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Using e-Infrastructures for Biodiversity Conservation

An introduction into the concept of Virtual Research Environments. Explaining how computer science can support communities.

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BlueBRIDGE receives funding from the European Union’s Horizon 2020
research and innovation programme under grant agreement No. 675680 www.bluebridge-vres.eu
Using e-Infrastructures
for Biodiversity
Conservation
Gianpaolo Coro
National Research Council (CNR), Pisa, Italy
This work is licensed under the Creative
Commons CC-BY 4.0 licence
Aims of the lecture
1. Introduce concepts around research e-Infrastructures
2. Overview of approaches for biodiversity data
management and analysis
3. Explain how computer science can support the needs
of a “community of practice”
4. Show tools used by large international organizations,
e.g. FAO, Unesco, ICES, IOTC
Outline
• E-Infrastructures
• i-Marine
• Biodiversity data
• Geospatial data
• Data processing
• Examples
Outline
• E-Infrastructures
• i-Marine
• Biodiversity data
• Geospatial data
• Data processing
• Examples
e-Infrastructures
e-Infrastructures enable researchers in different locations across the world
to collaborate in the context of their home institutions or in national or multinational scientific
initiatives. They can work together by having shared access to unique or distributed
scientific facilities (including data, instruments, computing and communications)*.”
Examples:
*Belief, http://www.beliefproject.org/
OpenAire, http://www.openaire.eu/
i-Marine, http://www.i-marine.eu/
EU-Brazil OpenBio,
http://www.eubrazilopenbio.eu/
e-Infrastructures
• Data e-Infrastructure: an e-Infrastructure promoting data sharing and
consumption. Addresses the needs of the research activity performed by a
certain community.
• Computational e-Infrastructure: an e-Infrastructures offering
computational resources distributed in a network environment. Uses Cloud
computing to execute calculations with a large number of connected
computers. Offers collaboration facilities for scientists to share experimental
results.

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Using e-Infrastructures for Biodiversity Conservation

  • 1. BlueBRIDGE receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 675680 www.bluebridge-vres.eu Using e-Infrastructures for Biodiversity Conservation Gianpaolo Coro National Research Council (CNR), Pisa, Italy This work is licensed under the Creative Commons CC-BY 4.0 licence
  • 2. Aims of the lecture 1. Introduce concepts around research e-Infrastructures 2. Overview of approaches for biodiversity data management and analysis 3. Explain how computer science can support the needs of a “community of practice” 4. Show tools used by large international organizations, e.g. FAO, Unesco, ICES, IOTC
  • 3. Outline • E-Infrastructures • i-Marine • Biodiversity data • Geospatial data • Data processing • Examples
  • 4. Outline • E-Infrastructures • i-Marine • Biodiversity data • Geospatial data • Data processing • Examples
  • 5. e-Infrastructures e-Infrastructures enable researchers in different locations across the world to collaborate in the context of their home institutions or in national or multinational scientific initiatives. They can work together by having shared access to unique or distributed scientific facilities (including data, instruments, computing and communications)*.” Examples: *Belief, http://www.beliefproject.org/ OpenAire, http://www.openaire.eu/ i-Marine, http://www.i-marine.eu/ EU-Brazil OpenBio, http://www.eubrazilopenbio.eu/
  • 6. e-Infrastructures • Data e-Infrastructure: an e-Infrastructure promoting data sharing and consumption. Addresses the needs of the research activity performed by a certain community. • Computational e-Infrastructure: an e-Infrastructures offering computational resources distributed in a network environment. Uses Cloud computing to execute calculations with a large number of connected computers. Offers collaboration facilities for scientists to share experimental results.
  • 7. Virtual Research Environments Virtual Research Environments: virtual organizations of communities of researchers for helping them collaborating. • Define sub-communities inside an e-Infrastructure; • Allow temporary dedicated assignment of computational, storage, and data resources to a group of people; • Very important in fields where research is carried out in several teams which span institutions and countries. e-Infrastructure VRE VRE VRE
  • 8. Outline • E-Infrastructures • i-Marine • Biodiversity data • Geospatial data • Data processing • Examples
  • 9. Outline i-Marine is both a Data and a Computational e-Infrastructure (Hybrid Data Infrastructure) • Used by several Projects: i-Marine, EUBrazil OpenBio, ENVRI, BlueBRIDGE; • Implements the notion of e-Infrastructure as-a-Service: it offers on demand access to data management services and computational facilities; • Hosts several VREs for Fisheries Managers, Biologists, Statisticians…and Students. DILIGENT 2004 BlueBRIDGE Today
  • 10. Social Network A continuously updated list of events / news produced by users and applications Share News Application- shared News User-shared News
  • 11. Workspace A folder-based file system allowing to manage complex information objects in a seamless way Information objects can be • files, dataset, workflows, experiments, etc. • organized into folders and shared • disseminated via URIs • accessed via WebDAV
  • 12. Services Storage Databases Cloud storage Geospatial data Metadata generation and management Harmonisation Sharing Processing Data management Cloud computing Elastic resources assignment Multi-platform: R, Java, Fortran
  • 13. Architecture Large Set of Biodiversity and Taxonomic Datasets connected A Social Network to share opinions and useful news Algorithms for Biology- related experiments Distributed Storage System to store datasets and documents A Network to distribute and access to Geospatial Data
  • 14. Online examples: the i-Marine Web portal and basic functions http://portal.i-marine.d4science.org
  • 15. Outline • E-Infrastructures • i-Marine • Biodiversity data • Geospatial data • Data processing • Examples
  • 16. Biodiversity Data • Taxonomies • In biology, a taxon (plural taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. • Introduced by Linnaeus's system in Systema Naturae (10th edition, 1758). • A taxon is usually known by a particular name and given a particular ranking, especially if (and when) it is accepted or becomes established • An accepted taxon is given a formal scientific name, according to nomenclature codes, e.g. Gadus morhua (Linnaeus, 1758)* • A "good" or "useful" taxon is one that reflects evolutionary relationships * More on scientific names here: http://wiki.i-marine.eu/index.php/Taxa_Merging_Discussion
  • 18. Biodiversity Data Specimen, Human Observations (direct/indirect) Records of species presence, usually provided by scientific surveys Occurrence data
  • 19. Biodiversity Data Providers i-Marine hosts biodiversity datasets coming from several data providers: • Some are remotely accessed and are maintained by the respective owners; • Other ones are resident in the e-Infrastructure. Currently, the accessible datasets are: • Catalogue of Life (CoL), • Global Biodiversity Information Facility (GBIF), • Integrated Taxonomic Information System (ITIS), • Interim Register of Marine and Nonmarine Genera (IRMNG), • Ocean Biogeographic Information System (OBIS), • World Register of Marine Species (WoRMS), • World Register of Deep-Sea Species ( WoRDSS ). Some data providers are collectors of other data providers, but the alignment is not guaranteed! The datasets allow to retrieve: • Occurrence points (presence points or specimen) • Taxa names
  • 20. Biodiversity Data Retrieval Merge OBIS GBIF Catalog of Life Visualise and explore Format 1 Format 2 Format 3 SameFormat:DarwinCore i-Marine SPD service
  • 22. Remote i-Marine Species Products Discovery Species Products Discovery allows to retrieve detailed information from several data providers We can visualize the occurrence points on a map and visually detect the errors We can inspect the points metadata
  • 23. i-Marine Species View Species View allows to discover species information from FishBase FishBase Also images and GIS maps may be attached to the species
  • 24. Online example: the i-Marine Species Products Discovery https://i-marine.d4science.org/group/biodiversitylab/species- data-discovery
  • 25. Outline • E-Infrastructures • i-Marine • Biodiversity data • Geospatial data • Data processing • Examples
  • 26. Geospatial data • Data that identify the geographic location of features and boundaries on Earth • Usually stored as coordinates and topology • Accessed and processed through Geographic Information Systems (GIS)
  • 28. OGC Standards Some standards: Web Maps Service (WMS): XML-based protocol that allows to display the datasets on an interactive map viewer Web Coverage Service (WCS): XML-based representation of space-time varying phenomena (especially used for raster maps) Web Features Service (WFS): XML-based representation for discrete geospatial features (especially used for polygonal maps) The Open Geospatial Consortium (OGC) is an international organization involving more than 400 organizations. Promotes the development and implementation of standards to describe geospatial data content and processing.
  • 29. i-Marine Geospatial data access and visualisation GeoExplorer is a web application (Portlet) for geo-spatial layers to: • Discover • Inspect • Overlay • Save WMS, WCS, WFS The map depicts the native range (~actual distribution) of Latimeria chalumnae
  • 30. GeoExplorer: Data Discovery and Visualization 30 Layers Stack Functions Visualization Discovery Metadata
  • 32. Outline • E-Infrastructures • i-Marine • Biodiversity data • Geospatial data • Data processing • Examples
  • 34. Supporting information sharing and collaborative research Reusability, Reproducibility, Repeatability of Science Sharing methods, data and findings via social networking Supporting data intensive Science Free access to scientific discoveries Science 2.0: next generation scientific research and technologies
  • 35. The Statistical Manager is a set of web services that aim to: • Help scientists in computational biology experiments • Supply precooked state-of-the-art processes as-a-Service • Perform calculations by using Cloud computing • Share input, results, parameters and comments with colleagues by means of Virtual Research Environment Statistical Manager Statistical Manager D4Science Computational Facilities Sharing Setup and execution
  • 36. Data processing rationale External Computing Facility OGC WPS Interface Data preparation Data processing WPS 1. Prepare data 2. Analyse 3. Recommend actions to decision makers
  • 37. Innovation through integration Vision: integration, sharing, and remote hosting help informing people and taking decisions
  • 38. Users 2015 Avg Users per month ~20 430 Number of Algorithms ~100 Organizations providing algorithms 1. CNR 2. Geomar 3. FIN 4. FAO 5. T2 6. IRD 7. Agrocampus 8. Ifremer 9. ICES 10. Univ. of Salerno 11. Univ. Fed. de Mato Grosso FishBase (CA,US,PHL) 44% Naturhistoriska Riksmuseet 23% Academia Sinica (Taiwan) 14% Universitaet Kiel 13% Museum National D'histoire Naturelle, Paris 5% Beijing 1% King Abdullah University Of Science And Technology 0% Consiglio Nazionale Delle Ricerche (PISA) 0% Inra - Centre De Recherches De Rennes 0% Other (individuals) 0% FishBase (CA,US,PHL) Naturhistoriska Riksmuseet Academia Sinica (Taiwan) Universitaet Kiel Museum National D'histoire Naturelle, Paris Beijing King Abdullah University Of Science And Technology Consiglio Nazionale Delle Ricerche (PISA) Inra - Centre De Recherches De Rennes Other (individuals)
  • 39. Computational boost Processes developed by scientist usually require long computational time and come under several programming languages. E.g. FAO stock assessment process has been imported on the D4Science e-Infrastructure with several benefits. Standard R environment • Sequential execution • For R experts only • Requires 30 days D4Science • Cloud computation • Web interface available for non experts • Requires 15h and 20 min • Produces the same output as the R process • 97.8% processing time reduction Output snippet
  • 41. Outline • E-Infrastructures • i-Marine • Biodiversity data • Geospatial data • Data processing • Examples
  • 42. Biodiversity Fill knowledge gaps on marine species Account for sampling biases Define trends for common species Plankton regime shift Herring recovered after the fish ban LME - MEOW
  • 43. 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 i-Marine reduced time-to-market: State-of-the-art models to estimate Maximum Sustainable Yield computational time reduced of 95% in average
  • 46. Geospatial data processing Maps comparison NetCDF file Data extraction Signal processing Periodicity detection Maps generation
  • 48. The giant squid - Architeuthis 16th century 2012 The giant squid (Architeuthis) has been reported worldwide even before the 16th century, and has recently been observed live in its habitat for the first time.
  • 49. Why rare species? • Biological and evolutionary investigations • Fisheries management policies and conservation • Vulnerable Marine Ecosystems • Key role in affecting biodiversity richness • Indicators of degradation for aquatic ecosystems
  • 50. Detecting rare species • How to build a reliable distribution from few observations? • How to account for absence locations? • Is there any approach for rare species?
  • 51. Data quality For rare species, data quality is fundamental: • Reliable presence data • Reliable absence locations • High quality environmental features • Non-noisy environmental features
  • 52. Tools From i-Marine: • Retrieve presence data • Generate absence data • Get environmental data • Model, adjust data and produce maps • Share results
  • 53. 1. Presence data of A. dux from i-Marine https://i-marine.d4science.org/group/biodiversitylab/species-data-discovery
  • 54. 2. Simulating A. dux absence locations from AquaMaps https://i-marine.d4science.org/group/biodiversitylab/processing-tools 0<Prob. < 0.2AquaMaps Native
  • 55. 3. Environmental Features https://i- marine.d4science.org/group/biodiversitylab/ge o-visualisation https://i- marine.d4science.org/group/biodiversitylab/pr ocessing-tools Most of these layers were available in D4Science Depth and Distance from land were imported using the Statistical Manager
  • 56. 4. MaxEnt model as filter https://i-marine.d4science.org/group/biodiversitylab/processing-tools MaxEnt Env. features most correlated to the giant squid Presence data Env. data
  • 58. 5. Presence/absence modelling: Artificial Neural Networks (ANN) Model trained on positive and negative examples In terms of env. features Trained model https://i-marine.d4science.org/group/biodiversitylab/processing-tools Presence/absence data Filtered env. features 1 (presence data) 0 (absence data)
  • 59. 6. Projection of the Neural Network https://i-marine.d4science.org/group/biodiversitylab/processing-tools
  • 60. 7. Comparison MaxEnt (presence-only) 22.01% 21.68% Similarity calculated using Maps Comparison, by Coro, Ellenbroek, Pagano DOI: 10.1080/15481603.2014.959391 Expert map, Nesis, 2003 Aquamaps Suitable (expert system) Neural Network (presence/absence) 42.83% https://i- marine.d4science.org/group/bio diversitylab/processing-tools
  • 61. Conclusions • Using data quality enhancement produces high performance distribution • A presence/absence ANN combines these data • Biological, observation and expert evidence confirm the prediction by the ANN
  • 62. Summary: modelling rare species distributions 1. Retrieve high quality presence locations by relying on the metadata of the records, 2. Use expert knowledge or an expert system to detect absence locations. Select absence locations as widespread as possible, 3. Select a number of environmental characteristics correlated to the species presence, 4. Use MaxEnt to filter the environmental characteristics that are really important with respect to the presence points, 5. Train an Artificial Neural Network on presence and absence locations and select the best learning topology, 6. Project the ANN at global scale, using the a resolution equal to the maximum in the environmental features, 7. Train a MaxEnt model as comparison system.
  • 63. Coelacanth (Latimeria chalumnae, Smith 1939) Coelacanths were thought to have gone extinct in the Late Cretaceous, but were rediscovered in 1938 off the coast of South Africa. Its current form is closely related to its form 400 million years ago. It is related to lungfishes and tetrapods.
  • 64. Coelacanth’s distribution Coelacanth, Smith 1939 GARP MaxEnt AquaMaps Neural Network Coro, Gianpaolo, Pasquale Pagano, and Anton Ellenbroek. "Combining simulated expert knowledge with Neural Networks to produce Ecological Niche Models for Latimeria chalumnae." Ecological Modelling 268 (2013): 55-63.