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. »


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)


• 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

Antarctic Biodiversity Information Networks


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 data

standardize

DwC-A

upload publish

IPT ANTABIF

publish

Data Paper

(your point of view)


Data flow(our point of view)


Applications


BENTHOS

PLANKTON

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


All species


21

Benthic species


Birds and Mammals (nice and fluffy)

Clarke AH, Danis B, Griffiths HJ, DSRII 2011


Nematoda (small and ugly)



Echinodermata (in between)


Echinodermataa b


2,8 isopod species described per year

600+ discovered during ANDEEP expeditions

214 years to describe them!

De Broyer C & Danis B, DSRII 2011

Yet another problem


•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

Biogeographic Atlas


Hedgpeth 1969’s Folio


http://share.biodiversity.aq/Atlas/Resources/AntarticMapFolio11.pdf

http://share.biodiversity.aq/Atlas/Resources/AntarticMapFolio11.pdf

Mashing (and sharing) data layers

SlopeBathymetryChlorophyll

Distance to the continentDistance to bird colonies

Distance to iceDistance to shelf

Distance to canyonFloor temperature

...


Functionalities


• organized in subdomains: “.aq” = Antarctica

• www.biodiversity.aq

• data.biodiversity.aq

• ipt.biodiversity.aq

• afg.biodiversity.aq

• scratchpads.biodiversity.aq

• ogc.biodiversity.aq

biodiversity.aq


http://www.antabif.be


• general website

• latest news

• contact

• sponsors

• governance

• RSS feeds: blog, PIC, photostream, slideshare, Mendeley

www. biodiversity.aq




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


Antarctic Field Guidesafg.biodiversity.aqafg. biodiversity.aq


afg.biodiversity.aqafg. biodiversity.aq


Carrots


Data PaperMetadata document

Reward data publishing


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


• 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

Step-by-Step


• 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.

Once paper is accepted


• 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

Important to consider


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 canjust 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


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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


www.biodiversity.aq

image © NY Times

Thanks


http://www.biodiversity.aq

http://www.biodiversity.aq

http://www.polarcommons.org

http://www.polarcommons.org

antarctic biodiversity networks: new architecture, new tools

Technology

data papertuesday

occurrence data

nd primary biodiversity

metadata push data

gbif data management

antarctic treaty

obis antarctic node

grifths hj