![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]](https://image.slidesharecdn.com/symposium7agosti20140723ishcuzcoagosti-140723120645-phpapp02/85/A-Step-Towards-From-Read-to-Write-Access-to-Taxonomic-Publications-9-320.jpg)
A Step Towards (From) Read to Write Access to Taxonomic Publications
- 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
- 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…
- 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
- 28. Solution Blue List elements of taxonomic information that are not subject to copyright… e.g. treatments (Patterson et al., 2014)
- 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
- 36. Solution: Digital object identifiers Publications Treatments Images / digital objects Data
- 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