Case study 2: (Plazi) Treatment Repository

Donat Agosti & Willi Egloff (Plazi, Bern) March 27, 2014

Dublin, RDA Third Plenary Meeting,RDA/CODATA Legal Interoperability IG

Overview

Who are we?

The issue

The Plazi workflow

The legal aspects

Synopsis

Extensive decentralized biodiversity infrastructure

Plants3,400 Herbaria worldwide10,000 Associate curators and specialists350,000,000 specimens in collections 180,000,000 specimens digitized2,000,000,000 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 are unstructuredCollections are incompleteData are not linkedMost data are not open

Names as information tags in life sciences

Names

Characteristics

Publications

GenesCollections

Specimens

Distribution

A global reference system for spatial data

60°48'9.75"N50°50'1.23"E

A global reference system for species related data

(http://www.yourwildlife.org/wp-content/uploads/2013/02/Common-ant-collage.jpg)

2D78C98D-0B15-4362-8DD8-185983C468FE

A global reference system for species related data

Spatial data Taxonomic data

Entity Location Species

Entity name Location name Scientific Name

Reference Geo-Coordinate UUID

Reference System Coordinate System Hierarchical System

Reference Data Global Map / Global Satellite coverage

Global Names Archictecture

Needed:

Global Names Architecturehttp://globalnames.org

(Reference system for all names)

SEE also: RDA Biodiversity Data Integration IG; RDA Data publishing IG

A global reference system for species related data

Formica obsoleta Linnaeus 1758, 580

zoobank.org:act:2D78C98D-0B15-4362-8DD8-185983C468FE

Taxonomic name usage defined by a treatment

A global reference system for species related data

A global reference system for species related data

Treatment: sections of publications documenting the features or distribution of a related group of organisms (called a “taxon”, plural “taxa”) in ways adhering to highly formalized conventions. (Catapano, 2010)

Formica obsoleta, Linnaeus 1758: 580

Formica obsoleta Linnaeus 1758, 580

zoobank.org:act:2D78C98D-0B15-4362-8DD8-185983C468FE

Taxonomic name usage defined by a treatment

treatment.plazi.org/id/2D78C98D-0B15-4362-8DD8-185983 C468FE

A global reference system for species related data

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

Formalization of taxonomic publications

Links

Conversionn

The way forward or prospective publishing

Fresh of press: fully automated distribution of data from publications

From discovery to publcation in three weeks …

What does this mean?

Linked Open Data Cloud

http://www.w3.org/wiki/SweoIG/TaskForces/CommunityProjects/LinkingOpenData

Plazi workflow: overview

1 Million Treatment Goal to complement Global Names Architecture name usages with the respective treatments

Semantic enhanced linked publishing

$$$$Funding

The real issue

BUT

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)

The real issue: copyright

Restrictions to information exchange:

- National security / data protection (n/a)

- Copyright (only "works")

- Database protection (only private commercial databases)

- Data use agreements

Copyright issues

Obstacles to Plazi workflow:

- Scanning / reproduction of works

- Scanning / reproduction of databases

- Making available of works

Copyright issues

Legal base for actual workflow

- Legal license for internal use in organizations / institutions (Art. 19 CH-Copyright Act)

- No database protection in CH

- Legal license overrules data use agreements

Copyright issues

Making available:

- Only non copyrighted data (names, treatments, references, ... See http://plazi.org/?q=blue_list)

- Works (original publications) restricted to internal use

Copyright issues

Removing further hurdles to information exchange:

- Suggest mandatory legal licenses for research purposes at EU-level

- Explore application of extended collective licenses (Scandinavian countries)

- Introduce extended collective licenses into CH-copyright law

Copyright issues

For further reading:http://plazi.org/?q=plazi_publications

http://plazi.org

Thank you very much!

Donat Agosti & Willi Egloff

agosti@plazi.org