1. 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

2. Overview
Who are we?
The issue
The Plazi workflow
The legal aspects
Synopsis

3. Extensive 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

4. 200,000,000+ printed pages
1,900,000 species described
20,000,000+ species treatments
17,000 new species per year
Biodiversity libraries
BUT: The data are hidden
Incomplete digitization
Publications are
unstructured
Collections are incomplete
Data are not linked
Most data are not open

5. Names as information tags in life sciences
Names
Characteristics
Publications
GenesCollections
Specimens
Distribution

6. A global reference system for spatial data
60 48'9.75"N
50 50'1.23"E

7. 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

8. 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

9. Needed:
Global Names Architecture
http://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

10. 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

11. 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

12. 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

13. 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.
1.30, SI 137, PW 0.73, ML 0.38. Mandible oute
to a sharp apical tooth, the apex parallel to
(Holotype with material in mandibles, so mand
$ described below from paratypes.) Median cly
....
</treatment>
Enhanced and linked text
Formalization of taxonomic publications

14. Links
Conversionn

15. The way forward or prospective publishing
Fresh of press: fully automated
distribution of data from publications
From discovery to publcation in three weeks …

16. What does this mean?
Linked Open Data Cloud
http://www.w3.org/wiki/SweoIG/TaskForces/CommunityProjects/LinkingOpenData

17. Plazi workflow: overview

18. 1 Million Treatment Goal
to complement Global Names Architecture
name usages with the respective treatments
Semantic enhanced linked publishing

19. Funding

20. The real issue

21. 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
The real issue: copyright

22. Restrictions to information exchange:
- National security / data protection (n/a)
- Copyright (only "works")
- Database protection (only private commercial databases)
- Data use agreements
Copyright issues

23. Obstacles to Plazi workflow:
- Scanning / reproduction of works
- Scanning / reproduction of databases
- Making available of works
Copyright issues

24. 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

25. 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

26. 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

27. For further reading:
http://plazi.org/?q=plazi_publications
http://plazi.org
Thank you very much!
Donat Agosti & Willi Egloff
agosti@plazi.org