The document summarizes Bruno Danis' presentation on Antarctic Biodiversity Networks at the GBIF Science Symposium 2011. Some key points:
- Antarctic Treaty of 1959 inspired sharing of scientific data from Antarctica freely.
- SCAR-MarBIN and ANTABIF facilitate open access to Antarctic biodiversity data through various tools and portals.
- Achievements include the Reference Antarctic Marine Species database, over 1 million georeferenced records published through GBIF and OBIS, and community projects like the Antarctic Field Guides and Biogeography Atlas of the Southern Ocean.
- Future challenges include continued technological improvements and promoting a culture of open data sharing in the Antarctic community.
Using multi-temporal benchmarking to determine optimal sensor deployment: adv...DART Project
A presentation given by Anthony Beck at EARSeL Gent on 20/09/12 describing some of the multi-temporal issues associated with archaeological detection. This presentation is primarily based on the research of David Stott.
Biodiversity Information Networks: dataflows for interdisciplinary scienceBruno Danis
In this paper, we present SCAR’s Marine Biodiversity Information Network (SCAR-MarBIN, www.scarmarbin.be), introduce the new Antarctic Biodiversity Information Facility (ANTABIF, HYPERLINK "http://www.biodiversity.aq" www.biodiversity.aq) and argue that it has become vital and practicable to support an international mechanism for the exchange of scientific data. This approach allows to integrate large data volumes, and helps modern biologists to face a “data deluge” using new techniques and technologies currently developed in the field of biodiversity informatics. Biodiversity is an example of data-intensive science, and certainly requires an interdisciplinary, scalable approach to address complex systemic problems such as environmental change and its impact on marine ecosystems. This paper discusses the experience of data scientists seeking to collect, curate, and provide data during the timeframe of the International Polar Year. The data content of the SCAR-MarBIN and ANTABIF holdings has been explored, and recent published analyses are used to illustrate concrete examples. We find that while technology is a critical factor to address this dimension, the greater challenges are more socio-cultural than technical. We describe a vision of discoverable, open, linked, useful, and safe data and suggest the need for a rapid socio-technical evolution in the overall science data ecosystem.
This document provides an overview and objectives of an ANTABIF training session. The training will familiarize participants with ANTABIF's architecture, functionalities, tools and standards. It will include hands-on exercises with dummy and real data. The objectives are to learn about ANTABIF, see demonstrations of its features, and collect feedback on its usefulness. The agenda includes technical overviews, standards, publishing tools, and hands-on sessions.
A new atlas, providing the most thorough audit of marine life in the Southern Ocean, is published this week by the Scientific Committee on Antarctic Research (SCAR). Leading marine biologists and oceanographers from all over the world spent the last four years compiling everything they know about ocean species from microbes to whales. It’s the first time that such an effort has been undertaken since 1969 when the American Society of Geography published its Antarctic Map Folio Series.
In an unprecedented international collaboration 147 scientists from 91 institutions across 22 countries (Australia, Belgium, Brazil, Canada, Chile, Denmark, France, Germany, Ireland, Italy, Japan, the Netherlands, New Zealand, Norway, Poland, Portugal, Russia, South Africa, Spain, Switzerland, the UK and the USA) combined their expertise and knowledge to produce the new Biogeographic Atlas of the Southern Ocean. More than 9000 species are recorded, ranging from microbes to whales. Hundreds of thousands of records show the extent of scientific knowledge on the distribution of life in the Southern Ocean. In 66 chapters, the scientists examine the evolution, physical environment, genetics and possible impact of climate change on marine organisms in the region.
Chief editor, Claude De Broyer, of the Royal Belgian Institute of Natural Sciences, said: “This is the first time that all the records of the unique Antarctic marine biodiversity, from the very beginnings of Antarctic exploration in the days of Captain Cook, have been compiled, analysed and mapped by the scientific community. It has resulted in a comprehensive atlas and an accessible database of useful information on the conservation of Antarctic marine life.”
VERSO: Ecosystem Responses in the Southern OceanBruno Danis
General presentation of the BELSPO funded vERSO (Ecosystem Resoponses to Changes in the Southern Ocean) project. More information on www.versoproject.be
Using multi-temporal benchmarking to determine optimal sensor deployment: adv...DART Project
A presentation given by Anthony Beck at EARSeL Gent on 20/09/12 describing some of the multi-temporal issues associated with archaeological detection. This presentation is primarily based on the research of David Stott.
Biodiversity Information Networks: dataflows for interdisciplinary scienceBruno Danis
In this paper, we present SCAR’s Marine Biodiversity Information Network (SCAR-MarBIN, www.scarmarbin.be), introduce the new Antarctic Biodiversity Information Facility (ANTABIF, HYPERLINK "http://www.biodiversity.aq" www.biodiversity.aq) and argue that it has become vital and practicable to support an international mechanism for the exchange of scientific data. This approach allows to integrate large data volumes, and helps modern biologists to face a “data deluge” using new techniques and technologies currently developed in the field of biodiversity informatics. Biodiversity is an example of data-intensive science, and certainly requires an interdisciplinary, scalable approach to address complex systemic problems such as environmental change and its impact on marine ecosystems. This paper discusses the experience of data scientists seeking to collect, curate, and provide data during the timeframe of the International Polar Year. The data content of the SCAR-MarBIN and ANTABIF holdings has been explored, and recent published analyses are used to illustrate concrete examples. We find that while technology is a critical factor to address this dimension, the greater challenges are more socio-cultural than technical. We describe a vision of discoverable, open, linked, useful, and safe data and suggest the need for a rapid socio-technical evolution in the overall science data ecosystem.
This document provides an overview and objectives of an ANTABIF training session. The training will familiarize participants with ANTABIF's architecture, functionalities, tools and standards. It will include hands-on exercises with dummy and real data. The objectives are to learn about ANTABIF, see demonstrations of its features, and collect feedback on its usefulness. The agenda includes technical overviews, standards, publishing tools, and hands-on sessions.
A new atlas, providing the most thorough audit of marine life in the Southern Ocean, is published this week by the Scientific Committee on Antarctic Research (SCAR). Leading marine biologists and oceanographers from all over the world spent the last four years compiling everything they know about ocean species from microbes to whales. It’s the first time that such an effort has been undertaken since 1969 when the American Society of Geography published its Antarctic Map Folio Series.
In an unprecedented international collaboration 147 scientists from 91 institutions across 22 countries (Australia, Belgium, Brazil, Canada, Chile, Denmark, France, Germany, Ireland, Italy, Japan, the Netherlands, New Zealand, Norway, Poland, Portugal, Russia, South Africa, Spain, Switzerland, the UK and the USA) combined their expertise and knowledge to produce the new Biogeographic Atlas of the Southern Ocean. More than 9000 species are recorded, ranging from microbes to whales. Hundreds of thousands of records show the extent of scientific knowledge on the distribution of life in the Southern Ocean. In 66 chapters, the scientists examine the evolution, physical environment, genetics and possible impact of climate change on marine organisms in the region.
Chief editor, Claude De Broyer, of the Royal Belgian Institute of Natural Sciences, said: “This is the first time that all the records of the unique Antarctic marine biodiversity, from the very beginnings of Antarctic exploration in the days of Captain Cook, have been compiled, analysed and mapped by the scientific community. It has resulted in a comprehensive atlas and an accessible database of useful information on the conservation of Antarctic marine life.”
VERSO: Ecosystem Responses in the Southern OceanBruno Danis
General presentation of the BELSPO funded vERSO (Ecosystem Resoponses to Changes in the Southern Ocean) project. More information on www.versoproject.be
What the deep sea tells us about sampling biases in the fossil recordGraeme Lloyd
The document discusses biases in the fossil record by comparing deep sea and land-based records of coccolithophores. It finds that coccolithophore diversity correlates strongly with the amount of rock recovered from each record. Modeling suggests a more uniform diversity regardless of record used. It also finds that the ratio of coccolithophore species to genera changes over time in correlation with sampling effort and number of taxonomists, suggesting these factors influence the pattern observed in the fossil record.
A presentation by Anthony Beck presented at the workshop "Potential of satellite images and hyper/multi-spectral recording in archaeology"
Poznan – 31st June 2012
Different records give different curves: comparing deep sea and land-based pa...Graeme Lloyd
This document compares records of coccolithophorid diversity from deep sea and land-based rock records over the last 150 million years. It finds that diversity strongly correlates with the shape of the rock record it is recovered from. However, after accounting for sampling biases, the true underlying diversity appears more uniform over time irrespective of the rock record used. This supports the hypothesis that the rock record, not the underlying biology, is driving patterns in the fossil record.
The document provides an overview of various topics in archaeology, including key figures, subfields of anthropology, methods used in archaeology such as surveys, excavations, dating techniques, and examples of important archaeological sites. It discusses concepts like stratigraphy, seriation, and site formation processes. The document serves as a reference for archaeological terminology, techniques, and examples.
The document discusses SCAR-MarBIN and ANTABIF, which provide free and open access to Antarctic biodiversity data. Their goals are to exchange scientific data and results from Antarctica freely to promote international cooperation and adaptive conservation/management. They have developed web portals and databases containing over 850,000 visitors and 35 million data records downloaded. Their philosophy is to build an open electronic ecosystem offering access to taxonomic and geospatial biodiversity data using open source solutions.
This document discusses the SCAR-MarBIN (Marine Biodiversity Information Network) project which aims to quantify Antarctic marine biodiversity. It notes that Antarctic biodiversity is highly endemic but understudied, especially in deep-sea environments. SCAR-MarBIN builds an open-access network of over 60 editors to aggregate data on over 16,000 Antarctic taxa and 9,234 species from 130 datasets. The project helps identify gaps in knowledge, promotes new initiatives to increase data, and builds bridges across disciplines and nations to advance conservation and management of Antarctic ecosystems.
DART - improving the science. Bradford 21022012DART Project
This document provides an overview of the DART project, which aims to improve the scientific understanding of archaeological detection. DART studies archaeological sites to better understand how their constituents generate observable contrasts and how sensors can detect these contrasts. The project conducts intensive ground observations and measurements at sites to analyze periodic changes in the sites. DART shares its data openly to maximize its impact and further innovation in archaeological detection.
This document provides an overview of Phillip Owens' career and research interests in digital soil mapping. It outlines his educational background in soil science and highlights some of his past roles, including working as a Congressional Science Fellow and USDA-ARS Research Scientist. It also summarizes some of his current interests and involvement in projects related to digital soil mapping, the development of soil classification systems, and using geospatial tools and data to better understand soil-landscape relationships.
The document discusses the DART (Detecting and Recording Archaeological Traces) project, which aims to improve archaeological detection techniques by taking a scientific approach. It involves intensive ground observation and data collection at sites to better understand how archaeological remains generate detectable contrasts and how those contrasts are influenced by environmental factors over time. The data collected includes spectro-radiometry, soil moisture and temperature probes, weather data, and aerial imagery. Preliminary analysis of temperature, moisture, and resistance data show changes seasonally that could help predict optimal times for detection. The open science approach seeks to further archaeological prospection methods.
SCAR-MarBIN and ANTABIF are open access biodiversity data portals for Antarctic species. They provide taxonomic and geospatial data for over 50 million records through their websites and web services. The portals aim to build an open ecosystem for sharing Antarctic biodiversity data through standardization and community involvement. Upcoming products will include georeferenced genetic data and interactive atlases.
This document summarizes a project that mapped riverine habitat in the Rio Grande to support the experimental reintroduction of the endangered Rio Grande silvery minnow. Researchers used high-precision GPS to map habitat types at different river flows. They collected data on physical characteristics and fish assemblages. The resulting spatial database will help understand habitat variability and fish distributions to aid conservation of the silvery minnow.
This document discusses the applications of geospatial systems and their importance in supporting green economic development. Geospatial technologies can be used to monitor biodiversity, assess natural resource use, and measure ecological footprints across various spatial and temporal scales. The convergence of remote sensing, GIS, modeling, and other geospatial tools allows issues to be analyzed and addressed in an integrated manner from local to global levels. Geospatial systems can locate resources, identify land use patterns, monitor environmental conditions over time, and assess impacts to support sustainable resource management and linkages between development and conservation.
Mark Thomas_A digital soil mapping approach for regolith thickness in the com...TERN Australia
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This document describes a new DNA metabarcoding approach for high-throughput biodiversity assessment using environmental DNA. Short DNA barcode markers are amplified from bulk soil or water samples and sequenced on next-generation platforms to identify all taxa present, without needing to isolate individual organisms. The method was tested on soil samples from an alpine meadow, identifying 8 earthworm species from sequence reads of short mtDNA markers. Future applications could include capturing DNA with hundreds of probes and shotgun sequencing of soil eDNA for comprehensive biodiversity surveys at large scales.
Encyclopedia of Life: Use cases for phenotypesCyndy Parr
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This document provides an introduction to analyzing lake sediment cores to study past climate change. It discusses why lake sediments are useful climate archives, as they form layers over time that record environmental changes. The document outlines how scientists describe and analyze sediment cores to develop climate histories. This includes taking high-resolution images, measuring properties like magnetic susceptibility, and defining different sediment facies that indicate past conditions. The goal is to characterize changes in climate and the landscape over time to better understand dynamics and improve future predictions.
Effects of density on spacing patterns and habitat associations of a Neotropi...Nicole Angeli
Presentation at Ecological Society of America, August 2013. Minneapolis, USA. –Oral Paper
Angeli, N. F., K. Lips, G. V. DiRenzo, and A. Cunha. “Effects of density on spacing patterns
and habitat associations in the Neotropical Glassfrog Espadarana prosoblepon.”
This document summarizes the work of the Marine Biology Lab at the Université Libre de Bruxelles led by Bruno Danis. It describes the lab's research focusing on various topics related to marine biology in Antarctica such as symbiosis, eco-physiology, biogeography, and biodiversity informatics. It lists the biological models, approaches, and objectives for each research topic. It also provides information on the lab's partners, funding, timelines, and publications. The lab operates the biodiversity.aq ecosystem which includes tools and databases for taxonomy, occurrences, an atlas, field guides, and microbial data.
Register of Antarctic Marine Species - AquaRESBruno Danis
RAMS (the Register of Antarctic Marine Species) is a free and open access database that contains taxonomic and biogeographic data for over 18,000 accepted Antarctic marine species. It is a community-driven project with a board of 60 editors. RAMS is part of the larger WoRMS (World Register of Marine Species) database. It serves as a taxonomic backbone for many Antarctic biodiversity projects and is aimed at supporting science, conservation, and management efforts. RAMS data is accessible on the biodiversity.aq website.
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Leveraging the Graph for Clinical Trials and Standards
An overview of Antarctic biodiversity networks
1. GBIF Science Symposium 2011
An overview of Antarctic Biodiversity Networks
Bruno Danis
Project Manager
Antarctic Biodiversity Information Facility (GBIF)
October 5, 2011
2. Layout
• Background
• Our vision
• Achievements and products
• Uptake of GBIF tools
• The Future: Technological and Cultural challenges
4. Antarctic Treaty
(our inspiration)
« In order to promote international cooperation in
scientific investigation in Antarctica, […], the Contracting
Parties agree that, to the greatest extent feasible and
practicable: […]
Scientific observations and results from Antarctica shall be exchanged
and made freely available. »
50+ years ago...
5. Specifics about Antarc7ca
• Antarc7c Treaty system (no government): the con7nent is devoted
to peace and science (but doesn’t appear on maps)
• SCAR ‐ the Scien7fic CommiCee on Antarc7c Research
• Rather sophis7cated logis7cs makes it expensive
• Biodiversity
– Highly adapted
– Mostly marine
– Extreme(ly stable) environment
– Extremely sensi7ve
5
6. SCAR‐MarBIN & ANTABIF
• www.scarmarbin.be: marine biodiversity informa7on network
• www.biodiversity.aq: biodiversity informa7on facility
• Core funding: BELSPO.be (un7l June 2012)
• Interna7onal Polar Year 2007/08
• Census of Antarc7c Marine Life
• Ocean Biogeographic Informa7on System
• Global Biodiversity Informa7on Facility
7. General philosophy
• Build an electronic ecosystem
• Offer free and open access to data and technology
• Expose all the (biodiversity) data and metadata, in mul7ple contexts
• Remain community‐driven, and collabora7ve
• Adopt strong standardiza7on
• Work for science, conserva7on, management
7
20. Community projects
(the carrots)
• Antarc7c Field Guides
• Gap analysis
• Biogeography Atlas of the
Southern Ocean
20
21. Antarc7c Field Guides
afg.biodiversity.aq
• (nice‐looking) Iden7fica7on aid
• Publica7on/sharing plajorm for customized Field Guides
• Best available pictures
• Expert Descrip7ons
• Many contributors, building the content
• Dynamically built from various sources (incl. RAMS and GBIF)
21
28. Gap analysis
share.biodiversity.aq
• Quick gap analysis on full dataset
• A small group of enthusiasts
• Cleaned full SCAR‐MarBIN dataset
• Produce visual products
• Produce a scien7fic paper
• How ignorant are we?
28
35. Yet another little problem
2,8 isopod species described per year
De Broyer C & Danis B, DSRII 2011
36. Yet another little problem
2,8 isopod species described per year
600+ discovered during ANDEEP expeditions
De Broyer C & Danis B, DSRII 2011
37. Yet another little problem
2,8 isopod species described per year
600+ discovered during ANDEEP expeditions
214 years to describe them!
De Broyer C & Danis B, DSRII 2011
38. Biodiversity Atlas of the SO
atlas.biodiversity.aq
• Re‐do of a “classic”: Hedgepeth 1969
• BASO: Paper and digital versions
• Predic7ve maps (93 env. parameters injected...)
• Build an interac7ve plajorm
• Crossdisciplinary capacity building
• Fill in gaps
• 60 contributors from 36 ins7tu7ons in 16 countries
35
44. Mashing (and sharing) data layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
45. Mashing (and sharing) data layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
46. Mashing (and sharing) data layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
47. Mashing (and sharing) data layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
48. Mashing (and sharing) data layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
49. Mashing (and sharing) data layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
50. Mashing (and sharing) data layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
51. Mashing (and sharing) data layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
52. Mashing (and sharing) data layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
53. Mashing (and sharing) data layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
58. More GBIF resources taken up
• Data transforma7on tools
• GBIF community site
• Collabora7on and Capacity building documents
• Communica7on channels
• Webservices
• Standards
43
59. impact of GBIF on SCAR [IPT]
• Communi7es have the possibility to push their data to GBIF
• BeCer impression of control over the data
• Data Paper concept
• Fast publica7on of new data
• Instances in different ins7tu7ons
• (makes my life easy)
44
60. impact of GBIF on SCAR [NPT]
• (many) Communi7es
• Poten7al to deploy many Antarc7c biodiversity portals
• SCAR Ac7on groups (thema7c)
• Polar ins7tutes, Na7onal Antarc7c Data Centers
• Research plajorms (vessels, bases,...)
• Overarching projects
• Training
• (will) make my life easy
45
61. impact of SCAR on GBIF
• (Mini‐GBIF)=>case study
• Interna7onal, interdisciplinary
• Antarc7c Treaty = 50 years of collabora7on
• SCADM (data managers): Data policy and Standards
• APECS (young scien7sts)
• A community in the star7ng‐blocks, happy to experiment
46
62. (near) Future
• Many IPTs
• Many NPTs
• Enhanced data flow
• The community feels responsibility to share data
• Op7miza7on of Biodiversity research efforts/resources
• Enhanced interoperability
• Integra7ve, connected science
• Factual, adapta7ve conserva7on and management
• => everyone’s happy
47
64. The Polar Informa7on Commons
www.polarcommons.org
• Climate change Magnifica7on
• => Emergency solu7on
• Setup of a commons
– IT cloud + GCMD
– Set of norms(!)
• All polar data (IPY)
• Simple procedure to upload data:
– badge dataset(s) (describe, choose a CC Licence)
– throw your data in the Cloud
– done
49
So starting with “Open”. I like this definition from wikipedia\n
OK. Linked. Again Wikipedia provides a good definition. The point is that data are more relevant and useful if they are associated and explicitly linked with other data, especially when they are linked in a way that computers can readily interpret.\n\n
Useful. I don’t define useful, because it depends on your perspective.\n\n
So if we think of interoperability of the actual data not just the metadata, there are two general approaches: A geospatial or map-based approach and a semantic approach that relies on common, well-defined concepts and relationships. Semantic work is really still in its infancy. There has been some work in specific domains and IPY has an agreement on basic terms, but major challenges remain. There has been progress in the geospatial realm.\n\n