Opendata repository-v2
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open data repository for scientific data
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Opendata repository-v2
- 1. Open data repository for scientific data sharing with the southern countries Desconnets J-C, Aventurier P., Banon S., Doucouré C., CoupinT., Soumaré A. Gaborone, on 8th November 2018
- 2. Working mainly in partnership with Mediterranean and inter-tropical countries on the science of global development issues. Multidisciplinary research: health and society, climate change, humanitarian and political crises, agriculture and biodiversity, IRD : French National Research Institute for Sustainable Development Publications : 1300/Year 65 Research Unit 52 % co-publications with South Countries 2048 Agents Budget : 230 M€/Year
- 3. 3 1- Generalizing Open Access to publications 2 - Structure research data and make it available through Open Access 3- Be part of a sustainable European and international Open Science dynamic http://cache.media.enseignementsup-recherche.gouv.fr/file/Recherche/50/1/SO_A4_2018_EN_01_leger_982501.pdf OLInFER'2018. IRD Open Science, nov 2018 General context french national plan for open science
- 4. sharing new papers new citations reuse IdentificationDescriptionDiscovery Storage deposit Current practises in research community science data life cycle 4 Research project design Start of project Data acquisition Data analysis scientific paper(s) End of project data cycle during the project data cycle in data repository project bounds memory lapse data destruction add value of research work Data acquisition Research project design Start of project Data analysis end of project Data management plan scientific paper(s) data cycle during the project data cycle in data repository project bounds add value of research work
- 5. 5 IRD data repository objectives First piece for the ecosystem « data management for open science » Short term objective (2019-2020) Provide a service (platform + support + curation) to researchers to control the dissemination of their data and their preservation Mid-term objective (2020-2025) Ensure the discovery of data archived in other repositories, data centres or research infrastructures (directory function)
- 6. 6 Internally Responding to the national plan for open science Improve the knowledge and management of datasets A first "concrete" element towards an open science policy at the IRD Specific objectives Institutional issues For our southern partners Define and control the data governance instead of private repositrories Improve the accessibility of our data to Southern partners Support open science initiatives in the South (replication of the data repository, capacity building) Europe and international level Meeting the requirements of European programmes Integrate into European EOSC (European Open Science Cloud) infrastructures
- 7. 7 Data repository scope Targeted data Unstructured, undigitised data, stored in PCs, historical data not linked to internally or externally accessible databases Observatories, data centres, online databases Statistical distribution of research data (Ferguson et al., 2014)
- 8. 8 Coming from various scientific domains with differents characteristics Genomics Exploited marine ecosystems Marine and agro biodiversity Health Environment sciences Targeted data and needs With various needs and expectations from researchers Data rescue, data preservation Reproducibility of experiments DOI allocation, data papers Data Sharing over the data producers
- 9. •Limit to data discovery and access facilities •Make available FAIR data •Support metadata harvesting from OAI-PMH protocol 9 Principles for design Metadata core model (DublinCore) Standard Identification system (DOI, ORCID…) Domain categorie s Harvest Control metadata value Use Extend Specific metadata domain standard Spatial location Species taxonomies extended discovery facilities interoperability
- 10. •Digital Object identifierAllocation for each dataset • Flexibility to describe a dataset (enrich core metadata model with metadata standard coming from a specific domain) • Possibility to put data management in the hands of researchers: each data folder can be managed by a different administrator • Publication workflow which allows • Obtaining a secure temporary link for reviewers of an article related to unpublished data • Data versioning • Metrics (download, view, guest book) 10 And key user requirements
- 11. • Open source software, created in 2006 by Harvard university • Set up a local Dataverse instance and participate in the Dataverse network (CIRAD, INRA, Science Po...) • Integrate an "ecosystem" of interoperable data repositories 11 Software for data repository dataverse.org https://dataverse.org/
- 12. Data serie Data set Full text search Faceted search Dataverse Web user interface – data discovery
- 13. Data citation Dataverse Web user interface – data citation and access Associated data files
- 14. Typical use of the data repository 14 • Creation of a repository folder and training of a referent person • research units, projects can create a customizable repository folder "Dataverse", ...) Description and data deposit by researcher Validation of the deposit by a general administrator Publication of the dataset FAIR data Researchers deposit, in accordance with the data management plan, a data set in their repository folder dedicated using standardised formats and metadata to describe their data (open/ closed /embargo/ only metadata )
- 15. 15 IRD Open data repository Spring 2019 Data management plan (DMPs). Design and availability of IRD DMPTemplate Training courses for researchers . Train scientific data experts and offer real careers in these professions, which will be the bridge between IT and thematic research Reform the research assessment to encourage data sharing First element for a open science policy at IRD
- 16. 16 Contact : Desconnets Jean-Christophe Head of Mission on Infrastructures and Digital data Mission Jean-Christophe.Desconnets@ird.fr
Editor's Notes
- My talk is about an on going project conducted by IRD to set up an open …… After introducing the context of the project, I will give some elements about the objectives and the scope in term of data I introduce also the design and user requirements which guide its implementation
- Few words about IRD. IRD stands for … The main role of IRD is to work … The research unit of IRD are involved on multi disciplinary challenges such as …. Some key informations (si je ne suis pas trop long)
- The general context of this project is the open science dynamic in general and particular the open science promotes by the european comission and since this summer, officially b the french ministery of the research. French goverment proposes a national plan for open science with a roadmap in three points : - The data repository is an official answerof the IRD to the point number two of the roadmap
- other element of the context are the current practises in scientific community, in term of data sharing and openess currently, the practises in research are often orthogonal with open data initiatives The schema describles in simple way science data cycle Generally, a research begins with the design of research project. After funding allocation, the project starts and one of the first phase is the data acquisition or data simulation, the second phase is data analysis which is concluded generally by a scientific paper. In most of the case, at the end of the project, the data produced could be forget or unuseable for an other purpose. A data repository service could introduce better practise for sustainable data management and will provide functionalities to identiffy, describe, store and make findable the data for others researchers than the data producer. So the setting up of data repository could really increase the visibility of research work and finally data can use for other research projects.
- The main objectives that data repository is to build the first piece In detail we have a short term objective which is : provide…including web plateform, user support and data curation The mid term objective is to… that we can call directory function of our platform
- Horizontal axis Vertical axis
- -Genomics which provides large amount of data coming from sequencing of rice genom or palm tree genom, for instance -Marine : Coral data collection and agro biodiversity -Health could be epidemilogical data, clinical data, ebola or HIV sequencing -Data rescue : a researcher is retiring, what’s happen with the database accumulated during this career ? -Data preservation the issue is to provide secure and sufficient storage capabilities - Data Sharing over the data producers for valorization through new citations in data papers or scientific communication
- The principles which guide the implementation of the data repository are quite simple : We want to limit … Make …according the Fair principles Support metadata harvesting from OAI-PMH protocol in the perspectives of directory data and to be harvestable by other repositories or search engine The schema below shows the approach that we choose in term of interoperability and discovery facilities. The key principles is to have a generic and concise metadata model based on dublin core metadata elements To ensure semantic consistency of data description , metadata value should be valuated using organisation, person and document standard identification system To ensure semantic discovery, metadata value will be controlled for instance by domain categories list, location places or species taxonomy according to scientific domain
- After several end-users meeting,, we are gathered (collected) a first set of requirements. The main are the following : Possibility to put data management in the hands of researchers: each data space can be managed by a different administrator : the description of dataset could be done by other person than the producer Obtaining a secure temporary link for reviewers of an article related to unpublished data : it is a requirement which is more frequent during the review process of an scientific publication
- - > Integrate an "ecosystem" of interoperable data repositories. It is essential to be harvest by french, european data repository or international search engines such as re3data.org, OpenAire, data cite search and so on..
- Dataverse user interface propose classical functionalities to discover, filter the data repository with full text search and faceted search. About faceted search. Interisting detail.: Each domain community could customized the faceted search by the selection of own faceted category such as spatial coverage for enviromental data or in situ observed property such meteorological variables
- A second screen shot of dataverse user interface. When you have chose a dataset. Associated data files to download. When is necessary, Dataverse propose various way to restrict data download or oblige the user to fill a guestbook to give the reason why he want to download the dataset
- In complement of dataverse plateform, we are working on organisation around repository data cycle The objective is to have an efficient data management cycle and deliver Fair data The typical use of the data repository that we define is the following : - Publication could be done under various status : fully open, closed, put an embargo of few months, years, put conditions on data use and so on. depending on the scientific, legal restriction on dataset Finally, the content of data repository will harvest by search engines or other data repositories
- To conclude the presentation,, i want to give some perspectives to this on going work Firstable, IRD data repository will open the next Spring (nineteen nine) At short term, the data repository will be completed by - Design and support to researchers and partners to build data Management plan - We also plan to work on Training courses catalog for Researchers on Computer literacy and data management challenges we should stenghten data scientist presence at IRD in research team which are the mediator between computer science and classical research thematics At mid term We have to work to reform the research assessement system in compliance with the San fransisco Declaration on Research assessment to introduce a better value of data sharing. it will be a very long term work