Presentation given at the Standing Groups meeting at the SCAR Open Science Conference. This presentation focuses on a facet of the ANTABIF architecture, the GBIF Integrated Publishing Toolkit
Presentation given at the Standing Groups meeting at the SCAR Open Science Conference. This presentation focuses on a facet of the ANTABIF architecture, the GBIF Integrated Publishing Toolkit
Biodiversity Information Networks: Dataflows for interdisciplinary sciencesGBIF_NPT
Danis and Parsons, presentation given at the World Conference on Marine Biodiversity, Aberdeen, September 2011.
ANSTRACT: In this paper, we present SCAR’s Marine Biodiversity Information Network (SCAR-MarBIN, www.scarmarbin.be), introduce the new Antarctic Biodiversity Information Facility (ANTABIF, 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.
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.
Andrew Baker_Supporting Science and Education With Flexible Cloud-Based Solut...Andrew Baker
Presentation given to "ICT in Schools" evening held at the Waite Laboratories on 24th May 2016. During the 2-hour session, ICTiS and SMiS partnerships, registered teachers and STEM professionals delved into computational thinking and technology resources for STEM education. This aim was to connect people and ideas in STEM education by showcasing ICTiS partnerships and hands-on technology.
Please feel free to download the presentation.
Researchers use government data in their work, the data derived from the research of others, and also produce data as part of their research processes. Generally, but not always, university based research is publicly funded; however there are few opportunities to re-disseminate these publicly funded data back to the public and to other researchers. Publicly funded research data are not managed nor preserved during the course of academic research and not once a research project is completed, furthermore there is uneven access to government produced data. This conversation session will therefore explore some of these issues by examining research practices at the GCRC and other community based organizations.
Building A Scalable Open Source Storage SolutionPhil Cryer
The Biodiversity Heritage Library (BHL), like many other projects within biodiversity informatics, maintains terabytes of data that must be safeguarded against loss. Further, a scalable and resilient infrastructure is required to enable continuous data interoperability, as BHL provides unique services to its community of users. This volume of data and associated availability requirements present significant challenges to a distributed organization like BHL, not only in funding capital equipment purchases, but also in ongoing system administration and maintenance. A new standardized system is required to bring new opportunities to collaborate on distributed services and processing across what will be geographically dispersed nodes. Such services and processing include taxon name finding, indexes or GUID/LSID services, distributed text mining, names reconciliation and other computationally intensive tasks, or tasks with high availability requirements.
GRC Integration And Management Of Diverse Environmental Data SetsCybera Inc.
Cameron Kiddle
Research Fellow, Grid Research Centre
University of Calgary
Presented at the Cybera/CANARIE National Summit 2009, as part of the session "New Frontiers in Data Integration." This session showcased a selection of leading-edge initiatives that are breaking new ground and setting new precedents around the collection and integration of data.
A presentation given at the "Data Stewardship: Increasing the Integrity and Effectiveness of Science and Scholarship" Session on Friday, June 8 2012 at the IASSIT 2012 conference in Washington DC.
This presentation introduced data publishing, using a social science (archaeology) case study to explore editorial processes and dissemination outcomes that increasingly demand “Linked Data” capabilities.
A presentation given by Anthony Beck at the Royal Agricultural College, Cirencester on 14th February 2012. This presentation describes the data collected by the DART project and encourages members of the local communities to exploit this data.
It covers data, formats, licences, software, applications. This introductory presentation was followed up with an afternoon hands-on workshop.
Biodiversity Information Networks: Dataflows for interdisciplinary sciencesGBIF_NPT
Danis and Parsons, presentation given at the World Conference on Marine Biodiversity, Aberdeen, September 2011.
ANSTRACT: In this paper, we present SCAR’s Marine Biodiversity Information Network (SCAR-MarBIN, www.scarmarbin.be), introduce the new Antarctic Biodiversity Information Facility (ANTABIF, 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.
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.
Andrew Baker_Supporting Science and Education With Flexible Cloud-Based Solut...Andrew Baker
Presentation given to "ICT in Schools" evening held at the Waite Laboratories on 24th May 2016. During the 2-hour session, ICTiS and SMiS partnerships, registered teachers and STEM professionals delved into computational thinking and technology resources for STEM education. This aim was to connect people and ideas in STEM education by showcasing ICTiS partnerships and hands-on technology.
Please feel free to download the presentation.
Researchers use government data in their work, the data derived from the research of others, and also produce data as part of their research processes. Generally, but not always, university based research is publicly funded; however there are few opportunities to re-disseminate these publicly funded data back to the public and to other researchers. Publicly funded research data are not managed nor preserved during the course of academic research and not once a research project is completed, furthermore there is uneven access to government produced data. This conversation session will therefore explore some of these issues by examining research practices at the GCRC and other community based organizations.
Building A Scalable Open Source Storage SolutionPhil Cryer
The Biodiversity Heritage Library (BHL), like many other projects within biodiversity informatics, maintains terabytes of data that must be safeguarded against loss. Further, a scalable and resilient infrastructure is required to enable continuous data interoperability, as BHL provides unique services to its community of users. This volume of data and associated availability requirements present significant challenges to a distributed organization like BHL, not only in funding capital equipment purchases, but also in ongoing system administration and maintenance. A new standardized system is required to bring new opportunities to collaborate on distributed services and processing across what will be geographically dispersed nodes. Such services and processing include taxon name finding, indexes or GUID/LSID services, distributed text mining, names reconciliation and other computationally intensive tasks, or tasks with high availability requirements.
GRC Integration And Management Of Diverse Environmental Data SetsCybera Inc.
Cameron Kiddle
Research Fellow, Grid Research Centre
University of Calgary
Presented at the Cybera/CANARIE National Summit 2009, as part of the session "New Frontiers in Data Integration." This session showcased a selection of leading-edge initiatives that are breaking new ground and setting new precedents around the collection and integration of data.
A presentation given at the "Data Stewardship: Increasing the Integrity and Effectiveness of Science and Scholarship" Session on Friday, June 8 2012 at the IASSIT 2012 conference in Washington DC.
This presentation introduced data publishing, using a social science (archaeology) case study to explore editorial processes and dissemination outcomes that increasingly demand “Linked Data” capabilities.
A presentation given by Anthony Beck at the Royal Agricultural College, Cirencester on 14th February 2012. This presentation describes the data collected by the DART project and encourages members of the local communities to exploit this data.
It covers data, formats, licences, software, applications. This introductory presentation was followed up with an afternoon hands-on workshop.
Similar to Antarctic Biodiversity Networks: new architecture, new tools (20)
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
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.”
Presentation given at the Microbial Antarctic Resource System (mARS), during the SCAR Open Science Conference 2012, in Portland. Presented by Alison Murray and Bruno Danis.
This presentation was given as a keynote during the CAML session at the SCAR open science conference in Buenos Aires, August 2010. Its an introduction to Polar data sharing, focusing on SCAR's Marine Biodiversity Information Network (www.scarmarbin.be) and the new Antarctic Biodiversity Information Facility (www.biodiversity.aq). Both these projects aim at offering free and open access to raw scientific data pertaining to Antarctic biodiversity.
JMeter webinar - integration with InfluxDB and GrafanaRTTS
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Session Overview
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Antarctic Biodiversity Networks: new architecture, new tools
1. Antarctic Biodiversity
Networks
New Architecture, New Tools
Bruno Danis
Tuesday 13 December 11
2. Objectives
• get familiar with Antarctic Biodiversity
Networks
• learn about the new architecture, and
functionalities
• get you onboard
Tuesday 13 December 11
3. On the Menu Today
• Background
• (quick) Technical overview
• Applications
• Functionalities
• Carrots
• Future directions
Tuesday 13 December 11
5. Antarctic Treaty
« In order to promote international
cooperation in scientific investigation in
Antarctica, […],
Scientific observations and results from
Antarctica shall be exchanged and made
freely available. »
Tuesday 13 December 11
6. Antarctic Biodiversity
Information Networks
• SCAR Marine Biodiversity Information Network
• Antarctic Biodiversity Information Facility
• Core funding: BELSPO.be
• Also from: SCAR, CAML, AWI, DFG, NWO, AAD
• International Polar Year 2007/08 (IPY)
• Census of Antarctic Marine Life (CAML)
Tuesday 13 December 11
7. Antarctic Biodiversity
Information Networks
• Antarctic Node for OBIS
• Antarctic Node for GBIF
• Data management component for new SCAR PPGs:
ANT-ECO, ANT-ERA
• Biodiversity component of SOOS
• Antarctic Node for GEO-BON
Tuesday 13 December 11
8. General Philosophy
• Build an electronic ecosystem
• Offer free and open access to data and technology
• Expose all the (biodiversity) data and metadata, in
multiple contexts
• Remain community-driven, and collaborative
• Adopt strong standardization
• Work for science, conservation, management
Tuesday 13 December 11
10. Achievements: dataportals
• Portal up since Oct 2005
• open access
• 935,000 visitors
• 8,400,000 hits
• 60,000,000 dld records
• Citations: 183
Tuesday 13 December 11
11. Achievements: taxonomy
• The first RAMS
• Board of 60+ editors
• Feeds WoRMS, CoL and EoL
• 17,098 taxa (RAMS)
• Building a dynamic RAS
• 24,248 taxa (RAS)
Tuesday 13 December 11
22. Birds and Mammals (nice and fluffy)
Clarke AH, Danis B, Griffiths HJ, DSRII 2011
Tuesday 13 December 11
23. Nematoda (small and ugly)
Clarke AH, Danis B, Griffiths HJ, DSRII 2011
Tuesday 13 December 11
24. Echinodermata (in between)
Echinodermata
a b
Clarke AH, Danis B, Griffiths HJ, DSRII 2011
Tuesday 13 December 11
25. Yet another 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
Tuesday 13 December 11
26. Biogeographic Atlas
•Re-‐do
of
a
“classic”:
Hedgepeth
1969
•BASO:
Paper
and
digital
versions
•Predic=ve
maps
(93
env.
parameters
injected...)
•Build
an
interac=ve
plaPorm
•Crossdisciplinary
capacity
building
•Fill
in
gaps
Tuesday 13 December 11
28. 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
...
Tuesday 13 December 11
36. ipt. biodiversity.aq
• prepare and clean your data
• publish primary biodiversity data
• publish metadata
• push data and metadata to ANTABIF &
GBIF
• generate and submit a Data Paper
Tuesday 13 December 11
38. afg. biodiversity.aq
• Identification aid
• Publication/sharing platform for customized
Field Guides
• High quality (useful) pictures
• Expert Descriptions
• Built dynamically from various sources
• Generate a pdf for your taxa/area of
interest, and share
Tuesday 13 December 11
48. The Data Paper
• A scholarly journal publication whose primary purpose is to
describe a dataset or group of datasets, rather than to report a
research investigation.
• Benefits of the Data Paper
– Scholarly credit to Data Publishers
– Describe the data in structured human readable form
– Bring the existence of the data to the attention of the
scholarly community
Tuesday 13 December 11
50. Step-by-Step
• Complete metadata of a dataset using metadata editor in IPT
2.0.2
• Generate ‘Data Paper’ manuscript (menu: Manage Resource –
RTF Download)
• Submit the manuscript for possible publication in one of the
PenSoft publication (ZooKeys, PhytoKeys, BioRisks, NeoBiota,
Biodiversity Data Journal, Nature Conservation).
• Revision (if any) is carried out using metadata editor in IPT 2.0.2
and manuscript re-submitted to PenSoft Open Journal System
Tuesday 13 December 11
51. Once paper is accepted
• Digital Object Identifier is assigned to the Data Paper
• Paper is published in (a) print format, (b) PDF format, (c)
semantically enhanced HTML, and (d) XML is archived in
PubMedCentral
• DOI of the Data Paper is linked with the Persistent Identifier
of the metadata document in the GBIF Registry
• Data Paper is indexed by Web of Knowledge (ISI),
PubMedCentral, Scopus, Zoological Record, Google Scholar,
CAB Abstracts, Directory of Open Access Journal (DOAJ),
EBSCO.
Tuesday 13 December 11
52. Important to consider
• Metadata is complete in all the respect
• All the claims are adequately substantiated
• Data described in ‘Data Paper’ is freely available at
the time of submission of the manuscript
Tuesday 13 December 11
53. NPT
• GBIF - Nodes Portal Toolkit
• To deploy and maintain modular biodiversity data
portals
• Uses GBIF data
• Extensible to accommodate custom needs
• Open Source
• Community developments
Tuesday 13 December 11
54. The
basic
NPT
plaPorm
provides
everything
needed
to
start
a
web
site
Non-‐technical
staff
can
just
start
adding
content!
Tuesday 13 December 11
55. NPT
Startup
Summary
This
configura=on
is
a
star=ng
point
for
further
development
• Provides
a
customizable
website
/
portal
• Provides
founda=on
for
further
modules
to
be
added
• Displays
GBIF
portal
data
as
data
maps
for
your
country
or
region
Tuesday 13 December 11
63. Community
• A network of IPTs and NPTs
• Enhanced data flow
• Community involved in data management
• Enhanced interoperability
• Optimization of research efforts/resources
• Integrative, connected science
• Factual, adaptative conservation
Tuesday 13 December 11
64. Challenges
• Data intensive science
• Data deluge
• Digital divides
• Other data types and integration
• Orphan datasets
• Cultural change
Tuesday 13 December 11