#  INTRODUCTION

This document represents the **Data Management Plan** for the **EnvMetaGen**
project. The plan details what data the project will generate, how it will be
exploited and made accessible for verification and re-use, and how it will be
curated and preserved. The underlying principles informing this plan are that
the data should be managed so that it is findable, accessible, interoperable
and reusable (FAIR) – _Guidelines on FAIR Data Management in Horizon 2020_ .

#  TYPES OF DATA

The EnvMetaGen project will generate research products on Environmental
Metagenomics and its application to ecological problems. There are five main
data types that this project will produce:

  1. Nucleic acid sequence data; 

  

  2. Taxonomic information and associated metadata; 

  

  3. Molecular biological and field collection methods; iv. Data analysis methods; 

  

  

v. Ecological information based on the results of experimental work.

Each data type will be archived and disseminated in the ways that are
appropriate to its specific qualities.

#  DATA ARCHIVING

##  Nucleic acid sequence data

Nucleic acid sequence data can be archived in many ways depending upon the
degree of analysis and annotation of features that has been undertaken on it.
Raw reads will be archived either in the NCBI Short Reads Archive; or similar
appropriate archives of un-analysed sequence data; or a generic data archive
such as DRYAD (http://datadryad.org/). Sequences that have been carefully
inspected and associated with a clearly defined taxon verified by a recognized
taxonomic expert will be deposited in the GenBank  (
_https://www.ncbi.nlm.nih.gov/genbank/)_ ;  the Barcoding of Life Database  (
_http://www.barcodeoflife.org/)_ ;  or DRYAD. These approaches are the
international standard for the field ensuring data is openly accessible. This
is also the main way that nucleic acid sequence data is re-used by other
researchers.

##  Taxonomic data

Taxonomic information relating to DNA sequences that are generated in this
project will generally be archived in custom databases with links to the
sequences and organisms associated with them. Where appropriate, sub-sets of
this data will also be deposited in BOLD or GenBank. The custom databases will
be hosted by the EnvMetaGen project website  ( _http://inbio-envmetagen.pt/_ )
. In addition, where appropriate the data on species occurrences will be added
to the database of the Global Biodiversity Information Facility  (
_http://www.gbif.org_ )  . Associated metadata such as collection locations
for type specimens or photographs of them will be archived according to the
requirements of the data repositories.

##  Molecular biological or field methods

Molecular biological or field collection procedures for biological materials
will be archived either through peer-reviewed publication in Open Access
journals, or by making a transcript or video of the methods and making this
available on the EnvMetaGen website. This follows the H2020 principle of Open
Research Data (ORD) publication.

##  Data analysis methods

Data analysis methods such as scripts for Bioinformatic procedures or R
scripts or similar for statistical analysis and graphical display of data will
be archived either in supplementary material for published papers in Open
Access journals, or by placing the script or a description of Bioinformatic
procedures on the EnvMetaGen website.

##  Ecological results dissemination

Ecological information that is generated through the various projects that may
be funded and run under the capacities of the EnvMetaGen project will be
archived in peer reviewed articles for Open Access journals. Where Open Access
is not an option because of the cost of it, summaries will be archived in the
EnvMetaGen website. This follows the H2020 principle of Open Research Data
(ORD) publication.

#  DATA DISSEMINATION

EnvMetaGen will follow the H2020 principles of making its data findable,
accessible, interoperable and reusable. The EnvMetaGen website will provide
the primary passive mechanism for data dissemination and achieving FAIR
outcomes. This site will have sections for each project that is conducted
under the overall EnvMetaGen umbrella project. It will also have sections for
protocols and data archiving for anything that cannot be handled by DRYAD,
BOLD or GenBank.

Active data dissemination to specialists will be done primarily through
published papers and verbal and poster presentations at scientific
conferences. Data dissemination to non-specialists will be handled by the
“Knowledge Transfer and Dissemination Officer” (KTDO) employed by the
EnvMetaGen project. This will involve the KTDO liaising with schools,
organisations such as museums and potential commercial partners. The KTDO will
develop specific strategies appropriate to each of these groups to raise
community awareness of the work done by EnvMetaGen and to explore potential
commercial collaborations.

#  CONCLUDING REMARKS

EnvMetaGen will follow standard “best practice” for the field of environmental
metagenomics. It will do this in a way that conforms to the H2020 programme’s
principles of FAIR data dissemination and that also follows an ORD approach.
This is a rapidly changing field and the exact data types that will be
generated are not yet determined as this is a capacity building project
without specific scientific objectives. The EnvMetaGen management team will
follow changes in the field and adjust the data management plan as necessary.
This might be important if data archiving practices change within the wider
environmental metagenomics community.

Data security is ensured by redundancy in that we will archive all data in
established public repositories as well as in our own EnvMetaGen site and
databases. Ethical considerations for our data are all covered in the
EnvMetaGen Deliverables 8.1 - 8.9 that were already uploaded on the EC project
portal.