Donat Agosti, Plazi
ICD8
Potsdam
13.8.2014
From Read to Write Access to
Taxonomic Publications
Editing and writing privileges
Read Write
Plazi can help you make it happen
Why do you publish?
What do you expect from a publication?
What might others expect from publications?
What is a taxonomic publication?
http://wikisource.org/wiki/File:Brooklyn_Museum_-_Egypt-Gizeh_%28pd%29_%281%29.jpg
What about new insights?
Editing and writing privileges
Read Write
What about questions?
Taxonomic publications
PDFs are stupid –
only humen can
understand them
Content not Form
What is a taxonomic publication?
Taxonomic publication
Our means to document life on earth
Treatments as standard containers of taxononmic publications
http://en.wikipedia.org
Treatment
Treatment
Treatment
Treatment
Treatment
publications or (more frequently) sections of
publications documenting the features or distribution
of...
Treatment
Each taxonomic name usage has it’s treatment
Treatment
Formica obsoleta Linnaeus, 1758: 580
Plazi treatment elements schema
Treatment text
Cite Treatment 1
Cite DNA sequence 1
Cite Figure 1
Cite Abbreviation 1
Cite...
Countries (Region)
Australia (Queensland)
Export species materials citations (DwC)
DNA
Specimens Observations
Institution
Pharmacology/epidemiology
Publication
Treatment
Treatment
Treatment
Table
Appendix
...
Pseudomyrmex ants and Vachellia ant-acacias
are a classic example of mutualism in biology.
allenii
melanoceras
ruddiae
chi...
Treatment
Linking of treatments using persistent identifiers
Treatment
citation
Treatment
identifier
Treatment
Linking of treatments to external resources
Treatments
Treatments
Plazi Search and Retrieval
Server: Access to data
DwC-A
You
You
You
human
machine
What about questions?
Brazil
All content in Plazi (34,000 treatments)
14,590 specimens
8900 plottable specimens from
1138 unique locations
200,000,000+ printed pages
1,900,000 species described
20,000,000+ species treatments
17,000 new species per year
BUT: The...
Text
<tax:treatment>
<tax:nomenclature>
<tax:name>
<tax:xid source="HNS" identif
<tax:xmldata>
<dc:Genus>Mystrium</dc:Gen
...
Markup setup: definition of a vocabulary
Taxpub / TaxonX define the XML elements
Markup: Conversion
Plazi
SRS
find scan «OCR» markup store
?domain domaingeneric
Plazi Digitization and Markup Workflow:
Go...
Makup workflow: Biodiversity Literature Repository
Markup: GoldenGATE editor
Markup: linking to external resources
WINDOW 1 WINDOW 2
Markup: Conversion
Find the right mix of generic and domain specific solutions
Plazi
SRS
find scan «OCR» markup store
?
do...
Markup workflows
You External service
Treatment √
Publication √
Corpus √ √
Journal √
Epilogue
Blue List
elements of taxonomic information that
are not subject to copyright… e.g.
treatments
(Patterson et al.,...
Epilogue
Open Access
Epilogue
Bouchout Declaration
Links
Links
Further reading: http://plazi.org/?q=plazi_publications
Catapano, 2011 (http://www.ncbi.nlm.nih.gov/books/NBK4...
Thank you!
Donat Agosti
agosti@plazi.org
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Agosti 20140813 icd8_agosti_global_dipterology-2

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

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  • Notes:

    Add in Plazi and the idea of the treatment server
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  • Agosti 20140813 icd8_agosti_global_dipterology-2

    1. 1. Donat Agosti, Plazi ICD8 Potsdam 13.8.2014 From Read to Write Access to Taxonomic Publications
    2. 2. Editing and writing privileges Read Write
    3. 3. Plazi can help you make it happen
    4. 4. Why do you publish?
    5. 5. What do you expect from a publication?
    6. 6. What might others expect from publications?
    7. 7. What is a taxonomic publication?
    8. 8. http://wikisource.org/wiki/File:Brooklyn_Museum_-_Egypt-Gizeh_%28pd%29_%281%29.jpg
    9. 9. What about new insights?
    10. 10. Editing and writing privileges Read Write
    11. 11. What about questions?
    12. 12. Taxonomic publications PDFs are stupid – only humen can understand them
    13. 13. Content not Form
    14. 14. What is a taxonomic publication?
    15. 15. Taxonomic publication Our means to document life on earth
    16. 16. Treatments as standard containers of taxononmic publications http://en.wikipedia.org Treatment
    17. 17. Treatment Treatment
    18. 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. 19. Treatment Each taxonomic name usage has it’s treatment Treatment Formica obsoleta Linnaeus, 1758: 580
    20. 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. 21. Countries (Region) Australia (Queensland) Export species materials citations (DwC)
    22. 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. 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. 24. Treatment Linking of treatments using persistent identifiers Treatment citation Treatment identifier
    25. 25. Treatment Linking of treatments to external resources
    26. 26. Treatments
    27. 27. Treatments Plazi Search and Retrieval Server: Access to data DwC-A You You You human machine
    28. 28. What about questions?
    29. 29. Brazil
    30. 30. All content in Plazi (34,000 treatments) 14,590 specimens 8900 plottable specimens from 1138 unique locations
    31. 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. 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. 33. Markup setup: definition of a vocabulary Taxpub / TaxonX define the XML elements
    34. 34. Markup: Conversion Plazi SRS find scan «OCR» markup store ?domain domaingeneric Plazi Digitization and Markup Workflow: GoldenGATE
    35. 35. Makup workflow: Biodiversity Literature Repository
    36. 36. Markup: GoldenGATE editor
    37. 37. Markup: linking to external resources WINDOW 1 WINDOW 2
    38. 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. 39. Markup workflows You External service Treatment √ Publication √ Corpus √ √ Journal √
    40. 40. Epilogue Blue List elements of taxonomic information that are not subject to copyright… e.g. treatments (Patterson et al., 2014)
    41. 41. Epilogue Open Access
    42. 42. Epilogue Bouchout Declaration
    43. 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. 44. Thank you! Donat Agosti agosti@plazi.org
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