Danis keynote

SCAR-MarBIN and ANTABIF
CAML’s virtual heritage

www.scarmarbin.be
www.biodiversity.aq
Thursday 5 August 2010

Outline
• Polar data sharing - our vision
• SCAR-MarBIN V1
• SCAR-MarBIN V2
• ANTABIF
• Products
• Nuts and Bolts
• Food for thought

Polar data sharing


The Antarctic Treaty
« In order to promote international cooperation in
scientiﬁc investigation in Antarctica, as provided for in
Article III (1c) of the Treaty, 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. »


Mark Parsons [THANKS]

Our vision:
Data are discoverable, open, linked, useful, and
safe.

Copyright: © Christian Morel


Discoverable
Data should be accessible soon after collection (online wherever possible) in a
discovery portal such as the Global Change Master Directory.



Open
Open Data is a philosophy and practice requiring that certain data are freely
available to everyone, without restrictions from copyright, patents or other
mechanisms of control.—Wikipedia



Linked
The term Linked Data is used to describe a method of exposing, sharing, and
connecting data [using] the Web.—Wikipedia



Useful

Data from different projects, disciplines, and data centers should be
easily understood and used in conjunction with each other in
standard tools and analysis frameworks

Data should be well described so to be useful for a broad audience.



Interoperable

Metadata and data should be readily interchangeable between
different polar data systems to enable data discovery across multiple
portals.



Safe
Safe from hackers, from obsolescence, from undocumented change, from loss,
and from the ravages of time.


Some initial recommendations
for scientists and data centers

• Investigators should publish their IPY data immediately.
• The scientiﬁc community needs to recognize the value of good data
through citation, consideration of data publication in promotion and
tenure review, and by training young scientists in data management.
• Data centers must develop partnerships with other data centers in
other countries and other disciplines to enhance data accessibility and
interoperability.
• Data centers should partner with their scientiﬁc community to explicitly
meet their needs, provide easy submission tools, and make the data
more useful and integrated with other data.


SCAR-MarBIN
SCAR’s Marine Biodiversity Information Network
www.scarmarbin.be


General philosophy
• Build an electronic ecosystem
• Offer free and open access to data and technology
• Expose all the (biodiversity) data and metadata
• Remain community-driven
• Adopt strong standardization
• Work for science, conservation, management


SCAR-MarBIN
Marine Biodiversity Information Network

• www.scarmarbin.be
• Main funding: Belgian science Policy ofﬁce
• International funding
• International Polar Year 2007/08
• Census of Antarctic Marine Life
• Ocean Biogeographic Information System
• Global Biodiversity Information Network

The webportal

taxonomy, biogeography
vizualisation
open access
800,000 visitors
5,800,000 hits
39,000,000 dld records
V2alpha coming up


The Register of Antarctic
Marine Species
• The ﬁrst RAMS
• Board of 60+ editors
all taxa

all species
• Feeds WoRMS, CoL and
EoL
valid species
• 16,475 taxa
0 3.750 7.500 11.250 15.000
• 9,346 species

Biogeographic data

1,088,044 records
178 datasets
5,235 taxa
Feeds OBIS, GBIF
Downloadable
WebGIS
OGC Webservices


SCAR-MarBIN V2

• 100% Open Source
• Geo-oriented
• improved search engine
• improved interface, direct access to data
• all resources available through Webservices
• alpha version to be deployed soon

SCAR-MarBIN V2


[results]: webportal


ANTABIF
Antarctic Biodiversity Information Facility
www.biodiversity.aq


ANTABIF
Antarctic Biodiversity Information Facility

• www.biodiversity.aq
• Funding: Belgian science Policy ofﬁce
• International Year of Biodiversity
• Single Access to all Antarctic Biodiversity
data
• Australian Antarctic Division
• Global Biodiversity Information Network

ANTABIF
Technology: 100% Open Source

• Search engine: Full text (SOLR-Lucene)

• Database: PostGresql

• GIS: Geoserver, PostGIS, OpenLayers

• Web services: RESTish (all resources)

• Protocoles: DIF, DwCore, DwC archive, Tapir…etc

• GBIF tools : HIT, IPT…etc

• Hosting: BBPF

• Metadata system: Global Change Master Directory

Who’s in?


ANTABIF
• Webpresence:
• www.biodiversity.aq
• share.biodiversity.aq
• scratchpads.biodiversity.aq
• metadata portal (GCMD)
• social networks: FB, Twitter, LinkedIn, blablabla
• Building NOW on bulletproof technology and
standards

[projects] some examples
Antarctic Field Guides
Georeferenced genetic data
Polar Macroscope Synthesis
Biogeographic Atlas of the SO
Scratchpads


What is a Scratchpad?
A Toolkit for our community Vincent Smith [THANKS]

1 2 3
Your data Uploaded & “Published” & reviewed
tagged on your site

Fast Intuitive Fit for use


Scratchpads Vincent Smith [THANKS]

A multi-site implementation of Drupal

http://scratchpads.eu

Taxonomy Vincent Smith [THANKS]

Taxonomy import,
management and
navigation


Bibliographic data Vincent Smith [THANKS]

Reference manager /
Endnote support for
bibliographies


Images Vincent Smith [THANKS]

Image galleries,
image upload &
annotation


Phylogeny Vincent Smith [THANKS]

Nexus / Newick import for
visualizing phylogenies


Character Matricies Vincent Smith [THANKS]

Molecular & morphological character matricies (discrete,
morphometric and text characters)

Distribution Maps Vincent Smith [THANKS]

Presence absence
country maps


Specimens & locations Vincent Smith [THANKS]

Specimen & location
records (DwC)


Pages, Forums, Blogs, Newsletters
Vincent Smith [THANKS]

Static web pages

Web fora with e-
mail integration

Newsletters with e-
User blogs mail integration


Mass Import Vincent Smith [THANKS]

Import from CSV text file to any content type


Multilingual Support Vincent Smith [THANKS]

Create & switch between content in any language


Taxon Pages Vincent Smith [THANKS]

Integrating data & “publishing” in a Scratchpad

Including 3rd party content

Products


[apps]: examples
• Challenging [biogeographic] theories
• Conservation
• Modeling
• Predicting change
• Expedition design
• Data exploration
• Gap analysis
• Observing systems
Jan Strugnell [THANKS]

Huw and me [THANKS]

All
Species


Huw and me [THANKS]

Benthic
Species


Huw and me [THANKS]

Planktonic
Species


Huw and me [THANKS]

Birds
&
Mammals


Biogeo Atlas Gang [THANKS]

Limopsis prediction (0.04 – 0.53)



Limopsis Random Forest



Bivalve Richness (0.05-7.2)


SCAR-MarBIN in the
literature


Convinced?


Nuts & Bolts


METADATA
• WHAT?
• Contact, abstract, citation
• much more can be entered
• HOW?
• online form: Datasets>Submit a dataset
• download data toolkit then email to me
• contact me

Your data is
DISCOVERABLE


DATA
• WHAT?
• ScientiﬁcName, Latitude, Longitude, Date
• much more can be added
• HOW?
• enter the metadata (!!!!)
• use DTK, or your own stuff, or more advanced
techniques
• contact your data center or me

PIC
Polar Information Commons


GBIF
Global Biodiversity Information Facility
www.gbif.org


Your data is OPEN


Your data is CITABLE


Your data is LINKED


Your data is
INTEROPERABLE


Your data is USEFUL


Your data is SAFE


Food for thought
• its a time of rapid change, need for timely change
in our behavior regarding data publication:
NORMS
• IPY/CAML’s virtual legacy
• save the whales? save the birds? SAVE THE DATA
FIRST! [in as many contexts as possible]
• ﬂying across disciplines is exciting!
• information networks are organic
• this is just a beginning!

Jump in!


Thanks!
bruno.danis@scarmarbin.be

www.scarmarbin.be

www.biodiversity.aq

www.slideshare.net/scarmarbin


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