#  1 INTRODUCTION

##  1.1 PURPOSE OF THE DOCUMENT

The goal of this document is to provide a technical description and the
guidelines of Raft4Biotech data management plan version 1. The Deliverable
outlines how the research data collected or generated will be handled during
and after the Raft4Biotech action, describes which standards and methodology
for data collection and generation will be followed, and whether and how data
will be shared. This document follows the template provided by the European
Commission in the

Participant Portal  1  .

Although a DMP is not required for this call Biotec-03-2016 because this
particular call is not adhered to the Open Research Data Pilot, we
nevertheless considered data sharing as an important component of our
dissemination strategy and also an important component of our Responsible
Research and Innovation (RRI) actions. We therefore endeavour to delineate the
main actions to generate a DMP and to identify specific datasets that will be
disseminated using free access/use and also the numbers of channels chosen for
their dissemination. The _Rafts4Biotech_ project DMP will be written in
reference to the Art 29.3 in the Annotated Model Grant Agreement  2  called
“Open Access to Research Data” (research data management). Open access refers
to a practice of giving online access to all scholarly disciplines information
that is free of charge to the end-user. In this way data becomes re-usable,
and the benefit of public investment in the research will be improved. Project
participants must deposit their data in a research data repository and take
measures to make the data available to third parties. The third party should
be able to access, mine, exploit, reproduce and disseminate the data. This
should also help to validate the results presented in scientific publications.
In addition Article 29.3 suggests that participants will have to provide
information, via the repository, about tools and instruments needed for the
validation of project outcomes.

The Data Management plan is a document that is submitted to the EU as project
**Deliverable 8.1.** in June 2017, at early stage of the project. It is
therefore important to note that the document will evolve and further develop
during the project’s life cycle.

#  3  RAFT4BIOTECH DATA MANAGEMENT PLAN

##  2.1 OBJECTIVE OF THE RAFT4BIOTECH PROJECT

The objective of the _Rafts4Biotech_ project is to develop a new and versatile
generation of microbial chassis to produce industrially relevant reactions
confined in subcellular membrane compartments, allowing their fine regulation
to achieve optimal performance and isolation from cellular metabolism to
prevent toxic cross-reactivity. The _Rafts4Biotech_ project will produce a new
generation of reliable and robust synthetic microbial chassis platforms
(SMCPs) in which industrial production processes are confined in bacterial
lipid rafts, thus SMCPs will be released from their classical off-genome
limitations and optimized for the industrial production of numerous
biochemical processes. The _Raft4Biotech_ project will use two of the most
biotechnologically relevant microbial systems, the gram-positive bacterium
_Bacillus subtilis_ and the gram-negative bacterium _Escherichia coli_ , to
engineer synthetic bacterial lipid rafts to optimize the performance of three
challenging biochemical processes of growing biotechnological interest,
including 1) the production of a new class of lipophilic antibiotics to fight
resistant infections. The industrial production of these antimicrobials cannot
be achieved in conventional cell factories because of their inherent toxicity
to bacterial cells and the natural capacity of these lipophilic molecules to
inhibit essential activity in bacterial membranes. 2) the implementation of
complex biochemical pathways of commercial value spatially confined in
synthetic bacterial lipid rafts. Subcellular confinement of these processes in
specific highly lipophilic areas of the bacterial membrane will increase the
efficiency of the targeted enzymatic processes that can be applied to
industrial manufacturing. The general aim of the _Rafts4Biotech_ project is
therefore to develop an innovative technology to optimize multistep enzymatic
processes using a new generation of SMCPs.

dissemination stands, different dissemination channels will be considered
depending on whether the dataset comes in form of a scientific publication or
in contrast, is a large dataset, likely produced by the number of -omics
research disciplines of _Rafts4Biotech_ project.

In the flow-chart below, we delineated the main actions to identify the
specific datasets that will be disseminated.

**Figure 1 Flowchart of the Data Management Plan designed for _Rafts4Biotech_
. **

#  3 DATA SET DESCRIPTION

The data for the _Rafts4Biotech_ project will be produced by various
researchers from the participating laboratories using general guidelines and
procedures to standardize the operative procedure of data and help to decide
which data is dedicated to dissemination and which data requires IPR
protection.

##  3.1 TRANSCRIPTOMIC DATA

Transcriptomic data will be generated via RNA-Seq using high-throughput
sequencing platforms. The resulting raw data (fastq files) and the alignment
information (BAM files) will be stored in the European Nucleotide Archive  4
(ENA) which accepts sequence reads and associated analyses. Data submitted to
ENA is automatically exchanged between International Nucleotide Sequence
Database Collaboration  5  (INSDC) partners: NCBI and DDBJ. These data bases
make data publically available to the community allowing for new discoveries
by comparing these raw data sets with others. Secondly, analyzed data files
will be deposited in the EBI Array Express Archive of Functional Genomics Data
6  . This ensures that transcriptome experiments are available for reuse and
combined analyses. Both, the EBI and the NCBI curates data that is deposit to
their archives, which ensure uniformity of the transcriptome data and its
cognate experiments.

##  3.2 PROTEOMIC DATA

Proteomic data will be generated by LC-MS/MS and SRMlabel-free. Upon
publication data will be freely made available through public databases and
supplementary material. Processed and raw data will be stored either in
ProteomeXchange international public database  7  or PRIDE European repository
7  .

##  3.3 METABOLOMIC DATA

The metabolomic data will be made available freely in the standard formats
defined by the Metabolomics Standards Initiative  8  to enable free and open
sharing of metabolomics data. The specific format will depend on whether
targeted or untargeted methods are being used. Besides the specific data
format the reported metadata are possibly even more crucial and are routinely
reported in our internal storage system. Within the project we will use the
OpenBis platform to store, annotate, and exchange metabolomics data  9  . Upon
publication data will be freely made available through public databases,
supplementary material and public accessible ETH storage for larger sets,
thereby ensuring preservation and re-use.

##  3.4 GENETIC TOOLS AND CONSTRUCTS

Regarding genetic tools and constructs that become available during the
completion of _Rafts4Biotech_ , plasmids and useful genetic constructs that
are released from IPR protection will be deposited at the Addgene non-profit
public repository  10  . Genetic sequences will be available to any requesting
laboratory. Addgene develops a strong interaction between participating
laboratories to implement data curation and standardization of the samples
that are stored in their DNA bank.

#  4 DATA SET STORAGE

During the life cycle of the project data will be stored and systematically
organised in a repository called ‘Data4Raft‘. A website will be generated not
only to be the showcase of all online communication material and also all the
dissemination material (papers, conference abstracts, conference talk videos,
posters), but also (via internal access-restricted intranet to the Data4Raft
repository) to share, preserve, cite, explore and analyse research data. It
will facilitate to make data available to others at the end of the project,
and allows to replicate others work.

#  5 DATA DISSEMINATION

Following the recommendation of the Exploitation Committee of _Rafts4Biotech_
to the Steering Committee, dataset will be disseminated by appropriate
channels, mostly depending on whether the dataset comes in form of a
scientific publication or in contrast, is a large omics dataset.

##  5.1 PUBLICATIONS

Open access will be mandatory for research publications. Open access
publishing (gold open access) will be the preferred option when is available.
However, high-impact journals such as _Science_ and _Nature_ do not provide
this option. Even in the cases of the high-impact journals that offer the gold
open-access option, the publication fees are excessive in such this precludes
many laboratories to publish in gold open access. As we have a clear intention
to cause the highest impact as possible, publication in high-impact journals
will be pursued during the course of this project. In case that the journal
does not have the gold open access option or the publication fees for open
access cannot be assumed by the reporting laboratory, we will choose self-
archiving publishing (green open access) as an option to publish in open
access. This option is free and suitable for such already accepted manuscripts
that become public after a defined embargo period of 2-6 months.

As reference, we will use Europe PubMed Central (Europe PMC) repository  11
This repository is the recommended repository for Green Open Access
publication in other European Funding actions such as ERC grants (European
Research Council). EuropePMC provides access to life sciences articles, books,
patents and clinical studies as well as links to online databases such as
Uniprot, European Nucleotide Archive (ENA), Protein Data Bank Europe (PDBE)
and BioStudies.

Europe PMC meets the agreed definition of a repository as determined by Jisc
and endorsed by RLUK, SCONUL, ARMA and UKCoRR.

##  5.2 IPR AND PUBLIC AVAILABILITY OF DATA

While the data produced and collected in the framework of the _Rafts4Biotech_
project will be publicly available, precautious will be taken regarding
intellectual property rights (IPR). To protect IPR, the ECR will be free to
choose any available form of protection (Patent, Trademark, Industrial design,
Copyright, Trade-secret, Confidentiality). The choice of the most suitable
form should be made on the basis of the specificities of the action and the
type of result. The ECR will develop the IPR section that has been previously
defined in the Consortium Agreement (CA). Rules of confidentiality established
in the CA will define access rights, license agreements and timing for public
availability of the data sets.

##  5.3 PRESERVATION OF THE FINAL DATA SET

Although the WEB-based ‘Data4Raft’ is a useful tool to store the data during
the life cycle of the project, it is not geared towards the long-term
preservation of the data. Therefore, at the completion of the project, the
final dataset will be transferred to a sustainable repository, which ensures
sustainable archiving of the final research data.

Several such repository services promoting sustained access to digital
research data are currently offered and the ECR will search and attempt to
identify a repository promoting sustained access to digital research data.

**END OF THE DOCUMENT**

Project: Rafts 4 Biotech D8.1 Presentation of the Data Management Deliverable
ID: D.8.1 Plan (DMP)

Grant Agreement: 720776 Call ID: H2020-NMBP-BIO-2016 Page: 10 of 12