A Step Towards (From) Read to Write Access to Taxonomic Publications


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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

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A Step Towards (From) Read to Write Access to Taxonomic Publications

  1. 1. Donat Agosti, Plazi ISH Conference Cuzco 23.7.2014, Cuzco A Step Towards (From) Read to Write Access to Taxonomic Publications
  2. 2. Acknowledgement Pensoft Pro-iBiosphere / EU FP7 Zenodo / CERN
  3. 3. Why do you publish?
  4. 4. What do you expect from a publication?
  5. 5. What might others expect from publications?
  6. 6. What is a taxonomic publication?
  7. 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. 8. Treatment Treatment
  9. 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. 10. Treatment Each taxonomic name usage has it’s treatment Treatment Formica obsoleta Linnaeus, 1758: 580
  11. 11. Treatments as standard containers http://en.wikipedia.org Treatment
  12. 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. 13. Countries (Region) Australia (Queensland) Export species materials citations (DwC)
  14. 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. 15. Treatment Linking of treatments using persistent identifiers Treatment citation Treatment identifier
  16. 16. Treatment Linking of treatments to external resources
  17. 17. Treatment Plazi Search and Retrieval Server: Access to data DwC-A You You You human machine
  18. 18. What are taxonomic publications? Taxonomic publictationS
  19. 19. Journal of Hymenoptera Research 5170 specimens 4062 plottable specimens from 1138 unique locations
  20. 20. Brazil
  21. 21. All content in Plazi (34,000 treatments) 14,590 specimens 8900 plottable specimens from 1138 unique locations
  22. 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. 23. Taxonomic publications PDFs are stupid – only men can understand them but…
  24. 24. GoldenGATE editor
  25. 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. 26. Solution for the future Publish semantically enhanced: Journal of Hymenoptera Research
  27. 27. Solution Open Access
  28. 28. Solution Blue List elements of taxonomic information that are not subject to copyright… e.g. treatments (Patterson et al., 2014)
  29. 29. Solution Bouchout Declaration
  30. 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. 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. 32. Solution
  33. 33. Solution
  34. 34. Solution Linking
  35. 35. Solution DOI persistent identifiers
  36. 36. Solution: Digital object identifiers Publications Treatments Images / digital objects Data
  37. 37. Solution DOI for publications DOI
  38. 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. 39. Solution
  40. 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. 41. Solution
  42. 42. Solution
  43. 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. 44. Solution Why don’t we assure that all the legacy taxonomic literature is in the Biodiversity Literature Repository?
  45. 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. 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. 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. 48. Thank you! Donat Agosti agosti@plazi.org