  
  
<table>  
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ATOL

</th>  
<th>

https://www.ebi.ac.uk/ols/ontologies/atol

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EOL

</td>  
<td>

https://www.ebi.ac.uk/ols/ontologies/eol

</td> </tr>  
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<td>

UBERON

</td>  
<td>

https://www.ebi.ac.uk/ols/ontologies/uberon

</td> </tr>  
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CL

</td>  
<td>

https://www.ebi.ac.uk/ols/ontologies/cl

</td> </tr>  
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<td>

BTO

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<td>

https://www.ebi.ac.uk/ols/ontologies/bto

</td> </tr>  
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<td>

CLO

</td>  
<td>

https://www.ebi.ac.uk/ols/ontologies/clo

</td> </tr>  
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<td>

SO

</td>  
<td>

_https://www.ebi.ac.uk/ols/ontologies/so_

</td> </tr>  
<tr>  
<td>

GO

</td>  
<td>

_https://www.ebi.ac.uk/ols/ontologies/go_

</td> </tr>  
<tr>  
<td>

NCIT

</td>  
<td>

https://www.ebi.ac.uk/ols/ontologies/ncit

</td> </tr>  
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<td>

CHEBI

</td>  
<td>

https://www.ebi.ac.uk/ols/ontologies/chebi

</td> </tr> </table>

###  2.4. Increase data re-use (through clarifying licences)

GENE-SWitCH data will be publicly released in the EMBL-EBI archives at the
earliest opportunity and pre-publication. This will be submitted to the
archives without embargo so that it is immediately released to the public.
This is in accordance with the FAANG data sharing principles

( _https://www.faang.org/data-share-principle_ )  , that is based upon the
principles of the Toronto

( _https://www.nature.com/articles/461168a_ )  and Fort Lauderdale

( _https://www.genome.gov/Pages/Research/WellcomeReport0303.pdf_ )
agreements. This reserves the right for GENE-SWitCH to make the first
publication with the data, whether a dataset has an associated publication is
tracked clearly in the FAANG data portal (  _https://data.faang.org/home_ )  .
All datasets will be clearly labelled with these data sharing principles, with
the following statement:

_**"** This study is part of the FAANG project, promoting rapid prepublication
of data to support the research community. These data are released under Fort
Lauderdale principles, as confirmed in the Toronto Statement (Toronto
International Data Release Workshop. Birney et al. 2009. Pre-publication data
sharing. Nature 461:168-170). Any use of this dataset must abide by the FAANG
data sharing principles. Data producers reserve the right to make the first
publication of a global analysis of this data. If you are unsure if you are
allowed to publish on this dataset, please contact the FAANG Consortium
(faang@iastate.edu) to enquire. The full guidelines can be found at _ _
_http://www.faang.org/data-share-principle_ .  **"** _

This enables the wider community to immediately make use of the data that
GENE-SWitCH produces to provide maximal value to researchers. All software
developed by the consortium will be openly licensed for reuse, an example of
this is in the GENE-SWitCH RNA-Seq pipeline  ( _https://github.com/FAANG/proj-
gs-rna-seq/blob/master/LICENSE_ )  . In accordance with GENE-SWitCH coding
standards, this license file will be displayed in the root folder of all
repositories.

Data quality assurance processes and metrics will be investigated and
implemented by work package 2 as part of the pipeline development process.

It is intended that through the accurate recording of metadata, associated
protocols and analysis software, and deposition in public archives that the
data will remain available for long after the project grant ends, for the
lifetime of the underlying public archives. The data will therefore be
reusable by any party, at some point the datasets may be superseded by those
produced on newer technologies. There will be no restriction on third party
use of the data. The data generation work packages will apply the latest
recommended community standards for data quality, comply with any standards
set by FAANG working groups or the public archives, and for the generation and
execution of bioinformatics analysis will utilise the latest open source,
published and recognised analysis software for the construction of its
pipelines.

#  3\. Allocation of resources

GENE-SWitCH directly funds the activity of the FAANG Data Coordination centre
(DCC) to conduct data management and coordination for the project. The
proposal has specific tasks and deliverables that will ensure the data
generated in the project will conform to FAIR data principles. This in
particular enhances the existing FAANG metadata standards, archival support
tools, data portal discovery and data visualisations to improve findability,
accessibility, interoperability and reusability of GENE-SWitCH data. These
enhancements will also benefit the entire FAANG community as improvements will
apply to all FAANG data. Thus the costs associated with ensuring GENE-SWitCH
data is FAIR have been fully factored into the costs provided to EMBL-EBI in
work package 3. All work packages that generate and analyse data have
appropriate funding for the accurate recording and provision of metadata,
through the validation and submissions software provided by the DCC. Data
management is the responsibility of the FAANG Data Coordination Centre at
EMBL-EBI that is operated by Peter Harrison and Guy Cochrane.

GENE-SWitCH will use the EMBL-EBI public archives for the long-term
preservation of its generated data, these resources have separate long term
funding that will persist the data long after the grant ends. The inclusion of
the data within the FAANG consortium data portal

( _https://data.faang.org/home_ )  and Ensembl browser (
_https://www.ensembl.org/index.html_ )  also ensures the functional annotation
of genomes will remain accessible by the community in the long term, as these
are likely to continue to receive separate funding.

#  4\. Data security

GENE-SWitCH will at the earliest opportunity submit all data to the public
archives at EMBL-EBI. Intermediate results and ongoing analyses will be
conducted and stored on the EMBL-EBI embassy cloud platform that is located in
the same data centre as the public archives. Access to the GENESWitCH embassy
cloud analysis platform is controlled by user specific ssh keys only issued to
consortium members. As soon as an analysis is finished it will be submitted to
the relevant EMBL-EBI archive for immediate public release without embargo.

The EMBL-EBI archives are internationally recognised repositories for the
long-term secure storage of scientific data. The EMBL-EBI archives are
recognised Core Elixir data resources (
_https://elixireurope.org/platforms/data/core-data-resources_ )  . All data
will be assigned a unique identifier for long term identification and
preservation of the datasets. The EMBL-EBI data centres that host the public
archives providing the long-term data storage, and the embassy cloud platform
for the analysis and intermediate processing of GENE-SWitCH data are state of
the art. EMBL-EBI uses three discrete Tier III plus data centres in different
geographical locations to ensure long-term security. Research data is also
replicated through the International Nucleotide Sequence Database
Collaboration (INSDC;  _http://www.insdc.org/_ )  agreements that sees the
data replicated at the National Center for Biotechnology Information (NCBI;
_https://www.ncbi.nlm.nih.gov/_ )  and DNA Databank of Japan (DDBJ;
_https://www.ddbj.nig.ac.jp/index-e.html_ )  that agree to recognise each
other centres accessioned datasets.

EMBL-EBI commits to store the data for the lifetime that the archives remain
active, this will be far beyond when the GENE-SWitCH grant ends, ensuring this
data remains available to the scientific community for years to come.

#  5\. Ethical aspects

The proposed GENE-SWitCH data management plan complies fully with all
international, EU and national legal and ethical requirements. GENE-SWitCH
data sharing and long-term preservation is not subject to informed consent.
GENE-SWitCH will fully comply with General Data Protection Regulations for its
activities and web services.

#  6\. Other issues

As well as complying with H2020 procedures for data management, the GENE-
SWitCH project will abide by the data sharing policy of the Functional
Annotation of Animal Genomes (FAANG) coordinated action (
_https://www.faang.org/data-share-principle_ )  . This statement outlines the
expectations of all FAANG projects that contribute to the coordinated action
in terms of data recording, archiving and sharing. The statement includes the
principles of the Toronto  ( _https://www.nature.com/articles/461168a_ )  and
Fort Lauderdale

( _https://www.genome.gov/Pages/Research/WellcomeReport0303.pdf_ )
agreements. The requirements set out in the FAANG data sharing principles do
not conflict with those imposed by the EU H2020 data management principles.

5.2 FAANG Data Sharing Statement

This document describes the principles of data sharing held by the FAANG
consortium. This document is subject to approval by the FAANG steering
committee. Any queries about this

document should be sent to _faang@iastate.edu_ .  
  
<table>  
<tr>  
<th>

**Definitions**

**Archive** means one of the archives hosted at the EBI, NCBI or DDBJ. These
include the ENA, Genbank, ArrayExpress and Geo. A full list of the FAANG
recommended archives is available as part of the FAANG metadata
recommendations.

**Submission** means data and metadata submission to one of the FAANG
recommended Archives.

**FAANG member** means an individual who has signed up to the FAANG consortium
through the FAANG website and agreed to the FAANG core principles.

**Data** means any assay or metadata generated for or associated with FAANG
experiments.

**Analysis** means any computational process where raw assay data is aligned,
transformed or combined to produce a new product.

**Internal** means data that is only accessible via the FAANG private shared
storage.

**Private** shared storage means a storage space hosted at EMBL-EBI that has
password access via FTP, aspera and Globus Grid FTP technologies.

**Public** means all data available through the FAANG public FTP site, which
has no password and is accessible to everyone.

</th> </tr> </table>

FAANG recognizes that quickly sharing the data generated by the consortium
with the wider community is a priority. Rapid data sharing before publication
ensures that everyone can benefit from the data created by FAANG and can take
advantage of improved understanding of the functional elements in these animal
genomes to aid their own research.

All raw data produced for a FAANG associated project will be submitted to the
archives without any hold until publication date, thus allowing the data to be
publicly available immediately after successful archive submission and useful
to the community as soon as possible.

The FAANG analysis group will turn the raw data into primary and integrated
analysis results. Primary analysis results consistent of sample level analysis
such as alignment to a reference genome or quantification of signal in the
assay. Integrated analysis results represent analyses which drawn together
data from multiple samples and/or experiments such as genome segmentation or
differential analysis results.

The majority of these analysis results

will not be archived before publication but FAANG recognizes the need to share
them both within the consortium and with the community. Initially all files
that are not archived will be shared between FAANG members in private shared
storage hosted at the EMBL-EBI. Any individual who signs up to FAANG and
agrees to  **_the Toronto principles_ ** 1  will be allowed access to this.
There will be metadata files in the private data sharing area, which make
credit for different datasets as clear as possible.

FAANG expects to make multiple releases each year. A data release will involve
declaring a data freeze and copying all files associated with that data freeze
from the private shared storage to the public FTP site. In the first instance
these data freezes will contain the primary analysis results. As FAANG's
analyses progress, the data freeze will be expanded to include integrative
analysis too. The data freeze process will be coordinated by the FAANG Data
Coordination Centre and will be based on consultation with FAANG members.
FAANG will also aim to release all data associated with a paper before
publication even if it lies outside this standard freeze cycle. The public
data will be available to the whole community.

All FAANG public data is released under  **_Fort Lauderdale principles_ ** 2
. The FAANG website, data portal and FTP site will all have clear data reuse
statements on them.

When considering internal FAANG data, if one FAANG member wishes to publish
using data generated by another FAANG member they should first contact the
data generator and clarify the member's publication strategy. Collaboration is
for everyone's benefit and is strongly encouraged. The FAANG Steering
Committee commits to report to journal editors and the laboratories involved
any event that disregards the rights of data creators (including biological
measurements as well as analysis of such measurements).

All members of FAANG can and will continue to do experimental and analysis
work outside of FAANG and the other data generated is not required to meet the
same data sharing expectations.

Only FAANG data can be distributed through the private storage and public FTP
site.