Research Ideas and Outcomes : Research Idea
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Corresponding author: Annalisa Minelli (annalisa.minelli@ve.ismar.cnr.it)
Received: 04 Feb 2018 | Published: 06 Feb 2018
© 2018 Annalisa Minelli, Alessandro Oggioni, Alessandra Pugnetti, Alessandro Sarretta, Mauro Bastianini, Caterina Bergami, Fabrizio Bernardi Aubry, Elisa Camatti, Tiziano Scovacricchi, Giorgio Socal
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Minelli A, Oggioni A, Pugnetti A, Sarretta A, Bastianini M, Bergami C, Bernardi Aubry F, Camatti E, Scovacricchi T, Socal G (2018) The project EcoNAOS: vision and practice towards an open approach in the Northern Adriatic Sea ecological observatory. Research Ideas and Outcomes 4: e24224. https://doi.org/10.3897/rio.4.e24224
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The Open Science approach delineates high and inspiring principles. In order to really root them into the scientific community, a cultural shift must occur that can be fostered and achieved mainly through the development of practical case studies. This is particularly relevant in the field of ecology, a highly multidisciplinary science, where the Open Science issue has become a matter of discussion only in very recent years. In particular, in the context of long-term ecological research, enabling open sharing of in-situ and derived long-term ecological data is required to advance research and education in the European and global networks.
The creation of marine ecological observatories, able to arrange and maintain integrated, harmonized and coherent long-term ecological observations, is stressed as a relevant step at the European level, for sustaining European marine policies. The Italian national flagship project RITMARE (“Italian research for the sea”, http://www.ritmare.it/en/) fostered the development of a marine ecological observatory in the Northern Adriatic Sea (NAS), one of the 25 research parent sites belonging to the Italian Long-Term Ecological Research Network (LTER-Italy, http://www.lteritalia.it), through a dedicated research line. Within this context, we developed a specific task, aimed at testing and applying the Open Science approach to the NAS ecological observatory: “EcoNAOS - Ecological Northern Adriatic Open Science Observatory System”. We present our plans and ideas for the application of the Open Science principles, starting from the 50-year ecological dataset of plankton and related biogeochemical parameters collected in the NAS, mainly in the Gulf of Venice. We introduce each of the different steps needed for “opening science”: research ideas statement, raw data collection, data harmonization (structural, syntactic and semantic), ancillary data collection/recovery and metadatation, data and metadata publication, software publication, publication of results, and data citation. In order to share different expertise and include different points of view as essential outcomes themselves, researchers from the field of LTER and data management were involved in EcoNAOS since its start. Our final goal is to demonstrate that a change of vision is possible, leading from “publishing ASAP” to “sharing data and information and collaborating ASAP”.
LTER-Italy, Northern Adriatic Sea, Open Science, marine ecological data, Open Access, Research project lifecycle
A critical global and regional issue is the man-induced changing of the marine ecosystem, which threatens its sustainable use by present and future generations. Significant challenges still persist in developing and delivering the sound ecological knowledge necessary to assess the on-going changes and their impact on the sustainable use of the sea and on the consequences for the protection strategies. This requires an innovative integration of ecological and oceanographic research and conservation monitoring programmes, across a wide range of temporal and spatial scales. The creation of marine ecological observatories, able to arrange and maintain integrated, harmonized and coherent long-term ecological observations, is actually stressed as a relevant step at the European level, for sustaining European marine policies (see, e.g., the
The Northern Adriatic Sea (NAS) is a significant geographical zone for the establishment of a marine ecological observatory, due to the concomitant presence of high degree of biodiversity, sensitive habitats and ecosystems, numerous on-going monitoring and research activities, as well as of heavy and diversified human pressures and economic interests, based on the marine resources of the area. It is one of the 25 parent sites belonging to the LTER-Italy (Long-Term Ecosystem research) network: it is composed by 4 LTER research sites (Fig.
The LTER-Italy parent site "Northern Adriatic Sea". The four research sites that compose it, together with the fixed point observatories, are evidenced. 1: Gulf of Trieste and Mambo buoy, 2: Gulf of Venice and Acqua Alta Tower, 3: Po Delta and Romagna Coast and S1-GB and E1 buoys, 4: Senigallia-Susak Transect and TeleSenigallia Pylon (
The Italian national flagship project RITMARE (“Italian research for the sea”), funded by the Italian Ministry of University and Research, dedicated a Research Line to the establishment of a marine ecological observatory in the NAS: building on the existing facilities, infrastructures and long-term ecological data, it aims at enhancing and aligning the marine observational capacities and at activating synergies among the main conservation management questions and key ecological and oceanographic variables.
Along this process, it is crucial to start the implementation of the Open Access and Open Science principles, by creating an open research lifecycle, which involves sharing each step of the process, including not only results (scientific papers) but also data (raw and processed), metadata, methods and software. We introduce here each of the different steps planned for “Opening Science” in this context: research ideas statement, raw data collection, data harmonization (structural, syntactic and semantic), ancillary data collection/recovery and metadatation, data and metadata publication, software publication, publication of results, and data citation. The whole process of application of the Open Science principles to the NAS ecological observatory will be referred in the text, from now on, as the project "EcoNAOS” (Ecological Northern Adriatic Open Science Observatory System).
The Open Science concept comes as far back as the early 1980s, when the need for an Open Source code was first expressed and formalized by R. M. Stallmann with the GNU project (
Open Science is actually also one of the key thematic elements of RRI - Responsible Research and Innovation (
From the researchers point of view, open practices can give advantage to gain more citations, media attention, potential collaborators, job and funding opportunities (
In the field of ecology, the Open Science issue is a matter of interest and discussion only in quite recent years (
The Open Science approach delineates high and inspiring principles to be followed. However, in order to really root them into the scientific community, a cultural shift must occur. This can be fostered and achieved mainly through the development of practical case studies and projects, where the cultural resistances and uncertainties could be evidenced, appreciated instead of neglected, and included as parts of the path towards Open Science. In this article we present plans and ideas for the application of the Open Science principles to the marine domain in LTER Italy, in the context of the establishment of the NAS marine ecological observatory. The focus will be, as a starting point, on the long-term data on plankton and related abiotic factors produced in 50 years of oceanographic cruises in the NAS, prevalently in one of its 4 research sites: the Gulf of Venice (Fig.
Publishing and sharing the different phases of the research process involves not only results, but also ideas, data collection and elaboration, metadata and tools construction. Many possible integrations, reuse and different implementations in the frame of Open Science could lead to growth, improvement, and widening of the research process as a whole. Starting from the circular model conceived by
The spiral model can be applied to many different research topics, because it follows the entire lifecycle of the research, from data collection to results publication. We used as input a specific dataset: 50 years of data on abiotic parameters, phytoplankton and zooplankton, gathered from 1965 until 2015 at the LTER-Italy parent site NAS, prevalently in the Gulf of Venice, from oceanographic cruises and, more recently, fixed observation points. The dataset has been produced by the Institute of Marine Sciences of the National Research Council of Italy (ISMAR-CNR), located in Venice, using different methodologies, which changed according to sampling and laboratory instruments and technologies available in different times or to research interests. The data is composed by parameters quite heterogeneous in type, number, geographical distribution and semantics. An example is reported in Fig.
An extract from data collected since 1965 to today in the NAS.
The data have been stored in paper registries and in spreadsheets. Old data have been recovered from paper registries and transcribed. Due to its relatively small dimension (about 60.000 records) the dataset currently is managed as a unique spreadsheet. A lot of raw (coming directly from sensors), semi-elaborated (first pruned data, e.g. from on board instruments) and elaborated data (e.g. coming from laboratory analysis) are available.
The elaboration of the datasets will be worked out by a small group of plankton ecologists and data management experts, with the aim of sharing and harmonizing as well the different experiences, needs and points of view. This collaboration is an important step to contribute overcoming cultural differences, barriers and fragmentation that might represent an obstacle for Open Science. The inclusion of the different attitudes and specificities allows flexibility and fosters finding jointly proper solutions and incentives.
A participatory process will be set up, for the whole duration of EcoNAOS. In fact, it is fundamental in order for the project to be successful, to involve and interest each researcher working with the specific dataset, receiving and accepting feedbacks, suggestions and evaluations at each step of EcoNAOS, driven by the spiral model and described in detail in the following paragraphs. The concepts and the outcomes of EcoNAOS will be tested on its applicability involving researchers from the LTER-Italy network in order to verify, within a wider but related community, the opening process effectiveness, its limits and strengths. In fact, it is important to understand perceptions and barriers (technical or cultural) with regard to Open Science and in particular Open Access applied to data, in order to find the right way to communicate Open Science and try to overcome existing obstacles.
During the whole project, we will collect impressions on the EcoNAOS ideas and development through workshops, involving institutions and research groups dealing with similar data at the LTER research sites of the NAS and at another LTER-Italy research site in the Tyrrhenian Seas (LTER Marechiara site). In these workshops we plan also to propose to our colleagues testing the opening process by the calculation of some relevant environmental quality indicators that could be executed by each institution/group using its own LTER dataset.
EcoNAOS will be organized in six main steps:
First step - Harmonization of the database. A complete harmonization, aimed to a real interoperability, includes standardisation of semantic, schemes and structure of a database (
Second step - Description of data through the collection of all the available metadata, such as information about the specific sampling cruise, the used instruments and probes, the involved researchers and operators, and so on. These metadata are supposed to be found in papers or digital archives and the aim of this specific task is not only to better describe and enrich the information related to specific data, but also to build up fundamental and affordable tools for the successive quality and consistency data check phases, and the reliability and the actual meaning of each sampled datum.
Third step - Integration of all the data in the well-established technological infrastructure created in the wider RITMARE project (
Fourth task (crosscutting all the others) - Publication of ideas, results, tools, data and metadata after an accurate Open Science framing. In this particular phase, it is important to choose the best tools in relation to the principles that guide our work and to the structure of our data. It is primarily important to us that everything could be published as soon as possible and in an Open Access environment (preferably gold road Open Access). Some solutions have already been studied: an example is the choice of RIO journal to publish these research ideas. We took this decision because it is Open Access and has a fully open and citable review process; another preferable choice appears to be the use of Github platform to share the code written from time to time. Some others solutions are still under discussion.
Fifth step - Implementation of a proper data citation system dealing also with the dynamic character of long-term data and versioning. So the issue of citing a dynamic and growing dataset (or portions of it) soon will arise. Querying an oceanographic database temporally, semantically or in relation to one or more numerical parameters is not yet a standard process, no specific rules or protocols have been created purposely (
Sixth step - Development of guidelines aimed to better explain the whole opening process. The guidelines development can only be carried on after all the others steps and it is useful to clarify each step for future applications, summarize strengths and weaknesses of EcoNAOS and express a final opinion on the efficiency/utility of the whole process. These guidelines will categorize interventions in two main principal groups: (i) interventions aimed to open the process (data policy, software, publication, citation) and (ii) interventions aimed to create F.A.I.R. data (e.g. database structure, semantic harmonization, efforts on interoperability, services available).
EcoNAOS can deliver an effective contribution to the application of the Open Science in marine ecology since:
This activity is fully in line with the data management plan of the LTER networks, at the national, European and global level, since one of the LTER mandates is actually to foster open sharing of LTER data, in order to advance socio-ecological research and education (
Lastly, this pilot project is not aimed to force the complete opening of any on-going and future research process. Instead, it has the goal to provide an overview on the current situation, as detailed as possible, on data opening and to test the feasibility of the process, identifying perspectives on the short and long-term, existing obstacles and solutions. EcoNAOS will offer as well a support to researchers in data management, using an integrated approach and stimulating cooperation among all the researchers involved , collecting their requests, doubts and observations on the wider Open Science principles applied to LTER marine themes.
The RITMARE ("La ricerca Italiana per il Mare" - "The Italian Research for the Sea") Flagship Project is one of the National Research Programmes funded by the Italian Ministry of University and Research. The funding period for the present work is 2017-2018. Funds have already been allocated.
The authors declare that there are no conflicts of interest regarding the publication of this article.