lecture presented at 8th International Congress of Dipterology, Potsdam, Germany, 10-15 August 2014, http://www.icd8.info/

1. Donat Agosti, Plazi
ICD8
Potsdam
13.8.2014
From Read to Write Access to
Taxonomic Publications

2. Editing and writing privileges
Read Write

3. Plazi can help you make it happen

4. Why do you publish?

5. What do you expect from a publication?

6. What might others expect from publications?

7. What is a taxonomic publication?

8. http://wikisource.org/wiki/File:Brooklyn_Museum_-_Egypt-Gizeh_%28pd%29_%281%29.jpg

9. What about new insights?

10. Editing and writing privileges
Read Write

11. What about questions?

12. Taxonomic publications
PDFs are stupid –
only humen can
understand them

13. Content not Form

14. What is a taxonomic publication?

15. Taxonomic publication
Our means to document life on earth

16. Treatments as standard containers of taxononmic publications
http://en.wikipedia.org
Treatment

17. Treatment
Treatment

18. 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]

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

20. 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

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

22. DNA
Specimens Observations
Institution
Pharmacology/epidemiology
Publication
Treatment
Treatment
Treatment
Table
Appendix
Biology/ecology
Reference to other biota
Publication
Treatment
Publication
Treatments in a publication
Var sections
Bib. refs

23. 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 gracilis
Treatment: redescription
Associated ant-acacia: Acacia gentlei
Ants Plants
Photocredits: Alex Wild
Treatment
Treatments linked
through citations
Interactions inherent between treatments

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

25. Treatment
Linking of treatments to external resources

26. Treatments

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

28. What about questions?

29. Brazil

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

31. 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

32. Text
<tax:treatment>
<tax:nomenclature>
<tax:name>
<tax:xid source="HNS" identif
<tax:xmldata>
<dc:Genus>Mystrium</dc:Gen
<dc:Species>leonie</dc:Spe
</tax:xmldata>
Mystrium leonie
</tax:name>
<tax:status>n. sp.</tax:status>
Fig 1 D - F
</tax:nomenclature>
<tax:div type="description">
<tax:p>HOLOTYPE WORKER: TL 3.95
1.30, SI 137, PW 0.73, ML 0.3
to a sharp apical tooth, the
(Holotype with material in ma
$ described below from paraty
....
</treatment>
Semantically enhanced text
From human to machine readable text

33. Markup setup: definition of a vocabulary
Taxpub / TaxonX define the XML elements

34. Markup: Conversion
Plazi
SRS
find scan «OCR» markup store
?domain domaingeneric
Plazi Digitization and Markup Workflow:
GoldenGATE

35. Makup workflow: Biodiversity Literature Repository

36. Markup: GoldenGATE editor

37. Markup: linking to external resources
WINDOW 1 WINDOW 2

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

39. Markup workflows
You External service
Treatment √
Publication √
Corpus √ √
Journal √

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

41. Epilogue
Open Access

42. Epilogue
Bouchout Declaration

43. 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

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