Antarctic Biodiversity Networks: new architecture, new tools

Antarctic Biodiversity
Networks

New Architecture, New Tools

Bruno Danis

Tuesday 13 December 11

Objectives

• get familiar with Antarctic Biodiversity
Networks
• learn about the new architecture, and
functionalities
• get you onboard


On the Menu Today
• Background
• (quick) Technical overview
• Applications
• Functionalities
• Carrots
• Future directions

Background


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. »


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)


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


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

Achievements: dataportals

• Portal up since Oct 2005
• open access
• 935,000 visitors
• 8,400,000 hits
• 60,000,000 dld records
• Citations: 183


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)


Achievements: biogeography
• 1,288,441 records
• 198 datasets
• 5,235 taxa
• Feeds OBIS, GBIF
• Downloadable
• WebGIS
• Webservices

Achievements: Progress

Records MarBIN ANTABIF Progress

Metadata 198 7.200 36,4

Occurrence 1.300.000 3.300.000 2,5

Taxonomy 17.000 30.500 1,8


Nuts and Bolts


100% Open Source
• Language: Ruby

• Framework: Rails(ActiveRecord) and YUI

• (smart) Search engine: Full text (Elasticsearch-Lucene)

• Database/GIS server/SpatialDB: PostGresql/Geoserver/PostGIS

• Mapping client: OpenLayers

• Web services: RESTish (all resources)

• Protocols/Standards: DIF, DwC, DwC-A, Tapir…etc

• GBIF tools : HIT, IPT

• Hosting: BeBIF (ULB/VUB joint IT Center)

• Metadata systems: GCMD API (DIF)


Data ﬂow
(your point of view)

Your data DwC-A IPT ANTABIF

standardize upload publish

publish

Data Paper


Data ﬂow
(our point of view)


Applications


Gaps
in
our
knowledge
(spa=al)
Clarke AH, Danis B, Grifﬁths HJ, DSRII 2011
BENTHOS

PLANKTON


All species


Benthic species

21


Birds and Mammals (nice and ﬂuffy)



Nematoda (small and ugly)



Echinodermata (in between)
Echinodermata
a b



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


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

Hedgpeth
1969’s
Folio


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
...


Functionalities


biodiversity.aq
• organized in subdomains: “.aq” = Antarctica
• www.biodiversity.aq
• data.biodiversity.aq
• ipt.biodiversity.aq
• afg.biodiversity.aq
• scratchpads.biodiversity.aq
• ogc.biodiversity.aq

www. biodiversity.aq

• general website
• latest news
• contact
• sponsors
• governance
• RSS feeds: blog, PIC, photostream, slideshare,
Mendeley

www. biodiversity.aq


data. biodiversity.aq
• ﬁnd primary biodiversity data
• visualize occurrence data on map
• view taxonomic data
• download data
• view metrics
• send feedback
• access technical documentation

data. biodiversity.aq


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

ipt. biodiversity.aq


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

afg.biodiversity.aq
Antarctic Field Guides


afg.biodiversity.aq


Carrots


Reward data publishing

Metadata document Data Paper


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


Incentivising Data Discovery


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


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.


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


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

The
basic
NPT
plaPorm
provides
everything
needed
to

start
a
web
site

Non-‐technical
staﬀ
can
just
start
adding
content!

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


Perspectives


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

Challenges
• Data intensive science
• Data deluge
• Digital divides
• Other data types and integration
• Orphan datasets
• Cultural change

Antarctic Biodiversity Networks: new architecture, new tools

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