D4.1 Data Management Plan

#  DATA SUMMARY

DELTA-FLU participates by default in the H2020 Open access to research data
pilot, which aims to improve and maximize access to and re-use of research
data generated by H2020 funded projects. This initial Data Management Plan
(DMP) will detail the management of the research data generated and collected
during the project, in compliance with article 29.3 of the H2020 Grant
Agreement. The DMP will follow the principles of FAIR data management as set
out in the Guidelines on FAIR data management in H2020. This DMP will include
information on the handling of research data during and after the project,
what data will be collected, processed and/or generated, which methodology and
standards will be applied, whether data will be shared/made open access, and
how data will be curated and preserved. The initial DMP will be updated over
the course of DELTA-FLU, whenever significant changes arise, such as the
generation of new data, or changes in consortium composition. DELTA-FLU will
be advised by the data access committees available at partner institutes
and/or the ethical body overseeing consent-giving procedures, regarding the
appropriate management and use of the research data.

##  PURPOSE OF DATA COLLECTION/GENERATION AND RELATION TO THE OBJECTIVES OF
THE PROJECT

The primary aim of data collection and generation within DELTA-FLU is to
advance knowledge on the key viral, host-related, and environmental factors
that determine the dynamics of avian influenza (AI) in poultry and other host
species, with the ultimate goal to improve prevention and control strategies
against this disease. By establishing interdisciplinary research focusing on
key questions of AI, DELTA-FLU will collect and generate data to determine 1)
potential for some highly pathogenic avian influenza viruses (HPAIV, e.g. H5N8
clade 2.3.4.4) to be maintained in wild bird populations and spread over long-
distances, 2) key viral, host, and environmental factors for incursion of
HPAIV from wild birds into poultry holdings, 3) roles of viral, host, and
environmental factors in the transition of low pathogenic avian influenza
virus to HPAIV in poultry, 4) effect of flock immunity against AI on early
detection and viral genetic drift, and 5) viral genetic factors that allow
reassortants of avian and mammalian influenza viruses to transmit efficiently
among pigs. Data will be used to inform about experimental design, analytic
tools and methods, as well as modelling and simulation tools, in order to
achieve these primary aims.

##  TYPES AND FORMATS OF DATA TO BE GENERATED/ COLLECTED

DELTA-FLU will collect and generate a range of data based on which targeted
prevention and control strategies can be designed, as summarized in the table
below. These data will largely originate from public databases, databases
available from partner’s own projects and research activities in work packages
1 – 3. Standards for collecting, curating and preserving the data are
integrated in the research activities of DELTA-FLU to ensure data is kept
securely and protected from inappropriate use or disclosure. Where
appropriate, DELTA-FLU will leverage existing standards, and continue to
develop existing ones for data representation, for example for sequence-based
experiments. The research data generated by DELTA-FLU will be curated in such
a way that the formats will be compatible with publicly available data
repositories.  
  
<table>  
<tr>  
<th>

Type of data

</th>  
<th>

Origin of data

</th>  
<th>

Format

</th>  
<th>

Expected size of data

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

Virus sequences

</td>  
<td>

Public databases (Genbank: https://www.ncbi.nlm.nih.gov/genbank/ or GISAID:
http://platform.gisaid.org), work packages 1 to 3)

</td>  
<td>

FASTA

</td>  
<td>

Depends on amount of metadata (order of MB)

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

Wild bird tracking data

</td>  
<td>

Public database

(https://www.movebank.org/), work package 1

</td>  
<td>

.csv,

Movebank format

</td>  
<td>

Depends on number of birds and duration of tracking (order or GB)

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

Animal trial data (tissue tropism of viruses, excretion dynamics of viruses,
virulence of viruses in infected birds)

</td>  
<td>

Public databases (PubMed: https://www.ncbi.nlm.nih.gov/pubmed or Web of
Science: http://apps.webofknowledge.com/), work packages 1 to 3

</td>  
<td>

Word, Excel

</td>  
<td>

Order of MB

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

##  RE-USE OF EXISTING DATA

In DELTA-FLU, partners will make use of specific existing datasets collected
from public databases, databases available from partner’s own projects and
research activities, or datasets made available by one or more partners to the
consortium. The re-use of existing data is necessary to value and integrate
obtained results into the current state of knowledge. These include the
following data, sources, and reuse:  
  
<table>  
<tr>  
<th>

Data/ source

</th>  
<th>

Re-use

</th>  
<th>

Expected size of data

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

Virus sequences / Genbank

</td>  
<td>

Creation of phylogenetic trees

</td>  
<td>

Order of MB

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

Virus sequences / GISAID

</td>  
<td>

Creation of phylogenetic trees

</td>  
<td>

Order of MB

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

Animal trial data / Pubmed, Web of Science, unpublished data of partners

</td>  
<td>

Evolution of genetic and phenotypic characteristics of viruses in different
avian hosts

</td>  
<td>

Order of MB

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

Before making datasets available amongst partners or via open access data
repositories, DELTA-FLU will review any agreement(s) with third parties to
evaluate any restrictive use of the data by the consortium partners, and
evaluate whether or not ethical and other restrictions on further use apply.
In addition, whether permissions for use of the data are needed from third
parties will be evaluated.

##  DATA UTILITY: TO WHOM WILL IT BE USEFUL

DELTA-FLU will collect and generate a range of data, as described above, based
on which targeted prevention and control strategies can be designed, including
policy strategies and risk assessment. These data might be useful to a wide
range of actors involved in prevention and control of avian Influenza virus
outbreaks. These actors include, but are not limited to:

  * Research institutes and their individual scientists (such as in the areas of virology, epidemiology, molecular biology, pathology, ecology, ornithology, risk assessment and modelling, and animal and human health) 

  

  * International public and animal health and food safety authorities (e.g. EU, FAO, EFSA, WHO, ECDC, OIE, OFFLU) 

  

  * International nature conservation organizations (e.g. Wetlands International, Wetlands and Wildfowl Trust) 

  

  * National governments and international policy-making authorities (e.g. EU) 

  

  * Poultry production industry, including poultry production companies, farmers, and international associations representing the industry (e.g. European Live Poultry and Hatching Egg Association, Association of Poultry Processors and Poultry Trade in the EU). 

  

#  FAIR DATA

##  MAKING DATA FINDABLE, INCLUDING PROVISIONS FOR METADATA

DELTA-FLU will ensure that all data stored provide sufficient information
about each data set. Typically, this will include information about
experimental protocols, samples, virus strains, reagents, experimental
conditions, and data analysis models and approaches. DELTA-FLU will use
internationally accepted naming conventions and indicators, such as the
taxonomic international accepted names for pathogens, the common pathogen
titration methodologies expressing doses such as TCDI50, PFU, etc., developed
and/or optimized specific detection and analyzing methods (e.g. WHO or OIE
standards), as well as modelling/simulation exercises. Scenario-based
mathematical models will be described in a publication submitted to an
appropriate (open access) peer-reviewed journal for publication, which will be
finable by its unique Digital Object Identifier. Sequence data will be
uploaded with additional information/metadata. Search keywords will be
provided e.g. for data in publications as well as for data in public
databases. In addition, version numbers will be provided to enable a clear
traceability of currentness of data and of documents

There is a broad range of metadata which will be created especially in
connection to sequencing data (location, origin of samples, species sampled
etc.) but also to data collected from satellite tracking (time, location,
species, other tracking data). The metadata will be collected following the
schemes provided within the working packages and also by related projects
(e.g. sequence metadata collection scheme of COMPARE).

##  MAKING DATA OPENLY ACCESSIBLE

Before making datasets available amongst partners or via open access data
repositories, DELTA-FLU will review any agreement(s) with third parties to
evaluate any restrictive use of the data by the consortium partners, and
evaluate whether or not ethical and other restrictions on further use apply.
In addition, whether permissions for use of the data are needed from third
parties will be evaluated. In cases where transferred data generates new data,
e.g. upon data analysis by one or more partners, the DELTA-FLU Consortium
Agreement will address Intellectual Property issues that may arise from
ownership of the processed data and use of the tools on these data. Prior to
sharing of data, all researchers in DELTA-FLU will review their data obtained
in the project for exploitation potential and adequate knowledge protection
where appropriate, and communicate without delay any decision to protect data
generated in DELTA-FLU to the Executive Board of DELTA-FLU. Adequate
protection of knowledge shall take into account the need for proper
dissemination of results and openly sharing of data without any unjustified
delay. DELTA-FLU will actively seek to publish the data in peer-reviewed
scientific journals, and will strive to publish in open access journals (“Gold
model”). In case publication in open access journals is not feasible, the
publications will be made available via the DELTA-FLU website, and the
repositories of the participating universities and institutes, respecting any
embargo periods of the journal (“Green model”).

The availability of the data generated in DELTA-FLU has three main access
levels. The first level is public data, in which data will be made permanently
and freely available through for example open access publication and data
storage in publicly accessible databases. The second level is managed access
data, in which data will be stored under strict security provisions and access
to these data will be provided to ( _bona fide_ ) researchers or actors able
to demonstrate that they meet the requirements for privacy protection and
security as assessed by the relevant data access committees (typically drawn
from the ethical body overseeing consent-giving procedures, or data access
committees available at partner institutes). The third level of access is
private data, in which data will be made available only to defined closed
consortia that will retain all access management functions. We anticipate that
private data will comprise only a minor portion of all DELTA-FLU data sets.
Typically, this concerns data for which potential dual use or biosecurity
issues have been identified in the ethical assessment.

Data sharing with third parties will be subject to a data-sharing agreement
established by the DELTA-FLU Steering Committee. The agreement will specify
the conditions of data use, criteria for access, and acknowledgements.
Consortium partners who wish to withhold patentable or proprietary data can do
so, and advice on this point will be given by the Steering Committee. Data
sharing and data access and related issues will in principle be discussed and
decided upon in the Steering Committee, duly advised by the consortium
partners’ data management officers, and the project’s Scientific Advisory
Board and Ethical Committee. If deemed appropriate and necessary, a data
access committee will be established during the course of the project.

In making data available, DELTA-FLU discriminates raw and final research data.
Raw research data that will not be considered for a patent application by
consortium partners, but has been used to generate scientific papers, will be
made publicly available two years after the project end at the latest, and
stored in a repository of the partner’s choice. Final research data will be
made publicly available only after i) relevant scientific publications based
on the data have been accepted, or ii) a patent application has been
published, or iii) two years after the project end at the latest.

The public data will be available following the access conditions of the used
databases (e.g. EPiFLU or Genbank for sequence data or Movebank for animal
movement data). Restricted data will be stored locally and access will be
granted by the responsible partners upon request, including information about
necessary software tools.

Movebank is a free online infrastructure created to help researchers manage,
share, analyze and archive animal movement data. The Movebank project is
hosted by the Max Planck Institute for Ornithology in coordination with the
North Carolina Museum of Natural Sciences, the Ohio State University and the
University of Konstanz. Movebank collaborates with numerous governmental
agencies, universities and conservation organizations, and has received
funding from the National Science Foundation, the German Aerospace Center, the
German Science Foundation and NASA. Movebank has long-term (>20 years) funding
through the Max Planck Society and the University of Konstanz and is intended
to serve as a global data archive for animal movement data. Movebank is a
resource open to all researchers and organizations regardless of species,
study area or source of funding. Movebank users retain ownership of their data
and can choose whether or not to make their data available to the public. The
database is designed for datasets that include multiple locations of
individual animals, commonly referred to as tracking data. It also supports
data collected by other bio-logging sensors attached to animals as well as
information about animals, tags and deployments. During data collection, data
on movement is continuously added to the database; this data can be made
visible to the public directly, via a map tool on the Movebank homepage. After
completion of specific project, data can be curated and metadata included and
published in the Movebank Data Repository with specific DOI and under Creative
Commons license, enabling the data to be used by other researchers.

GenBank is the NIH genetic sequence database, an annotated collection of all
publicly available DNA sequences. GenBank is part of the International
Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank
of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI.
These three organizations exchange data on a daily basis. There are several
ways to search and retrieve data from GenBank. The GenBank database is
designed to provide and encourage access within the scientific community to
the most up-to-date and comprehensive DNA sequence information. Therefore,
NCBI places no restrictions on the use or distribution of the GenBank data.
However, some submitters may claim patent, copyright, or other intellectual
property rights in all or a portion of the data they have submitted. NCBI is
not in a position to assess the validity of such claims, and therefore cannot
provide comment or unrestricted permission concerning the use, copying, or
distribution of the information contained in GenBank. Some authors are
concerned that the appearance of their data in GenBank prior to publication
will compromise their work. GenBank will, upon request, withhold release of
new submissions for a specified period of time.

GISAID EpiFlu database is a non-profit organization that provides public
access to the most complete collection of genetic sequence data of influenza
viruses and related clinical and epidemiological data. Furthermore, the
database provides rapid sharing of influenza virus data. “The Initiative
involves public– private partnerships between the non-profit organization
_Freunde von GISAID e.V._ [4] and governments of the Federal Republic of
Germany, the official host of the GISAID EpiFlu™ database” “The database
access agreement of GISAID ensures that contributors of virus sequence data do
not forfeit intellectual property rights to the data”.

PubMed comprises over 28 million citations for biomedical literature from
MEDLINE, life science journals, and online books. PubMed citations and
abstracts include the fields of biomedicine and health, covering portions of
the life sciences, behavioral sciences, chemical sciences, and bioengineering.
PubMed also provides access to additional relevant web sites and links to the
other NCBI molecular biology resources. PubMed is a free resource that is
developed and maintained by the National Center for Biotechnology Information
(NCBI), at the U.S. National Library of Medicine (NLM), located at the
National Institutes of Health (NIH).

Web of Science connects publications and researchers through citations and
controlled indexing in curated databases spanning every discipline. It allows
cited reference searches to track prior research and monitor current
developments in over 100 years’ worth of content that is fully indexed,
including 59 million records and backfiles dating back to 1898. It is
maintained by Clarivate Analytics, that provides a comprehensive citation
search. It gives access to multiple databases that reference cross-
disciplinary research, which allows for in-depth exploration of specialized
sub-fields within an academic or scientific discipline.

##  MAKING DATA INTEROPERABLE

To ensure the interoperability of data, where appropriate, DELTA-FLU will
leverage existing standards, and continue to develop existing ones for data
representation. DELTA-FLU will make the generated and collected research data
available via appropriate, dedicated, and, where possible, open access
archives and database repositories. In addition, DELTA-FLU will upload basic
datasets in standardized forms in a primary database as required by the
journal in which the consortium partners publish their results.

As the project activities and the consortium partners span multiple scientific
disciplines, partners will agree on standard vocabularies for all data types
present in DELTA-FLU generated and/or collected data sets, as well as on
common terminology, key words, units and formats to be applied to the data and
other documents.

##  INCREASE DATA RE-USE (THROUGH CLARIFYING LICENCES)

In DELTA-FLU, partners will make use of specific datasets collected from
public databases, data-bases available from partner’s own projects and
research activities, or datasets made available by one or more partners to the
consortium. Therefore, the majority of the data will be stored by the partner
who is performing the experiments or using the tools. In those cases, the data
remain under the control of the partner who delivered the data, and management
and ethical procedures will follow those of the original project under which
the data were made available.

Before making datasets available amongst partners, DELTA-FLU will review any
agreement(s) with third parties to evaluate any restrictive use of the data by
the consortium partners, and evaluate whether or not ethical and other
restrictions on further use apply. In addition, whether permissions for use of
the data are needed from third parties will be evaluated. In cases where
transferred data generates new data, e.g. upon data analysis by one or more
partners, the Consortium Agreement addresses IP issues that may arise from
ownership of the processed data and use of the tools on these data. Detailed
arrangements on the data use and related knowledge management issues have been
agreed upon in the Consortium Agreement.

The data generated and collected in the project will be made openly available
to third parties after the end of the project. Possible restrictions could be
put in place due to the need to finalize pa-tenting processes or publish
scientific works based on the data.

Final research data stored locally will remain re-usable until the end of the
project and for an additional 10-years term if adequate financial sponsors
will be found (if necessary). Raw and final re-search data stored in other
open repositories will remain re-usable for a minimum of 10 years.

All partners of DELTA-FLU have compromised about harmonizing methods and
protocols to assure quality (milestones and deliverables). The majority of the
applied diagnostic methods are standardized. In sum, only those methods will
be used which have already been validated and accredited in partners lab to
ensure highest quality standards. This ensures high quality data, which can be
compared between different partners and other laboratories.

#  ALLOCATION OF RESOURCES

Each partner in DELTA-FLU is responsible for data stored locally and for
complying with their own standard operating procedures (SOPs), and any DELTA-
FLU specific SOP that may be drawn up if deemed necessary, as well as for
complying to the relevant legal and ethical requirements. Data sharing, data
access and related issues will in principle be discussed and decided upon in
the Steering Committee.

Final research data stored locally will remain re-usable until the end of the
project and for an additional 10-years term if adequate financial sponsors
will be found (if necessary). Raw and final research data stored in open
repositories, such as EMBL-EBI ENA/GenBank and Movebank, will remain re-usable
for a minimum of 10 years.

Consortium partners strive to publish research data as supporting materials
together with their publications as much as possible, to facilitate future re-
use of data by other researchers. Cost for open access publications are
foreseen in the DELTA-FLU budget (around 2000 - 8000 euros per partner).
Currently, we do not have a cost estimate for the staff time necessary to make
data FAIR in this project.

#  DATA SECURITY

As mentioned above, each partner in DELTA-FLU is responsible for data stored
locally and for complying with their own standard operating procedures (SOPs),
and any DELTA-FLU specific SOP that may be drawn up if deemed necessary, as
well as for complying to the relevant legal and ethical requirements. The
following general terms regarding data protection will be followed by the
partners in DELTA-FLU with regard to raw and final research data which is not
stored in open repositories:

  * The amount of data collected is relevant and not excessive; 

  

  * Data are stored securely; 

  

  * Data are fairly and lawfully processed; 

  

  * Data accuracy is ensured (i.e. all reasonable efforts to ensure data accuracy are undertaken); 

  

  * Data are used only in ways that are compatible with the original consent or agreement; 

  

  * Relevant national and international regulations regarding data protection will be applied. 

  

Data storage facilities will be maintained in accordance with manufacturers’
guidelines. Data will be backed up at regular intervals, and stored safely and
securely, in accordance with the consortium partners’ organizational policy.

#  ETHICAL ASPECTS

Ethical issues that may have an impact on data sharing will be assessed during
the project as part of work package 4, task 4.3 (Management of the research
data generated and collected during the project). Animal trial data collection
follows all national and EU laws.

DELTA-FLU will not generate, collect or deal with personal data.