pro-ibiosphere towards open biodiversity knowledge coopeus 2013

Jeremy MillerNaturalis Biodiversity Center

Leiden, Netherlands, andPlazi, Switzerland

Pro-iBiosphereTowards Open Biodiversity Knowledge

with Soraya Sierra, Donat Agosti, Lyubomir Penev, and the Pro-iBiosphere team

http://www.pro-ibiosphere.eu/http://wiki.pro-ibiosphere.eu/wiki/Main_Page

Goals

• Address technical and semantic interoperability challenges– How to make taxonomic data, information and knowledge more

widely accessible and re-usable?– How to link taxonomic literature to external datasets?

• Gain a better understanding of how to sustain important workflows and services

Multi-Taxon Specimen Data for Setting Conservation Priorities

Source: Kremen C, Cameron A, Moilanen A, Phillips SJ, Thomas CD, Beentje H, Dransfield J, Fisher BL, Glaw F, Good TC, Harper GJ, Hijmans RJ, Lees DC, Louis E, Nussbaum RA, Raxworthy CJ, Razafimpahanana A, Schatz GE, Vences M, Vieites DR, Wright PC, Zjhra ML. 2008. Aligning conservation Priorities across taxa in Madagascar with high-resolution planning tools. Science 320: 222-226.

Conservation priority areas for six single-taxon solutions

Consensus conservation priority areas and actual and proposed protected areas

Antweb Monographs Field guide

Monograph MonographsField guide

Monographs

2003: Madagascar announces it will triple protected land to 10% coverage

Animals

Records: 230,000,000Species: 165,000Density: 1,400

Plants

Records: 80,000,000Species: 187,000Density: 427

Birds

Records: 183,000,000Species: 1,000Density: 18,000

Hymenoptera

Records: 4,000,000Species: 38,000Density: 112

Spiders

Records: 450,000Species: 15,500Density: 29

GBIF DataGBIF Records Species in GBIF

Plants

Birds

Hymenoptera

Spiders

Other

Plants

BirdsHymenoptera

Spiders

animalsOtheranimals

% D

escr

ibed

spe

cies

in G

BIF

R/Sp: 427

R/Sp: 18,000

R/Sp: 112

R/Sp: 29

Number of Collection Records in Physical Versus Digital Form, by Collection

Number of Collection Records in Physical Versus Digital Form, by Collection

Number of Collection Records in Physical Versus Digital Form, by Collection

the structure of taxonomic data…

Taxonomic article

References

Descriptions

Nomenclature

Images

Records

Na

me

Na

me

Na

me

Na

me

DNA

Taxonomic article

References

Descriptions

Nomenclature

Images

Records

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Na

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Na

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DNA

01001010010011011

0100111010001000100100110111001000Records

01001010010011011

0100111010001000100100110111001000Images

01001010010011011

0100111010001000100100110111001000References

01001010010011011

0100111010001000100100110111001000Nomenclature

01001010010011011

0100111010001000100100110111001000Descriptions

GU

ID

GUID

GUID

GU

ID

GU

ID

GU

ID

Taxonomic article

References

Descriptions

Names

Images

Records

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DNA

01001010010011011

0100111010001000100100110111001000Records

01001010010011011

0100111010001000100100110111001000Images

01001010010011011

0100111010001000100100110111001000References

01001010010011011

0100111010001000100100110111001000Nomenclature

01001010010011011

0100111010001000100100110111001000Descriptions

GU

ID

GUID

GUID

GU

ID

GU

ID

GU

ID

Taxonomic article

References

Descriptions

Names

Images

Records

01001010010011011

0100111010001000100100110111001000DNA

DNA

01001010010011011

0100111010001000100100110111001000Records

01001010010011011

0100111010001000100100110111001000Images

01001010010011011

0100111010001000100100110111001000References

01001010010011011

0100111010001000100100110111001000Nomenclature

01001010010011011

0100111010001000100100110111001000Descriptions

GU

ID

GUID

GUID

GU

ID

GU

ID

GU

ID

GBIF

ZooBank

Global Names

Morphbank

speciesID

EOL

Genbank

Taxonomists

Ecologists

Conservation

Policy

Public

the prospective approach…

Publication PDF

Publication PDF

XML: TaxPub

Publication PDF

XML: TaxPub

Publication PDF

XML: TaxPub

Publication PDF

XML: TaxPub

XML: TaxPub

Encyclopedia of Life

Pensoft: Biodiversity Data Journal

Pensoft: Biodiversity Data Journal

Pensoft: Biodiversity Data Journal

Pensoft: Biodiversity Data Journal

Pensoft: Biodiversity Data Journal

the retrospective approach…

200,000 Taxonomic Articles in Zoological RecordSince 1864

200,000 Taxonomic Articles in Zoological RecordSince 1864

Elements of a Taxonomic Treatment

Elements of a Taxonomic Treatment Nomenclature

Elements of a Taxonomic Treatment Nomenclature

DNA sequences

Elements of a Taxonomic Treatment Nomenclature

DNA sequences

Materials citations

Elements of a Taxonomic Treatment Nomenclature

DNA sequences

Materials citations

Distribution

Elements of a Taxonomic Treatment Nomenclature

DNA sequences

Materials citations

Distribution

Diagnosis

Elements of a Taxonomic Treatment Nomenclature

DNA sequences

Materials citations

Distribution

Diagnosis

Description

Elements of a Taxonomic Treatment Nomenclature

DNA sequences

Materials citations

Distribution

Diagnosis

Description

Natural history

Elements of a Taxonomic Treatment Nomenclature

DNA sequences

Materials citations

Distribution

Diagnosis

Description

Figures

Natural history

Distributing Elements to Biodiversity Databases

Thank you for your attention

Acknowledgments

Naturalis Biodiversity CenterSoraya SierraJan van TolEva Kralt

PlaziDonat AgostiGuido SauterTerry CatapanoWilli Egloff

Pensoft PublishingLyubomir PennevTeodor GeorgievPavel StoevJordan Biserkov

National Botanic Garden of BelgiumQuentin GroomRoyal Botanic Gardens, KewDon KirkupAllan PattonBotanischer Garten und Botanisches Museum BerlinWalter BerendsohnAnton GüntschMuseum für Naturkunde Leibniz Gregor HagedornSigma OrionisCamille Torrenti

COOPEUS-WP6Jesus Marco de Lucas

California Academy of SciencesStan Blum