#  INTRODUCTION

A new element in the Horizon 2020 is the use of data management plans
detailing what data a project generates and how this data is made accessible.
This document introduces the first version of the Data Management Plan (DMP)
of the INFERNET project funded by the European Union’s Horizon 2020 Program
under Grant Agreement #654206. The DMP describes the data management cycle for
datasets to be collected and/or generated by INFERNET. It covers:

  1. What research data will be collected and/or generated by INFERNET; 

  

  2. The handling of research data; 

  

  3. The methodologies that will be applied; 

  

  4. Data-sharing policies; 

  

  5. Data curation and preservation policies. 

  

  

Open data are becoming increasingly important for maximizing the excellence
and growth of the research activity in Europe. INFERNET is aligned with the
foundations of open data, namely

  * building a software-defined toolkit in an open source project for inference in biological networks; • building a permanent link to the open source community through case examples; 

  

  * sharing the data produced with the community. 

  

Note that primary data used in the scientific research of the INFERNET project
relative to WPs come from public open databases like UNIPROT, the XFAM suite
provided by the European EMBL-EBI. This gives us the full possibility of
redistributing processed data and results obtained on the basis of the primary
data.

The INFERNET DMP primarily lists the different datasets that will be produced
by the project, the main exploitation perspectives for each of those datasets,
and the major data management principles. The purpose of the DMP is to provide
an analysis of the main elements of the data management policy that will be
used by the consortium. The DMP is however not a “crystallized” document and
it will evolve during the lifespan of the project.

The DMP regards all the data sets that will be collected, processed and/or
generated within INFERNET. To generate this DMP, the consortium created a data
management policy based on a) the elements that the EU proposes to address for
each data set and b) the specific capability of the consortium to address each
of those element. The elements were then used to create a DMP template which
was refined with all partners.

The structure of the document is the following:

  * **Section 2** presents the General Principles to which the INFERNET consortium will adhere; 

  

  * **Section 3** details the types of data to be collected, processed and/or generated by the INFERNET consortium (which can be grouped as (a) research papers, (b) software codes and (c) data sets proper) and outlines the corresponding open data policies the consortium will follow; 

  

  * **Section 4** discusses the outreach strategies the consortium plans to implement; 

  

  * **Section 5** provides an overview of the content of the data collected and/or generated by the INFERNET consortium; 

  

  * **Section 6** draws conclusion and sets future goals. 

  

The intended audience for this document is the INFERNET consortium and the
European Commission.

#  GENERAL PRINCIPLES

##  Aims of the Data Management Plan

This DMP aims at providing insight into the facilities and criteria employed
for the collection, generation, storage, dissemination and sharing of research
data related to the INFERNET project. In particular, the DMP will focus on

  1. Embedding the INFERNET project in the EU policy on data management, which is increasingly geared towards providing open access to data that is gathered with funds from the EU; 

  

  2. Enabling verification of the research results of the INFERNET project; 

  

  3. Fostering the reuse of INFERNET data by other researchers; 

  

  4. Enabling the storage of INFERNET data in publicly accessible repositories; 

  

  

The INFERNET project has a very broad understanding to the notion of “data”
(to be detailed in Section 3). In the following, we shall outline the basic
principles on which we designed the INFERNET DMP.

##  Participation in the Pilot on Open Research Data

The INFERNET project participates in the Pilot on Open Research Data launched
by the European Commission along with the Horizon 2020 program.

The INFERNET consortium strongly believes that open access to research data
and publications is important within the context of responsible and
reproducible research and innovation, and agrees on the benefits that the
European innovation ecosystem and economy can draw from allowing reusing data
at a larger scale. Ensuring research data and publications can be openly and
freely accessed means that any relevant stakeholder can choose to cross-check
and validate whether research data are accurately and comprehensively reported
and analysed, and may also encourage the reuse of data. However, open access
to research data must comply with sound research ethics, ensuring for instance
that no directly or indirectly identifiable information is revealed.

##  Intellectual Property Rights and Security

Project partners keep Intellectual Property Rights (IPR) on their technologies
and data. As a legitimate result, the INFERNET consortium will have to protect
these data and consult the concerned partner(s) before publication.

IPR management is concerned also on preventing the leak or hack of the data.
Although we do not plan to collect human sample data, INFERNET will guarantee
that if the specific nature of the dataset requires, we will include secure
protection to it.

A holistic security approach will be undertaken to protect the three mains
pillars of information security:

  * Confidentiality, 

  

  * Integrity, ● Availability. 

  

The security approach will consist of a methodical assessment of security
risks followed by an impact analysis. This analysis will be performed on the
personal information and data processed by the proposed model.

##  Personal Data Protection

We are not planning to collect personal data such as full names, contact
details, background, etc. Should the development of the project require such
data, we will adhere with the EU's Data Protection Directive 95/46/EC1 aiming
at protecting personal data. National legislations applicable to the project
will also be strictly followed, such as the Italian Personal Data Protection
Code 2. In such case, all data will be collected by the project after
providing subjects with full details on the experiments to be conducted, and
after obtaining signed informed consent forms from them.

#  TYPES OF DATA HANDLED DURING THE PROJECT AND CORRESPONDING OPEN DATA
POLICIES IMPLEMENTED BY INFERNET

The INFERNET project will deal with three main sources of data that can be
subject of open data policies: _research papers,_ _software source code_ ,
_datasets_ . In the following we shall focus on how the INFERNET consortium
will handle each of these sources. It should however be emphasized that
INFERNET will also make use of secondary sources, including: literature
research, existing databases collecting experimental results, archives of
research papers (both preprints and published articles) and actively
maintained software repositories.

##  Research papers

Research papers published both in peer-reviewed journals and conference
proceedings, will be the main instrument to propagate our research
contributions to the appropriate audience. Where appropriate, INFERNET will
protect the intellectual property of the work prior to publication, but in
general, the consortium will privilege Open-Access journals. We will make
publications available through the project web portal and systematically use
other web resources like preprint servers ( _e.g._ ArXiv.org, bioRxiv.org
etc.), as is the tradition in physics research and which gain increasing
acceptance by the editorial policies of specific journals.

Currently, there are two main strategies to implement open data access on
research papers: _gold_ and _green_ open data [1]. Following _gold_ open data,
researchers can publish in an Open Access (OA) free online access journal.
According to _green_ open data, instead, researchers can deposit a version of
their published works into a subject-based or institutional repository. As not
all journals today comply with gold open data standards, all INFERNET related
publications will be made publicly available following _green_ open data
standards. Our concrete strategy to comply with the _green_ open data standard
will be:

  * **Self-Archiving** , i.e. the act of the author depositing a free copy of an electronic document online in order to provide open access to it. This is considered a reasonable route to make a research paper open data ( _green_ ). We have already deployed the INFERNET web site (http:/www.infernet.eu) where published papers will be uploaded in compliance with the embargo period of the journal to which the article will be submitted for publication. 

  

  * **Metadata:** Every INFERNET publication will be associated to metadata that describes the type and topic of the publication (abstract), as well as the original publisher, venue and Document Object Identifier (DOI). 

  

  * **Public Archives:** In compatibility with the journal embargo time, we aim at disseminating INFERNET publication on open archives. In particular arxiv ( _http://xxx.lanl.gov_ ), and biorxiv ( _http://www.bioarxiv.org_ ) will be the preferred online repositories. 

  

##  Software source code

All partners will be contributing to a public and centralized code management
system. This makes the development of the project open and transparent for the
public. In particular we will not only leverage the results at the end of the
project as open data, but it also makes the source code open for the entire
software life-cycle. In details

  * **Centralized repository:** we are going to create a GitHub ( _http://github.com_ ) also linked from and to our project website. GitHub is currently the most popular code management public repository due to the large availability of options to fork/branch/merge versions of a software project that enables third parties to easily extend the source code. 

  

  * **Long-term availability** will be guaranteed by the _cloud_ nature of the storage strategy implemented by the repository. 

  

  * **Licensing:** whenever possible we will license open source code under either Apache License 2.0 or GNU General Public License 3.0. Loosely speaking these licenses provide the user with the freedom to use the software for any purpose, to distribute it, to modify it, and to distribute modified versions of the software, under the terms of the license, without concern for royalties [2]. However, the intellectual property of the source code is kept: For instance, the Apache License requires preservation of the copyright notice and disclaimer, which are related to the project [3]. 

  

  * **Code usability:** thanks to the helpful extension of GitHub, code will be always complemented by upto-the-date documentation that will help the use of the code even even beyond the lifetime of INFERNET. 

  

##  Data sets

In many cases, research publications will be associated with a dataset, either
as a source of information to extract novel observations or as a result of the
research process. Our aim is to provide in an open format all research data
needed to validate the results of the associated publications. Again, as in
the case of scientific publications, we will try to adhere as much as possible
to _a green_ open data standard.

  * **Self-Archiving** : in analogy with what we already outlined for publications, datasets will be either directly uploaded, or referenced from the INFERNET website. 

  

  * **Availability** : The web site of the project will be extended to 6 years over the natural duration of the project guaranteeing long-term availability of the data. 

  

  * **Metadata and open formats:** Every INFERNET dataset will be organized with simple lightweight and well-established file format (such as CSV). We will avoid closed-source proprietary formats. Very relevant will be the use of metadata to understand the _topic_ , _purpose_ , _collection/generation methodology_ as well as an explanation of the different _fields_ of the dataset. 

  

#  OUTREACH STRATEGY AND DATA SHARING

To foster the re-use of INFERNET research data by third parties, consortium
members will be committed to implementing a strategy to disseminate results
for the benefit of the scientific community as well as for potentially
interested economic players.

The actions that will be undertaken to maximize the visibility of our results
will be:

  * **Reference to dataset and software in the publication:** papers produced for the project will contain a clear reference to where the data and related software actually live to maximize the awareness of INFERNET results in the scientific community; 

  

  * **Advertise available data in conference and public events:** we will leverage the presence of members of INFERNET in international conference to present not only scientific results, but also the software and related datasets. 

  

Data sharing will be achieved through publicly accessible web servers as
described in the previous section.

#  DATA DESCRIPTION

In this section we will describe the different items that will be produced
during the entire project lifetime. As already stated above, DMP is an ongoing
process and will be updated in the course of the project. This is the first
release of the document, and given the very early stage of the project, we do
not have at present material to describe. With respect to the data format we
will adhere to the following rules:

  * Research articles: PDF according to the guidelines outlined in section 3.1 of this document. 

  

  * Software codes: standard languages (C, C++, Julia, ) 

  

  * Data files: minimal machine readable formats (CSV, ASCII, TXT), suitable metadata, and manual and guidelines to use them. 

  

#  CONCLUSIONS

The purpose of this document was to provide the plan for managing the data
generated and collected during the project, i.e. the Data Management Plan
(DMP). Specifically, the DMP described the data management life cycle for all
datasets to be collected, processed and/or generated by a research project. It
covered the handling of research data during and after the project, including:
what data will be collected, processed or generated; what methodology and
standards will be applied; how data will be shared/made open and in what
formats; and how data will be curated and preserved.

Following the EU’s guidelines regarding the DMP, this document will be updated
during the project lifetime (in the form of deliverables).

#  BIBLIOGRAPHY

  1. E. Commission, “Guidelines on open access to scientific publications and research data in Horizon 2020.” http://ec.europa.eu/research/participants/data/ref/h2020/grants_manual/hi/oa_pilot/h2020- hi-oa-pilotguide_en.pdf, 2013. 

  

  2. Wikipedia, “Comparison of free and open-source software licenses.” https://en.wikipedia.org/wiki/Comparison_of_free_and_open-source_software_licenses. [3] Wikipedia, “Apache license.” https://en.wikipedia.org/?title=Apache_License.