6. Indicators as powerful widely understood tool
Reed Elsevier, Annual Reports and Financial Statements 2013
http://www.reedelsevier.com/investorcentre/reports%202007/Documents/2013/reed_elsevier_ar_2013.pdf
39% profit
7. Biodiversity research and conservation planning0
Multi-Taxon Specimen Data for Setting Conservation Priorities
Source: Kremen C, et al. 2008. Science 320: 222-226.
Consensus conservation priority areas and
actual and proposed protected areas
2003: Madagascar announces it will triple protected land to 10% coverage
9. EU-Political and Science Decision to support IPBES
EU-BON
European Biodiversity Observation Network
EU-FP7 funded
10. A EU decision in support of environmental policy making
EU-BON
• To build a European Biodiversity Observation
Network
• Measure and predict change over space and time
• Combine Remote Sensing data and on the ground
observation data in predictive modeling
• Tools to inform decision makers (EU-politicians)
11. The basic science question
Hardisty, Nature 502, 171 (2013)
BUT: predictive ecology has substantial data needs
Harfoot, BIH2013, Rome, 2013
What is the future of the biological world?
Imagine if we could:
…Predict community level dynamics of ecosystems at
scales from local to global, based on the ecology and
biology of all individual organisms
13. Communication
EU-BON a child of GEOSS
Global Earth Observation System of Systems
Open Access to remote sensing data from all over the
world
14. The impact of remote sensing data on understanding biodiversity
With sophisticated technologies we can identify different trees in the Amazon…
http://video.ted.com/talk/podcast/2013G/None/GregAsner_2013G-480p.mp4
15. Access to data
…we could create a link to the related data in our biodiversity literature
http://video.ted.com/talk/podcast/2013G/None/GregAsner_2013G-480p.mp4
16. Names as information tags in life sciences
Names
Characteristics
Publications
GenesCollections
Specimens
Distribution
17. Treatments as bits of information
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
18. Treatments as part of publications
DNA
Specimens Observations
Institution
Pharmacology/epidemiology
Publication
Treatment
Treatment
Treatment
Table
Appendix
Biology/ecology
Reference to other biota
Publication
Treatment
Publication
19. Text
(e.g. PDF)
<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
(XML: Taxonx / Taxpub JATS)
Plazi: Semantic enhanced treatments
20. Automatic extraction and visualization of treatment content
Countries
Madagascar
Anochetus grandidieri Forel
21. Datamining of treatments
Pseudomyrmex ants and Vachellia ant-acacias
are a classic example of mutualism in biology.
allenii
melanoceras
ruddiae
chiapensis
collinsii
cookii
cornigera
globulifera
hindsii
janzenii
mayana
sphaerocephala
boopis
flavicornis
hesperius
ita
janzeni
kuenckeli
mixtecus
nigrocinctus
nigropilosus
opaciceps
particeps
peperi
reconditus
satanicus
simulans
spinicola
subtilissimus
veneficus
ferrugineus
gentlei
gracilis
Transbiotic link network
Associated species linked through
references in taxonomic treatments
Acacia-ant species: Pseudomyrmex gracili
Treatment: original description
Treatment: redescription
Associated ant-acacia: Acacia gentlei
Ants Plants
Photocredits: Alex Wild
Treatment
Treatments linked
through citations
22. The Plazi approach
From treatment
to treatment repository
The Plazi approach
Agosti, D., W. Egloff. 2009. Taxonomic information exchange and copyright: the Plazi approach.
BMC Research Notes 2009, 2:53. doi:10.1186/1756-0500-2-53
24. Analyzing a large corpus of publications: Plazi repository
14,590 specimens
8900 plottable specimens from
1138 unique locations
25. Analyzing a journal: Journal of Hymenoptera Research
5170 specimens
4062 plottable specimens from
1138 unique locations
26. The biodiversity community
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
28. The taxonomy publishing world
12,000 Taxonomic Papers on 42,000 Spiders
Since 1757
Publications widely scattered
Source: Jeremy Miller
29. Why is the system broken?
WHY
does it NOTwork?
30. Access to data limited
…we cannotcreate a link to the related biodiversity data
http://video.ted.com/talk/podcast/2013G/None/GregAsner_2013G-480p.mp4
31. Communication
200,000,000+ printed pages
1,900,000 species described
20,000,000+ species treatments
17,000 new species per year
BUT: The data are hidden
Incomplete digitization
Publications are not
semantically enhanced
Collections are incomplete
Data is not linked
Most data are not open
32. Why is the system broken?
Access to a corpus
NOT
single PDF, data point
33. Why is the system broken?
Access to content
NOT
representations
34. Why is the system broken?
Legal issues
Technical issues
Social issues
35. Legal issues: Copyright
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)
41. Why is the system broken?
WHY
NOT
make it work?
42. European Open Biodiversity Knowledge Management System
European Open
Biodiversity Knowledge
Management System
European Union FP7 funded project
43. European Open Biodiversity Knowledge Management System
Prepare the ground for the creation of
a system for intelligent management
of biodiversity knowledge which will
improve the present system of
taxonomic literature.
44. Legal issues: Copyright: The Blue List
The Blue List
elements of taxonomic information that are not subject to copyright
Patterson, D. J., Egloff, W., Agosti, D., Eades, D., Franz, N., Hagedorn, G., Rees,
J. A. and Remsen, D. P. 2014. Scientific names of organisms: attribution,
rights, and licensing BMC Research Notes 7:79 doi:10.1186/1756-0500-7-79.
45. Legal issues: Copyright: Legal exceptions for research
Legal exceptions for research
Egloff W, Patterson D, Agosti D, Hagedorn G 2014. Open exchange of scientific knowledge and
European copyright: The case of biodiversity information. ZooKeys 414, 109-135. DOI:
10.3897/zookeys.414.7717
48. Technical issues: DOI
Persistent identifiers for data objects and physical objects
Linking data using agreed vocabularies
http://wiki.pro-ibiosphere.eu/wiki/Best_practices_for_stable_URIs
49. Technical issues: DOI
Biodiversity Literature Repository @ Zenodo
public repository for legacy literature using Data Cite DOI
CrossRef to cite (Zenodo) Data Cite DOI?!
50. Technical issues: semantic enhanced publishing
Semantic enhanced publishing
Taxpub JATS
Use DOI as widely as possible
52. Technical issues: semantic publishing
Advanced publishing and dissemination
Form based
Semantnic enhanced TaxPub JATS based publishing
53. Social issues: Bouchout Declaration
http://bouchoutdeclaration.org/ launched June 12, 2014
10 Principles
Free and open use of digital resources
Use of persistent identifiers and linking of data
Policy developments
Developing sustainable business models