Romain David

Romain David
Research fellow - Data Manager at ERINHA AISBL (European Research Infrastructure on Highly Pathogenic Agents) · ERINHA

PhD
FAIR data, sensitive data and data sharing for EOSC Life, BY-COVID, ISIDORe, Research Data Alliance and Go FAIR.

About

150
Publications
34,097
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Introduction
I'm Research fellow - Data Manager at ERINHA AISBL (European Research Infrastructure on Highly Pathogenic Agents) young PhD but I have 15 year exp both in terrestrial / marine ecological engineering data management - network animation. Data mining and graph approach addict and "Data Management Plan with FAIR Compliance" evangelizer. Follow @Romain_DAVID_13 on twitter https://cv.archives-ouvertes.fr/romain-david/
Additional affiliations
March 2019 - March 2020
MISTEA laboratory (UMR Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie)
Position
  • Research Associate
Description
  • Interoperability improvment for platforms (Phenotyping Hybrid Information System), ensure links between actors of different disciplines Develop activities on the development, adoption, choice and implementation of ontologies and standards
May 2011 - December 2016
French National Centre for Scientific Research
Position
  • Engineer
Description
  • Implementation of experimental protocols, organization of scientific work and sampling sessions, organization of workshops and seminars, writing of papers and scientific publications, animation of the network, organization of information systems and internal tools (http://www.cigesmed.eu) European coralligenous monitoring network (European program "CIGESMED"), involvement in work packages, Leader of WP6, Expertise manager for ZNIEFFs Mediterranean Sea: Validation of ZNIEFFs according to ecologic
January 2000 - September 2009
Regional Observatory of the Environment (O.R.E.) Poitou-Charentes
Position
  • Project Manager
Description
  • 2005 – 2009 : Project Manager "Natural Heritage": Creation and animation of the Partner Network of Natural Heritage Actors (40 structures, the first Regional Biodiversity Observatory in France),Technical support to Natural Heritage stakeholders (R.P.A.P.N., implementation of S.I.N.P. in Poitou-Charentes), 2000 – 2005 : Internet and Databases Manager, Management and development of IT products related to environmental data, In charge of Internet sites / Regional Environmental Information System
Education
January 2013 - July 2018
Aix-Marseille Université
Field of study
  • Oceanography and data mining
September 2009 - September 2010
University of Paris 6 Pierre et Marie Curie - Sorbonne University (France), Oceanographic station of Roscoff (France), Laboratory of Oceanography of Banyuls (France)
Field of study
  • Coastal Ocean Science
September 2004 - June 2005
Université de Poitiers
Field of study
  • Ecological Engineering

Publications

Publications (150)
Article
Full-text available
The challenges of Reproducibility and Replicability (R & R) in computer science experiments have become a focus of attention in the last decade, as efforts to adhere to good research practices have increased. However, experiments using Deep Learning (DL) remain difficult to reproduce due to the complexity of the techniques used. Challenges such as...
Preprint
The Horizon 2020 project EOSC-Life brings together the 13 Life Science 'ESFRI' research infrastructures to create an open, digital and collaborative space for biological and medical research. Sharing sensitive data is a specific challenge within EOSC-Life. For that reason, a toolbox is being developed, providing information to researchers who wish...
Poster
Full-text available
For many decades, the immunogenetics community has been among the frontrunners in sharing data and samples, ensuring a great scientific progress in this domain. International histocompatibility workshops and scientific meetings in immunogenetics societies as EFI and ASHI have largely contributed to this progress In many other fields it has now bee...
Poster
Full-text available
Profound changes in our world are exacerbating data availability challenges at the global level, in particular between scientists and other knowledge workers from regions separated by various features including historical, financial, cultural, political aspects, aside from time and space . Very few, if any, of our present problems such as biodivers...
Poster
Full-text available
The challenges of Reproducibility and Replicability (R&R) have become a focus of attention in order to promote open and accessible research. Therefore, efforts have been made to develop good practices for R&R in the area of computer science. Nevertheless, Deep Learning (DL) based experiments remain difficult to reproduce by others due to the comple...
Poster
Full-text available
In computer science, there are more and more efforts to improve reproducibility. However, it is still difficult to reproduce the experiments of other scientists, and even more difficult when it comes to Deep Learning (DL). Making a DL research experiment reproducible requires a lot of work to document, verify, and make the system usable. These chal...
Presentation
Full-text available
This presentation is a contribution from the PARSEC team. PARSEC is a project sponsored by the Belmont Forum as part of its Collaborative Research Action (CRA) on Science-Driven e-Infrastructures Innovation (SEI), with funding from FAPESP, the ANR, JST and the NSF, with collaborators from Australia, and support from the synthesis centre CESAB of th...
Presentation
Full-text available
Environmental science teams are characteristically multi-disciplinary, multi-national, and multi-organisational. The environmental and ecological challenges that face us make these characteristics unavoidable if the best open science is to be achieved. The importance of ensuring the terms that describe shared data, and indeed information, are well-...
Article
Full-text available
Sharing sensitive data is a specific challenge for research infrastructures in the field of life sciences. For that reason a toolbox has been developed, providing resources for researchers who wish to share and use sensitive data, to support the workflows for handling these kinds of digital objects. Common and community approved annotations are req...
Article
Full-text available
Socioeconomic indicators are essential to help design and monitor the impact of public policies on society. Such indicators are usually obtained through census data collected at 10-year intervals, which are not only temporally coarse but expensive. Over recent years other ways of collecting data and producing these indicators have been explored, in...
Article
Full-text available
Background In the French West Indies, more than 20 species of cetaceans have been observed over the last decades. The recognition of this hotspot of biodiversity of marine mammals, observed in the French Exclusive Economic Zone of the West Indies, motivated the French government to create in 2010 a marine protected area (MPA) dedicated to the conse...
Article
Full-text available
Background: The coronavirus disease 2019 (COVID-19) global pandemic required a rapid and effective response. This included ethical and legally appropriate sharing of data. The European Commission (EC) called upon the Research Data Alliance (RDA) to recruit experts worldwide to quickly develop recommendations and guidelines for COVID-related data sh...
Poster
Full-text available
We are now facing profound changes (biodiversity, climate, pandemic, etc.). Human impacts and their mitigation will depend on our ability to mobilize research at the global level. The sustainable development of the society will largely depend on the sustainable development of global science and scientific research tools, outputs, and research ecosy...
Data
Database collected as part of the Lorraine Coché master's 2 internship "Inventory and structuring of marine mammal observation data around Guadeloupe" in 2020 (Master Tropical marine ecosystems at the University of the Antilles). This database centralizes and harmonizes the data collected by the team of the Agoa Sanctuary (Aire Marine Protégée), th...
Poster
Full-text available
The IG objectives will be informed by the community. We take the following objectives as a starting point: • Develop a shared understanding and refined definition of sensitive data. • Define various levels of sensitivity for data and develop tools to assess this sensitivity. • Develop an understanding of how sensitivity relates to openness. • Ident...
Preprint
In this paper, we report on the outputs and adoption of the Agrisemantics Working Group of the Research Data Alliance (RDA), consisting of a set of recommendations to facilitate the adoption of semantic technologies and methods for the purpose of data interoperability in the field of agriculture and nutrition. From 2016 to 2019, the group gathered...
Article
Full-text available
Making data compliant with the FAIR Data principles (Findable, Accessible, Interoperable, Reusable) is still a challenge for many researchers, who are not sure which criteria should be met first and how. Illustrated with experimental data tables associated with a Design of Experiments, we propose an approach that can serve as a model for research d...
Article
Full-text available
In this paper, we report on the outputs and adoption of the Agrisemantics Working Group of the Research Data Alliance (RDA), consisting of a set of recommendations to facilitate the adoption of semantic technologies and methods for the purpose of data interoperability in the field of agriculture and nutrition. From 2016 to 2019, the group gathered...
Poster
Full-text available
Reducing the risk of misuse of data is particularly crucial in the context of research on highly pathogenic agents. But as demonstrated during the COVID19 crisis, sharing data of high quality is a sine qua non condition to compare research results at a large scale. Our actual challenge is to ensure compliance with the FAIR principles while taking i...
Poster
Full-text available
In the PARSEC project, our team of data science experts are partnering with our multi-country synthesis science research team to build relevant tools and processes for better data and software management that integrate into the research lifecycle and are to be shared with the wider research community. This poster articulates the technology challeng...
Article
Autonomous Reef Monitoring Structures (ARMS) have been applied worldwide to characterize the critical yet frequently overlooked biodiversity patterns of marine benthic organisms. In order to disentangle the relevance of environmental factors in benthic patterns, here, through standardized metabarcoding protocols, we analyse sessile and mobile (<2 m...
Presentation
Full-text available
présentation du RDA SHARC interet group (Sharing Rewards and Credit) Co-chairs: R. David, L. Mabile, A. Cambon-Thomsen https://www.rd-alliance.org/groups/sharing-rewards-and-credit-sharc-ig Observation: Malgré de nombreuses annonces / promotion active, le partage de données selon les principes FAIR n'est toujours pas effectif dans la plupart des c...
Article
Full-text available
The SHARC Interest Group of the Research Data Alliance was established to improve research crediting and rewarding mechanisms for scientists who wish to organise their data (and material resources) for community sharing. This requires that data are findable and accessible on the Web, and comply with shared standards making them interoperable and re...
Presentation
Full-text available
In addition to the iPoster prepared for the session, this presentation provides an overview of the Data and Digital Output Management Plan and Workbook developed for the PARSEC project. The Workbook and the supporting checklist are outputs designed to be shared broadly in the community with supporting materials for use by Earth, space, and environm...
Article
Full-text available
• 1. The coralligenous habitat was studied at the large Mediterranean scale, by applying a standardized, non‐destructive photo‐sampling protocol, developed in the framework of the CIGESMED project. • 2. The results provided evidence to support the following statements: (a) the assemblage pattern is not homogeneously distributed across the four Medi...
Technical Report
Full-text available
PARSEC Data and Digital Output Management Plan and Workbook for the Belmont Forum Collaborative Research Action (CRA) Science-driven e-Infrastructure Innovation (SEI) for the Enhancement of Transnational, Interdisciplinary and Transdisciplinary Data Use in Environmental Change Project Building New Tools for Data Sharing and Reuse through a Trans...
Poster
Full-text available
Despite the fact that the implementation of the FAIR principles (Findable, Accessible, Reusable, Interoperable) has become necessary in new research projects to meet the requirements of funding organisations and respond to some funders calls, many institutions do not consider data sharing through implementation of the FAIR principles as a research...
Preprint
Full-text available
Phenotyping experiments are made in various installations from greenhouses to lean field. These different experiments tend to answer agricultural challenges such as food security. The plant phenotyping handles a multitude of different objects, from biological and genetical material to weather data by phenotypic traits measures. This multitude of ob...
Technical Report
Full-text available
a mixed informative and interactive session with speakers and audience. Objectives of the joint meeting; Goals of the group’s project; current standing; A. Cambon-Thomsen, 5 min; Towards SHARC recommendations / guidance? L. Mabile 5 min FAIR criteria assessment survey results, Romain David 5 min How can the FAIR criteria best be employed in gu...
Presentation
Full-text available
RDA & RDA VRE interest groups and tools “Virtual Research Environments - Working towards building a common reference model and a catalogue of design patterns for VREs" Contenu tiré du site RDA Ateliers APSEM 2019
Poster
Full-text available
The EPPN2020 is a research project funded by Horizon 2020 Programme of the EU that will provide European public and private scientific sectors with access to a wide range of state-of-the-art plant phenotyping installations, techniques and methods. Specifically, EPPN2020 includes access to 31 plant phenotyping installations, and joint research activ...
Poster
Full-text available
FAIRisation: includes all the necessary processes to implement FAIR principles from the moment a political decision has been validated in this direction. It includes pre-Fairification steps, FAIRification steps and evaluation steps for each aspect of FAIRification. Pre-FAIRification: Processes necessary in a community to permit the FAIR principles...
Chapter
Improving data identification and tagging for more effective decision making in agriculture
Poster
Full-text available
The immunogenetics community is characterised by a widespread international collaboration between laboratories with exchange of biological samples and data. However, the researchers who are involved in building and curating bioresources do not always get the credit they deserve and this is an obstacle for sharing practices. Several international in...
Presentation
Full-text available
Object identification Objects: plants, plots, experiments, sensors, events, etc Identification: persistent, unambiguous, resolvable Variable naming and formalization Give (local or global) name to variables What (concept), How, Associated controlled contexts Data interoperability Formats, schemas, semantic Representation compatibility and consist...
Poster
Full-text available
The SHARC (SHAring Reward & Credit) interest group (IG) is an interdisciplinary group set up in the framework of RDA (Research Data Alliance) to improve crediting and rewarding mechanisms in the sharing process throughout the data life cycle. Notably, one of the objectives is to promote data sharing activities in research assessment schemes at nati...
Presentation
Full-text available
Short introduction describing the scope of the group and if any previous activities Data sharing statements and promotion face a challenging reality, as many obstacles remain on several fronts. Among them is the lack of relevant and recognized rewarding mechanisms for the very specific efforts required to share organized datasets and physical res...
Poster
Full-text available
Plant phenomics datasets are unprecedented resources for identifying and testing novel mechanisms and models. These datasets need to be reusable to the scientific community. Their analysis requires the understanding of relevant information on thousands of plants, sensors and events. The open-source Phenotyping Hybrid Information System (PHIS) is pr...
Article
Hard substrata Monitoring Settlement Scientific diving A B S T R A C T We investigated the validity of Autonomous Reef Monitoring Structures (ARMS) as monitoring tools for hard bottoms across a wide geographic and environmental range. We deployed 36 ARMS in the northeast Atlantic, northwest Mediterranean, Adriatic and Red Sea at 7-17 m depth. After...
Presentation
Full-text available
What for? to foster data sharing by improving recognition of the work required How? by providing a set of recommendations to guide researchers and other relevant stakeholders (research institutions administrators, funders, policy makers and publishers/editors) in moving through the necessary steps towards crediting and rewarding in the data/resourc...
Conference Paper
Full-text available
Coralligenous habitats are bioconstructed, emblematic habitats of the Mediterranean Sea, which display a remarkably complex tridimensional structure and are considered as one of the most important biodiversity hotspots of the Mediterranean Sea. In order to assess the specific diversity of these habitats we sampled small surfaces (10 cm 2) of these...
Poster
Full-text available
SHARC (SHAring Reward & Credit) est un groupe d'intérêt scientifique interdisciplinaire créé dans le cadre de RDA (Research Data Alliance) dans le but de faciliter le partage des données de recherche (et des ressources) par la valorisation de l'ensemble des activités pré-requises à ce partage, tout au long du cycle de vie des données. Dans ce cadre...
Article
The understanding of ecosystem services is essential to support sustainable use and preservation of ecosystems. Coralligenous habitats, main contributors of the Mediterranean marine biodiversity, are yet understudied in term of services provided. This study presents an original small-scale approach to investigate the services provided by coralligen...
Poster
Full-text available
The RDA-SHARC (SHAring Reward & Credit) interest group is an interdisciplinary volunteer member-based group set up as part of RDA (Research Data Alliance) to unpack and improve crediting and rewarding mechanisms in the sharing process throughout the data life cycle. Background and objectives of this group are reported here. Notably, one of the obje...
Presentation
Full-text available
Coralligenous habitats are emblematic biogenic constructions of the Mediterranean Sea built-up in dim light conditions by organisms from various phylogenetic groups such as calcareous coralline algae (CCA), bryozoans, polychaetes, cnidarians, mollusks, sponges, crustaceans and foraminiferans (Ballesteros 2006). The resulting framework harbors micro...
Article
Full-text available
In a world of declining biodiversity, monitoring is becoming crucial. Molecular methods, such as metabarcoding, have the potential to rapidly expand our knowledge of biodiversity, supporting assessment, management, and conservation. In the marine environment, where hard substrata are more difficult to access than soft bottoms for quantitative ecolo...
Thesis
Full-text available
Dans le domaine de l’environnement marin, des protocoles d’observation développés dans de nombreux cadres produisent un grand volume de données hétérogènes, difficiles à agréger car centrées sur l’utilisation souvent spécifique à un métier. L’accès et le partage des données à large échelle est pourtant incontournable pour mieux cerner les enjeux de...
Article
Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes...
Article
Full-text available
The one thing in common “archaeological”, “biodiversity” or “social systems” studies share is that data production is both expensive and few automated. Long time series and / or large spatial surveys are difficult to conduct, since it is necessary to use several observers. The robustness and reproducibility of the observation are also harder to get...
Article
Full-text available
The one thing in common “archaeological”, “biodiversity” or “social systems” studies share is that data production is both expensive and few automated. Long time series and / or large spatial surveys are difficult to conduct, since it is necessary to use several observers. The robustness and reproducibility of the observation are also harder to get...
Presentation
Full-text available
In the current context of climate change, variations in sea surface temperature, sea level change, and latitudinal shifts of currents and hydrological fronts are expected to affect marine biodiversity of the Sub-Antarctic Islands located near the Polar Front, such as the Kerguelen Islands, particularly in coastal waters. Characterizing the impact o...
Conference Paper
Full-text available
Journées Sciences de Données du GdR MaDICS Les journées MaDICS ont eu lieu les 22 et 23 juin à l’École de Management de Marseille (EDM), co-organisées localement par des laboratoires CNRS / Aix-Marseille Université (CPPM, IMBE, LAM). MaDICS (Masses de Données, Informations et Connaissances en Sciences) est un groupement de recherche (GdR) qui perm...
Poster
Full-text available
Data produced by biodiversity research projects that evaluate and monitor Good Environmental Status have a high potential for use by stakeholders involved in [marine] environmental management. The lack of specific scientific objectives, poor organizational logic, and a characteristically disorganized collection of information leads to a decentraliz...
Research
Full-text available
Since last year, the researchers of our institute organize public conferences: once a month (the last wednesday of each month) at the Endoume Marine Station (Marseille). join us!
Conference Paper
Full-text available
Artificial sampling units (ASUs) allow for standardized sampling in the marine environment. We deployed ASUs at three sites in the Bay of Marseille for 14 months to measure the diversity and community composition of macroinvertebrates within and among sites. Invertebrates were identified morphologically to the class level. At this resolution, varia...
Conference Paper
Full-text available
Coralligenous habitats are bioconstructed, emblematic habitats of the Mediterranean Sea which presents a remarkably complex 3D structure resulting of the permanent dynamics between bioerosion and bioconstructions. This highly complex framework represents an habitat for around 1600 species and is so considered as one of the most important biodiversi...
Presentation
Full-text available
Data produced by biodiversity research projects that evaluate and monitor Good Environmental Status have a high potential for use by stakeholders involved in [marine] environmental management. The lack of specific scientific objectives, poor organizational logic, and a characteristically disorganized collection of information leads to a decentraliz...
Technical Report
Full-text available
Coralligenous is a hard-bottom mainly biogenic habitat, produced by the agglomeration of calcareous encrusting algae growing in dim-light conditions. It is characterized by high structural complexity and spatial heterogeneity, thus supporting rich biodiversity and a variety of sessile assemblages, shaping a typical and one of the most important hab...