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Towards an e-infrastructure in agriculture?
The document discusses the BlueBridge project, which aims to develop e-infrastructure for agriculture and marine resource management, supported by the European Union's Horizon 2020 funding. It emphasizes the importance of virtual research environments (VREs) for data collection, sharing, and collaborative research among various stakeholders in fisheries and aquaculture. The project focuses on promoting interdisciplinary collaboration, effective data management, and innovation in resource management practices.
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Towards an e-infrastructure in agriculture?
- 1. BlueBRIDGE receives fundingfrom the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 675680 www.bluebridge-vres.eu Towards an e-infrastructure in agriculture? Donatella Castelli, CNR-ISTI CNR-ISTI donatella.castelli@isti.cnr.it Euragri Workshop Big data in agriculture: consequences for research and research organizations 9 March 2016, Paris
- 2. Outline • iMarine &its Virtual Research Environments • BlueBRIDGE Virtual (Research) Environments • Final remarks Euragri Workshop, 9 March 2016, INRA, Paris
- 3. Terminology (1) Euragri Workshop,9 March 2016, INRA, Paris e-Infrastructure Elecronic platform operated by a responsible entity offering an open set of basic enabling services (including access to resources) to a Community of Practice (CoP). Through the e-Infrastructure the CoP realises economy of scale. Data infrastructure “e-Infrastructure” offering services for collection, deposition, storage, preservation, access, retrieval, analysis/mining/processing, publication, etc.
- 4. Terminology (2) Euragri Workshop,9 March 2016, INRA, Paris The Community of Practice (the community) The e-infrastructure (the operational platform) The system (the enabling sw system)
- 5. Launch an initiativeaimed at establishing and operating an e-infrastructure contributing to the implementation of the principles of the Ecosystem Approach to Fisheries Management and Conservation of Marine Living Resources iMarine Euragri Workshop, 9 March 2016, INRA, Paris
- 6. iMarine CoP needs Howto facitate the implementation of the an Ecosystem Approach to fisheries management and conservation of marine living resources? Euragri Workshop, 9 March 2016, INRA, Paris Interdisciplinary & multifacets collaboration at the local, national, regional and international levels Knowledge generation - Access to large amount of heterogeneous, distribuited, across-domain data - Rich data mining, analysis and processing capabilities
- 7. Data Infrastructure forthe iMarine CoP Euragri Workshop, 9 March 2016, INRA, Paris Services “in the style of cloud”
- 8. Leveraging others’ resources Ownresources Third-party providers Euragri Workshop, 9 March 2016, INRA, Paris
- 9. Leveraging others’ resources Ownresources Third-party providers Euragri Workshop, 9 March 2016, INRA, Paris
- 10. Hetogeneous datasets Euragri Workshop,9 March 2016, INRA, Paris Semantic Data Biodiversity data Geospatial data Statistical data Documents OAI-PMH, DC, OpenSearch RDF, OWL DwC, DwC-A ISO19139 (OGC W*S) SDMX*
- 11. VRE as-a-Service Euragri Workshop,9 March 2016, INRA, Paris e-Infrastructure VRE VRE VRE • web-based working environment • providing access to services and resources tailored to serve the needs of a community of practice in accomplishing a specific goal • open and flexible with respect to service offering and lifetime • providing fine-grained controlled sharing of both intermediate and final research results • Very low cost of creation and operation Virtual Research Environment
- 12. VRE Definition Euragri Workshop,9 March 2016, INRA, Paris 3. Configure applications 2. Select applications1. Specify VRE metadata (including policies) 4. Select data collections Hardware setup and software deployment completely hidden Evolving needs of its users completely supported
- 13. Collaborative Environment Euragri Workshop,9 March 2016, INRA, Paris Share Updates User news feed VREs user is a member of A single point to Get status and updates from applications and other users they are interested in; Get notifications about messages, jobs completion, new generated products, etc.
- 14. Workspace A single placeto • Manage data, store and preserve them • Share data Euragri Workshop, 9 March 2016, INRA, Paris
- 15. Working within aVRE (1) The user • Stores data in a personal workspace • Visualizes and harmonizes data • Saves the results for further exploitations • Shares with his/her colleagues Euragri Workshop, 9 March 2016, INRA, Paris
- 16. Working within aVRE (2) The user • Stores software in a personal workspace • Prepares it for execution with a simple interface (one shot process, never to repeat) • Executes it and analyses the results • Modifies the code in the workspace • Shares software and/or results with his/her colleagues Euragri Workshop, 9 March 2016, INRA, Paris
- 17. iMarine VREs Euragri Workshop,9 March 2016, INRA, Paris iMarine Gateway https://i-marine.d4science.org/ • Public VREs (used to offer an application environment to a subset of users of a community) • Private VREs (used for experiments, data access and preparation, and data analytics)
- 18. Scalable Data MiningVRE Tabular Data Manager (TabMan) Statistical Manager (StatMan) Analytics Data preparation & access Monitoring the status of the computation Single environment Euragri Workshop, 9 March 2016, INRA, Paris
- 19. Tabular Data Manager(TabMan) • Manipulates Big Tabular Datasets • Prepares data for analyses • Makes data compliant with external code lists • Visualizes, represents and inspects data Euragri Workshop, 9 March 2016, INRA, Paris
- 20. TabMan imports datasetswith tuna catch statistics Yellowfin Skipjack TabMan Euragri Workshop, 9 March 2016, INRA, Paris
- 21. Modifying columns TabMan Euragri Workshop,9 March 2016, INRA, Paris
- 22. Data Curation b. Columnsplitting using regular expressions c. Changing columns types and Codelists compliancy e. Denormalization: one column per row value a. Duplicates deletion d. Produce a new codelist TabMan Euragri Workshop, 9 March 2016, INRA, Paris
- 23. Adding Geometries TabMan Euragri Workshop,9 March 2016, INRA, Paris
- 24. Csquare codes andFAO Ocean Areas codes TabMan Euragri Workshop, 9 March 2016, INRA, Paris
- 25. GIS maps publishedunder standard formats (WMS, WFS, WCS) TabMan Euragri Workshop, 9 March 2016, INRA, Paris
- 26. Tuna Atlas VRE •Represents world wide Tuna catches in an interactive map • Centralize and harmonize Tuna RFMOs Statistics with a common format • Share the approach with other institutions with different exploitations FAO Tuna Atlas • Create a Virtual Research Environment • Centralise and harmonise catch statistics coming from heterogeneous sources • Modify and analyse tabular datasets • Visualise and summarize information and trends D4Science support to Tuna Atlas FIC_ITEM NAME_E ALPHA 3CODE 2494 Skipjack tuna SKJ 2496 Albacore ALB 2497 Yellowfin tuna YFT 2498 Bigeye tuna BET 2500 Black marlin BLM 2501 Striped marlin MLS 2503 Swordfish SWO 3296 Atlantic bluefin t BFT 3298 Southern bluefin t SBF 3303 Blue marlin BUM 3305 Atlantic white mar WHM 18734 Pacific bluefin tu PBF
- 27. Statistical Data Manager(StatMan) • 100+ statistical models • Transparent use of cloud computing • Automatically generated interfaces • Integration with R Data access Monitoring the status of the computation
- 28. Statistical Manager (StatMan) External Computing Facility OGC WPS Interface Datastandardisation services Statistical services WPS
- 29. 100+ Hosted algorithms EuragriWorkshop, 9 March 2016, INRA, Paris
- 30. Algorithms categories Anomalies Detection(4) Classification (1) Climate (4) Correlation Analysis (1) Data Clustering (4) Filtering (2) Function Simulation (1) Occurrences (8) Performances Evaluation (2) Species Simulation (6) Training (2) Time Series (2) Euragri Workshop, 9 March 2016, INRA, Paris Taxa (5) Maps (7) Geo Processing (14) Bayesian Methods (5) Obis Observations Species Data (3) Obis Observations Trends (4) SPECIES Procedures (2) Vessels (3) Databases (9) Spread (4) Charts (4) Precipitations (2) Stock Assessment (7)
- 31. Stock assessment Length-Weight Relations:estimates Length- Weight relation parameters for marine species, using Bayesian methods. Developed by R. Froese, T. Thorson and R. B. Reyes SGVM interpolation: interpolation of vessels trajectories. Developed by the Study Group on VMS, involving ICES FAO MSY: stock assessment for FAO catch data. Developed by the Resource Use and Conservation Division of the FAO Fisheries and Aquaculture Department (ref. Y. Ye) ICCAT VPA: stock assessment method for International Commission for the Conservation of Atlantic Tunas (ICCAT) data. Developed by Ifremer and IRD (ref. S. Bonhommeau, J. Bard) CMSY:estimates Maximum Sustainable Yield from catch statistics. Prime choice for ICES as main stock assessment tool. Developed by R. Froese, G. Coro, N. Demirel, K. Kleisner and H. Winker Atlantic herring D4Science reduced time-to-market: State-of-the-art models to estimate Maximum Sustainable Yield computational time reduced of 95% in average
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- 34. Geospatial data processing Maps comparison NetCDF file Dataextraction Signal processing Periodicity detection Maps generation
- 35. Forecasting and analysisusing an online R development environment TabMan Euragri Workshop, 9 March 2016, INRA, Paris
- 36. Algorithm Importer Reduce computationtime Reduce integration time Publish algorithm as-a-Service Manage access policies Provenance Management Accounting No software required on desktop machines Code is not disclosed Euragri Workshop, 9 March 2016, INRA, Paris
- 37. Interfaces 1 - iMarine portal 2-QGIS (via WPS Client) 3 -WPS Euragri Workshop, 9 March 2016, INRA, Paris
- 38. Computations history and summary Data importing facilities Computationsand data Euragri Workshop, 9 March 2016, INRA, Paris
- 39. Data exploring and tablesvisualisation facilities Data Management Euragri Workshop, 9 March 2016, INRA, Paris
- 40. Data collection: SmartFormVRE Euragri Workshop, 9 March 2016, INRA, Paris Select a Fishery survey Define forms, controlled vocabularies, …. Validate& Enrich Deposit Analyse
- 41. BioDiversityLab: uniform access todata Euragri Workshop, 9 March 2016, INRA, Paris
- 42. Report production: VME-DB EuragriWorkshop, 9 March 2016, INRA, Paris The International Guidelines for the Management of Deep-Sea Fisheries on the High Seas. VME database to assist in informed decision making and the development of further measures to increase sustainability and reduce impacts. VME record Specific measures Description (Habitat & Biology) RFMO General Measures Meetings & other Sources of Information Historical information on fishing areas and closed areas Time
- 43. iMarine experience Euragri Workshop,9 March 2016, INRA, Paris Research Scientific advice Educa tion Product innovation
- 44. BlueBRIDGE (Sept. 2015 –Feb. 2018) Euragri Workshop, 9 March 2016, INRA, Paris Building Research environments fostering Innovation, Decision making, Governance and Education for Blue growth
- 45. Target stakeholders Euragri Workshop,9 March 2016, INRA, Paris SMEseducators scientific authorities reseachers
- 46. Expected impact Euragri Workshop,9 March 2016, INRA, Paris Support capacity building & Innovate current practices of interdisciplinary communities actively involved in increasing scientific knowledge about resource overexploitation, degraded environment and ecosystem More solid ground for informed advice to competent authorities Cost effective training & knowledge bridging between research and innovation Enlarged spectrum of growth opportunities Researchers Scientists producing indicators Trainers Enterprises
- 47. Six interrelated detailed objectives EuragriWorkshop, 9 March 2016, INRA, Paris Supporting the collaborative production of scientific knowledge required for assessing the status of fish stocks and producing a global record of stocks and fisheries Blue Assessment Supporting the production of scientific knowledge for analysing socio- economic performance in aquaculture Blue Economy Supporting the production of scientific knowledge for fisheries & habitat degradation monitoring Blue Environment Boosting education and knowl. bridging between research &innovation in the area of protection and mgmt of marine resources Blue Skill Developing and deploying service and resource commons across VREs to facilitate the exploitation of existing infrastructure resourcesBlue Commons Ensuring uptake of the BlueBRIDGE tools and services, with specifc focus on SMEs, other scientific domains & policy making contextsBlue Uptake
- 48. Specific Areas Euragri Workshop,9 March 2016, INRA, Paris • Stock Assessment VRE • Global record of Stocks and Fisheries VRE Blue Assessment • Performance evaluation, benchmarking and decision making in aquaculture VRE • Strategic Investment analysis and Scient. Planning/Alerting VRE Blue Economy • Aquaculture Atlas Generation VRE • Protected Area Impact Maps VRE Blue Environment • ICES Knowledge Bridging • IRD Knowledge Bridging • Knowledge Bridging Programmes Blue Skill
- 49. Supported Training Workflow Trainers •Trainers check the catalogue of applications and datasets • Request integration of new applications and datasets BB • BB Support team checks the course specification and support the integration • VRE is created Trainees • Trainees are invited to join the VRE • Use the VRE and interact with the trainers via VRE social facilities • Exploit the VRE tools to perform hands-on and examination Trainees • May still use the VRE for accessing data and tools • May still interact with other users • May still perform analysis and access course materials Euragri Workshop, 9 March 2016, INRA, Paris
- 50. Final Remarks • Themarine and agriculture sectors have many similar needs in term of data management services • By construction D4Science/iMarine have been built for being able to easy accomodates other needs (e.g. framework, standard protocols, integration of external algorithms, VREs) • Open to investigate collaborations and synergies Euragri Workshop, 9 March 2016, INRA, Paris
- 51. Euragri Workshop, 9March 2016, INRA, Paris www.i-marine.eu www.bluebridge-vres.eu https://www.gcube-system.org/ www.d4science.org
Editor's Notes
- #28 People can contribute with: R scripts Java programs Linux programs OGC-WPS services
- #29 Several formats: NetCDF, WFS, WCS, Esri-Grid, GeoTiff – CSV, RDB - DwC
- #41 The App Login form Username / Password Select a Fishery survey Behind the screens User must be registered to infrastructure At infra level users are assigned surveys
- #43 FishFinder - FAO Aquatic Species fact sheets DIAS - FAO Database on Introductions of Aquatic Species FIRMS - Marine Resource and Fishery fact sheets ABNJ - Deep seas SEAFO interactive mapping pilot
- #45 Today important societal challenges raise questions that are not restricted to a specific sector or discipline. Nevertheless, most of the data and knowledge exchange still occurs in “silos”. BlueBRIDGE fills this gap, by simplifying sharing and re-use of knowledge produced in these sectors and facilitating collaboration among their actors on relevant societal challenges or community specific questions. In particular, BlueBRIDGE supports activities contributing to the H2020 Blue Growth Societal challenge with a strong focus on sustainablegrowth. Trasform the research data in societal data