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2 donat agosti-1

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Interoperability of taxon treatments. Lecture at at the Final Meeting of the Pro-iBiosphere Conference, Meise, Belgium. http://wiki.pro-ibiosphere.eu/wiki/Final_Conference

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2 donat agosti-1

  1. 1. Interoperability of Taxon Treatments Donat Agosti Plazi Brussels, June 2, 2014 Supported by the European Commission through its FP7 research funding programme
  2. 2. The big question What is the future of the biological world? Imagine if we could: …Predict community level dynamics of ecosystems at scales from local to global, based on the ecology and biology of all individual organisms Harfoot, BIH2013, Rome, 2013 Hardisty, Nature 502, 171 (2013) BUT: predictive ecology has substantial data needs
  3. 3. Biodiversity libraries 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
  4. 4. Interoperability of taxa Can we build a system (e.g. Open Biodiversity Knowledge Management System) that includes a component that extracts, stores and serves and serves information on taxa in a system that is agnostic of Biota? Traditionally Floras, Faunas, Mycotas are dealt with by different communities
  5. 5. Pro‐iBiosphere project is to develop a blue print of an Open Knowledge Management System It is not building a system Pilots to demonstrate specific issues interoperability of taxa explore workflows to produce recommendations of «best» practices interoperability of infrastructures registration of names advanced publishing Do not expect production level products
  6. 6. Treatment Formica obsoleta Linnaeus, 1758: 580 Each taxonomic name usage has it’s treatment
  7. 7. Treatment as standard containers http://en.wikipedia.org
  8. 8. Pilot 1: Taxa used for markup Taxa Documents Treatments Mistletoes 3 124 Chenopodium 15 174 Fungi 5 5 Bryophyta 2 25 Nephrolepis 1 35 Centipedes 50 154 Ants 40 486 Spiders 30 219 TOTAL ca. 140 ca. 1500
  9. 9. Chenopodium pilot
  10. 10. Spider pilot: machine access to content through markup Pardosa logunovi
  11. 11. Spider pilot: overview of 34 OA Zootaxa publications 5170 specimens 4062 plottable specimens from 1138 unique locations
  12. 12. melanoceras chiapensis cookii sphaerocephala allenii collinsii ruddiae cornigera globulifera hindsii janzenii mayana boopis Pseudomyrmex ants and Vachellia ant‐acacias are a classic example of mutualism in biology. hesperius flavicornis Treatment: redescription opaciceps ita janzeni kuenckeli mixtecus nigrocinctus nigropilosus 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: original description Associated ant‐acacia: Acacia gentlei Ants Plants Photocredits: Alex Wild Treatment Treatments linked through citations Transbiotic interoperability
  13. 13. Pro‐iBiosphere 1,000 treatements Plazi 10,000 treatments Pensoft 23,000 Total 34,000 treatments Legacy literature Prospective literature
  14. 14.
  15. 15. All data in Plazi 14,590 specimens 8900 plottable specimens from 1138 unique locations
  16. 16. Brazil 5170 specimens 4062 plottable specimens from 1138 unique locations
  17. 17. Brasil
  18. 18. Journal of Hymenoptera Research 5170 specimens 4062 plottable specimens from 1138 unique locations
  19. 19. Interoperability of taxa Can we build a system (e.g. Open Biodiversity Knowledge Management System) that includes a component that extracts, stores and serves and serves information on taxa in a system that is agnostic of Biota? Yes, we can.
  20. 20. Isssues and Recommendations Legacy Prospective Digitization √ OCR / Text capture √ Markup √ (√) Standardization √ √ Strategies to markup √ External links √ (√) Semantic √ (√) enhancment Create content √ (√)
  21. 21. Plazi SRS Digitization and Markup Workflow: $$$$ ? find scan «OCR» markup store ? domain generic domain Find the right mix of generic and domain specific solutions
  22. 22. Create Content: selection strategy 200,000 Taxonomic Articles in Zoological Record Since 1864
  23. 23. Markup / data extraction strategies Dedicated external services, bulk Applications for individual contributor, small scale Involve community / crowd / wikimedia Ad hoc Web Services, individual Mixed strategies Combination with re‐publishing, small scale Create market for treatments, large scale
  24. 24. Variation in status labels Quality Control and Standardization TaxStatus ctd. Total ctd REVISED STATUS 10 s. str. 1 sp. n. 130 sp. nov. 4057 sp.n. 3 spec. nov. 34 stat. nov. 56 Status revised 9 subsp. nov. 26 var. nov. 80 (blank) Grand Total 5965 TaxStatus Total comb. nov. 246 G. N. 65 gen. nov. 19 gen.nov. 10 hybr. nov. «sp.nov.» 13 n sp 12 n. comb. 2 n. nom. 6 n. sp. 267 n. stat. 5 n. subg. 3 new combination 139 new species 651 NEW STATUS 114 nomen novum 6 nov. spec. 1 Standardize and apply in prospective publishing …
  25. 25. Standardization of markup Formica rufa Linnaeus 1758: 426 Genus name year of pub. Species epithet page of publicat Name Authority Bibliographic reference Treatment citation
  26. 26. Linking of treatment as an example for external links Treatment citation Treatment identifier
  27. 27. Conclusions • Biodiversity literature is very rich in data • BL has a basic structure (treatments) across all Biota • Legacy literature should be strategically marked up • Prospective literature should be semantically enhanced • Markup tools exist and should be optimized • Identifiers for treatments exist to link to treatments
  28. 28. Thank you very much! Donat Agosti Plazi agosti@plazi.org

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