Lecture provided at the 8th International Congress of Hymenopterists, Cuzco, Peru, July 23, 2014. The lectures makes a case to join the bibligraphies and pdf of hymenoptera taxonomy literature on the Biodiersity Literature Repository / Zenodo

1. Donat Agosti, Plazi
ISH Conference
Cuzco
23.7.2014, Cuzco
A Step Towards
(From) Read to Write Access to
Taxonomic Publications

2. Acknowledgement
Pensoft
Pro-iBiosphere / EU FP7
Zenodo / CERN

3. Why do you publish?

4. What do you expect from a publication?

5. What might others expect from publications?

6. What is a taxonomic publication?

7. DNA
Specimens Observations
Institution
Pharmacology/epidemiology
Publication
Treatment
Treatment
Treatment
Table
Appendix
Biology/ecology
Reference to other biota
Publication
Treatment
Publication
Taxonomic publication
Var sections
Bib. refs

8. Treatment
Treatment

9. Treatment
Treatment
publications or (more frequently) 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. Some of these are over a century old.
[Catapano, 2011]

10. Treatment
Each taxonomic name usage has it’s treatment
Treatment
Formica obsoleta Linnaeus, 1758: 580

11. Treatments as standard containers
http://en.wikipedia.org
Treatment

12. Plazi treatment elements schema
Treatment text
Cite Treatment 1
Cite DNA sequence 1
Cite Figure 1
Cite Abbreviation 1
Cite Table 1
Cite Appendix 1
Cite Reference 1
Cite supplementary
materials
Interaction sp. X
Trait 1 value = Y
Inline table
Treatment text, continued
Materials citation
Species interacted with
Cited by treatment
httpUri
httpUri
Map, Dashboard charts
Abbreviation 1
treatment x GUID
Trait database
Sequence in database
httpUri
RDF
Treatment citation ontology
Treatment (Plazi)
httpUri ?
Table 1
Appendix 1
Figure caption
Supplementary materials
Reference 1
Plazi treatment
Linked treatment elements
Other online source
Other links
Content from citations, instances
Content output from treatment
Hyperlink
httpUri
Figure image
Treatment

13. Countries (Region)
Australia (Queensland)
Export species materials citations (DwC)

14. 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: redescription
Associated ant-acacia: Acacia gentlei
Ants Plants
Photocredits: Alex Wild
Treatment
Treatments linked
through citations
Treatment

15. Treatment
Linking of treatments using persistent identifiers
Treatment
citation
Treatment
identifier

16. Treatment
Linking of treatments to external resources

17. Treatment
Plazi Search and Retrieval
Server: Access to data
DwC-A
You
You
You
human
machine

18. What are taxonomic publications?
Taxonomic publictationS

19. Journal of Hymenoptera Research
5170 specimens
4062 plottable specimens from
1138 unique locations

20. Brazil

21. All content in Plazi (34,000 treatments)
14,590 specimens
8900 plottable specimens from
1138 unique locations

22. 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
Taxonomic publictationS

23. Taxonomic publications
PDFs are stupid –
only men can
understand them
but…

24. GoldenGATE editor

25. Conversion
Find the right mix of generic and domain specific solutions
Plazi
SRS
find scan «OCR» markup store
?
domain domaingeneric
Digitization and Markup Workflow:
$$$$ ?

26. Solution for the future
Publish semantically enhanced:
Journal of Hymenoptera Research

27. Solution
Open Access

28. Solution
Blue List
elements of taxonomic information that
are not subject to copyright… e.g.
treatments
(Patterson et al., 2014)

29. Solution
Bouchout Declaration

30. Solution
Support reliable and permanent open access to digital biodiversity
records
Create identifiers, link provide direct access to digital objects of
biodiversity literature, specimens, multimedia, genes, etc.
Ensure global interoperability and sharing of biodiversity data,
information and knowledge
Ongoing dialogue to refine the concept and implementation
As signatories, we encourage an overarching approach to Open Biodiversity
Knowledge Management which is based on the following fundamental
principles:
http://bouchoutdeclaration

31. Solution
Institutional: 57; Individual: 58
Large Natural History Institutions (e.g BGBM, Naturalis,
MfN, RGBM, INBio, MCZ, CAS)
Scientific Networks (e.g. IUBS, Vertnet, CRIA, TaiBIF,
Canadensys, Creative Commons, DataOne)
Scientists
Global
Initial Signatories (June 12, 2014)

32. Solution

33. Solution

34. Solution
Linking

35. Solution
DOI
persistent identifiers

36. Solution: Digital object identifiers
Publications
Treatments
Images / digital objects
Data

37. Solution
DOI for publications
DOI

38. Solution
DOI: CrossRef
doi/10.5281/zenodo.10
doi/10.5281/zenodo.10697
doi/10
DOI: DataCite (Biodiversity Literature Repository)
DOI for publications

39. Solution

40. Solution
ZENODO @CERN
ZENODO builds and operate a simple and innovative service that
enables researchers, scientists, EU projects and institutions to
share and showcase multidisciplinary research results (data and
publications) that are not part of the existing institutional or
subject-based repositories of the research communities.
Zenodo is the digital repository of CERN
Zenodo agreed to host and support the Biodiversity Literature
Repository

41. Solution

42. Solution

43. Solution
Services or what you get:
Wide access
Refindit
Refbank
Legal Issues
Archiving
Distribution of publications resolved
Your legacy literature is for everybody directly from
your publications accesible

44. Solution
Why don’t we assure that all the legacy taxonomic
literature is in the
Biodiversity Literature Repository?

45. The future
Why not assure that all the legacy taxonomic
literature is in the Biodiversity Literature
Repository?
Why not make our community the first that can
publish in its journal with all publications linked
to a digital copy?

46. The future
Why not assure that all the legacy taxonomic
literature is in the Biodiversity Literature
Repository?
Why not make our community the first that can
publish in its journal with all publications linked
to a digital copy?

47. Links
Links
Further reading: http://plazi.org/?q=plazi_publications
Catapano, 2011 (http://www.ncbi.nlm.nih.gov/books/NBK47081/)
Bouchout Declaration (http://bouchoutdeclaration.org)
Blue List (http://plazi.org/?q=blue_list)
Biodiversity Literature Repository (https://zenodo.org/collection/user-biosyslit
Zenodo (https://zenodo.org/about)
Refindit (http://refindit.org)
Refbank (http://refbank.org)
Pro-iBiosphere (http://pro-ibiosphere.eu/)
Introduction to persistent identifiers (http://wiki.pro-
ibiosphere.eu/wiki/Best_practices_for_stable_URIs)
Twitter
@plazi_treat; @bouchoutdec, @myrmoteras

48. Thank you!
Donat Agosti
agosti@plazi.org