20140317 pi b_nmbe_journal_club

Towards an (European) Open Biodiversity Knowledge Management System

Donat Agosti (Plazi, Bern)

March 17, 2014

Berne, Journal Club @ NMBE

El Bulli: Cooking in Progress (2011) Ferran Adria (Actor), Gereon Wetzel (Director)

http://www.amazon.com/s?ie=UTF8&field-keywords=Ferran Adria&ref=dp_dvd_bl_act&search-alias=dvd

http://www.amazon.com/s?ie=UTF8&field-keywords=Gereon Wetzel&ref=dp_dvd_bl_dir&search-alias=dvd

The cook (Ferran Adriá) wants to know when he can expect what seafood for his kitchen.

He assumes that phenological data is open and accessible to anyone.

He has a question and needs to know: What seafood at what time?

His goal is to provide a service based on the use of observation data, i.e. treat you (and make some money).

The fishmonger knows when what seafood is available.

He considers his knowledge of seafood phenology as his asset to make money.

His goal is to make money with knowledge based on observation records and understanding the characteristics of seafood.

What do YOU want to know?

How do YOU expect to get to your information?

• What are the main online resources you use?

• Do you maintain your own digital library?

• Do you participate in an online project, egscratchpads, catalogue, digital archive andmake your data accessible?

• … ?

What does this mean?

Meredith Lane, e-biosphere Conference, London 2009

Hardisty, Nature 502, 171 (2013)

BUT: predictive ecology has substantial data needs

Harfoot, BIH2013, Rome, 2013

The big question

What is the future of the biological world?

Imagine if we could:

…Predict community level dynamics of ecosystems atscales from local to global, based on the ecology andbiology of all individual organisms

Decentralized biodiversity infrastructure

Plants

3,400 Herbaria worldwide

10,000 Associate curators and specialists

350,000,000 specimens in collections

180,000,000 specimens digitized

2,000,000,000 specimens including animals

Source: gbif.org; http://sciweb.nybg.org/science2/IndexHerbariorum.asp

200,000,000+ printed pages1,900,000 species described20,000,000+ species treatments 17,000 new species per year

Biodiversity libraries

BUT: The data are hidden

Incomplete digitization Publications areunstructuredCollections are incompleteData is not linkedMost data are not open

Nationaal Herbarium Nederland collection on GBIF

Source: http://www.gbif.org/dataset/7b33b040-f762-11e1-a439-00145eb45e9a

One collection’s view of the world

Another collection’s view of the world

http://www.gbif.org/dataset/82b0f51c-f762-11e1-a439-00145eb45e9a

What does this mean?

The Linking Open Data cloud diagram

Linked Open Data Cloud

Names as information tags in life sciences

Names

Characteristics

Publications

GenesCollections

Specimens

Distribution

The enhanced and linked treatments, extracted, stored on Plazi.org, and served in

a human readable form, are linked to the underlying data: Fisher & Smith, 2008,

PLoS ONE.

Towards an (European) Open Biodiversity Knowledge Management System

Coordination and Policy Development in Preparation for a European Open Biodiversity Knowledge Management

System

Supported by the European Commission through its FP7 research funding programme

pro-iBiosphere

pro-iBiosphere: Partners

Create digital objects+ Identifiers and resolvers

+ Open Access+ Adequate infrastructure

+ Sustainable and permanent infrastructure+ Reliable services for partners in research projects and society

Seamless Global Virtual Research Knowledge Management System

(European Open Biodiversity Knowledge Management System)

Biodiversity Knowledge Management System

Impact

Support reliable and permanent open access to digital biodiversity recordsCreate identifiers and link biodiversity literature, collections, digital objects, genes, etc.Ensure global interoperability and sharing of biodiversity data, information and knowledgeProvide new services in support of open scienceProvide the ground for modelling biosphereDevelop data policies to harness the potential of open access

European Open Biodiversity Management SystemThe envisaged

will:

Convert data into machine readable data

Literature as an example

Text

<tax:treatment>

<tax:nomenclature>

<tax:name>

<tax:xid source="HNS" identifier="193329"/>

<tax:xmldata>

<dc:Genus>Mystrium</dc:Genus>

<dc:Species>leonie</dc:Species>

</tax:xmldata>

Mystrium leonie

</tax:name> Bohn & Verhaagh

<tax:status>n. sp.</tax:status>

Fig 1 D - F

</tax:nomenclature>

<tax:div type="description">

<tax:p>HOLOTYPE WORKER: TL 3.95, HL 1.02, HW 0.95, CI 93, SL

1.30, SI 137, PW 0.73, ML 0.38. Mandible outer margin strongly curving

to a sharp apical tooth, the apex parallel to the anterior clypeal margin.

(Holotype with material in mandibles, so mandibles and anterior clypeus

$ described below from paratypes.) Median clypeus

....

</treatment>

Enhanced and linked text

Treatment

A publication or section of a publication documenting the

features or distribution of a related group of organisms

(called a “taxon”, plural “taxa”) in ways adhering to highly

formalized conventions.

http://terms.tdwg.org/wiki/tp:taxon-treatment

Catapano, 2010.

http://terms.tdwg.org/wiki/tp:taxon-treatment

Treatment

X-us c-us

(Treatment)

Citation

Description

Mate

X-us b-us

(Treatment)

Citation

Description

Material cit

X-us b-us

n.sp

(Treatment)

Citation

Description

Material cit

X-us b-us

(Treatment)

Citation

Description

Material cit

Treatments

X-us c-us

(Treatment)

Citation

Description

Mate

X-us b-us

(Treatment)

Citation

Description

Material cit

X-us b-us

n.sp

(Treatment)

Citation

Description

Material cit

X-us b-us

(Treatment)

Citation

Description

Mateerial cit

Title

(Article)

Bibliogra-phic references

Title

(Article)


Title

(Article)


Title

(Article)


Systema naturae

(Article)


Treatments

References

Treatments can be cited, like publications, with stable identifiers.

http://treatment.plazi.org/id/31F96F41E3E002BD88985A4F3A20E45A

Best practices for stable URIs:

http://wiki.pro-ibiosphere.eu/wiki/Best_practices_for_stable_URIs

Jeremy Miller, Work in Progress

Names can be linked automatically

Automated registration

MANUSCRIPT SUBMISSION

MANUSCRIPT ACCEPTED

XML Response

ARTICLEPUBLISHED

Taxon name available/valid (effectively published)

XML article metadata

XML Query

Peer review

The enhanced and linked treatments, extracted, stored on Plazi.org, and served in

a human readable form, are linked to the underlying data: Fisher & Smith, 2008,

PLoS ONE.

Penestomus egazini Miller, Haddad & Griswold, 2010

Progress

Treatments (% complete): 4/4 (100%)

Data summary

Specimen records: 41

adult femaleadult maleother

51%

2%

46%

Specimen collections

Institutions: 3

Distribution

Muséum National d'Histoire Naturelle, Paris

California Academy of Sciences, San Francisco

Albany Museum, Grahamstown

2%

5%

76%

20%

CountriesLesotho

South Africa

Georeferenced materials citations

Export species materials citations (DwC)

Export treatment materials citations (DwC)

02000400060008000

100001200014000160001800020000

Materials Citations Records by Researcher

Other

Donat Agosti

David Grimaldi

Toby Schuh

James Carpenter

Norman Platnick

American Museum of Natural History

Data summary

Materials citations 2004-2013: 111,364

Distribution



Ma

teria

ls C

ita

tion

s R

ecord

s

0

500

1000

1500

2000

2500

Materials Citations Records by Institution

Other

Muséum National d'HistoireNaturelle, ParisNatural History Museum,LondonMuseum of ComparativeZoologySmithsonian Institution

American Museum of NaturalHistory

Zootaxa

Data summary

Materials citations 2004-2013: 11,476

Distribution



Ma

teria

ls C

ita

tion

s R

ecord

s

Better:

Create data as machine readable data

Unified marked up final outputTaxon treatments, keys, images, localities

PROSPECTIVE PUBLISHING | HISTORICAL LITERATURE

Legacy and new taxonomic literature

Content management systems &repositories (e.g., Plazi, EOL, GBIF, SCRATCHPADS, EDIT)

TaxPub XML schemaPENSOFT MARK UP tool

Marked up publicationsPDF, HTML and XML

archiving

WIKISpecies-ID, Wikispecies

Wikipedia

Indexing (IPNI, ZooBank, Myco-

Bank, GNA)

Aggregators(EOL, GBIF)

Electronic archives; Data

Centers

END

USERS

TaxonX schema PLAZI’ GOLDEN GATE editor

Automated submission; peer-

review

http://biodiversitydatajournal.com/articles.php?id=995

Access to ant taxonomic publications through antbase.org /Smithsonian Institution, including currently the entire

body of non-copyrighted publications since 1758 (>4,000 publications or 85,000 pages)

Open Access

Knowledge wants to be free

Before antbase.org, Harvard‘s Museum of

Comparative Zoology could claim to be the only

location with a complete set of ant systematics

publications from 1758 - present.

Before antbase.org, Harvard‘s Museum of

Comparative Zoology could claim to be the only

location with a complete set of ant systematics

publications from 1758 - present.

Through antbase.org‘s

digital library, access

to this body of

literature is worldwide,

and it is actively used

(>10,000 visits in one

month only).

Knowledge has to be free

Bouchout Declaration, 2014

Umsetzung durch den Schweizerischen Nationalfonds, 2007

Berlin Declaration, 2003

• The free and open use of content, services and other digital resources about biodiversity;

• Licenses that grant all users a free, irrevocable, world-wide, right to copy, use, distribute, transmit and display the work publicly as well as build on the work and making derivative works, subject to proper attribution consistent with community practices;

• Policy developments that will foster free and open access to biodiversity data;

• Tracking the use of information to ensure that sources and suppliers of data are assigned credit for their contributions;

• An agreed infrastructure, standards and protocols to improve access to and use of open data;

Bouchout Declaration, 2014 (1)

• Registers for content and services to allow discovery, access and use of open data;

• Persistent, dereferenceable identifiers for data objects and physical objects such as specimens, images and taxonomic treatments;

• Linking data using agreed vocabularies, both within and beyond biodiversity, that enable participation in the Linked Open Data Cloud;

• Dialogue coordinated by the leading signatories to refine the concept, priorities and technical requirements of Open Biodiversity Knowledge Management.

• A sustainable Open Biodiversity Knowledge Management that is attentive to scientific, sociological, legal, and financial aspects.

Bouchout Declaration, 2014 (2)

Knowledge has to be made free

Reduce costs – future publishing

Don’t waist money:

Focus on Open Access enhanced linked publications – not pdf only

founded in 2008

Swiss based NGO with members in

Switzerland, Germany, Bulgaria, US and

Iran

research based think tank with the

mission to promote open access to

scientific content

five pillars: Legal advice,

technical innovations and solutions,

maintenance of a treatment repository

and Biowikifarm, consultancy, advocacy

Modify copyright legislation to serve

better the scientific needs

Taxpub TaxonX

DTD Schema

Prospective publications Legacy publications

Constraint loose

Derivative of JATS independent

Self-contained Allows import of other schemas

Plazi workflow: overview

Plazi Search and Retrieval Server: Access to data

Darwin Core-Archive

You

You

You

human

machine

Biowikifarm

founded in 2008

Swiss based NGO with members in

Switzerland, Germany, Bulgaria, US and

Iran



scientific content





Plazi GmbH founded in 2012 as

service SME owned by Plazi



scientific content







Funding from public donors, eg. EU,

corporate and private

Funding:

EU

EU-BON

Pro-iBiosphere

Private sector

Inkind

Voluntary work

five pillars: Legal advice, technical

innovations and solutions, maintenance

of a treatment repository and

Biowikifarm, consultancy, advocacy



Funding from public donors, eg. EU,

corporate and private

Clients are global

Consultancies and Services:

Consulting publishers on how to

produce XML semantically enhanced

output (eg. EJT, Zootaxa, Smithsonian

Institution)

Service to mark-up literature

http://plazi.org

Thank you very much!

Donat Agosti

[email protected]

This project is funded under the European Union's Seventh Framework

Programme (FP7/2007-2013) under grant agreement №312848.

20140317 pi b_nmbe_journal_club

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