This document discusses a schema for describing and exchanging the content of taxonomic publications in a way that allows both human and machine access. It proposes using semantic markup like XML to tag elements in publications like names, descriptions, and references in a way that links related data across sources. This would allow content to be more accessible for tasks like data mining while maintaining context. The schema is part of ongoing work by Plazi to apply semantic markup to digitize existing publications and structure new ones for improved dissemination and reuse of taxonomic knowledge.

1. A Schema for Description and Exchange of TaxonomicPublication's Content Donat Agosti, Terry Catapano, Lyubomir Penev & Guido Sautter Plazi, Bern, Switzerland 25. July 2011, IBC, Melbourne

2. WHY?

3. disseminate access knowledge

4. New York Times, July 19, 2011

5. “JSTOR's the one that should be in prison, man, for locking up knowledge.”Hufpost Politics, July 19, 2011http://www.huffingtonpost.com/2011/07/19/huffpost-hill----gang-vio_n_904027.html

6. Open Access

8. CNS classified abstracts: 874,727

9. text mining recognized: 368,688

10. text mining processed: 94,381

11. extracted graph of 30,000+ relationships and 5,500 genes and proteins“protein-protein interaction networks” John Wilbanks, Neurocommons

12. 27,266 papers 128,437 papers 41,985 papers 4,563 papers 10,365 papers In a semantic Web environment (where machines talk to each other and do most of our work), data need to be able to talk to each other: “protein-protein interaction networks” John Wilbanks, Neurocommons

13. “protein-protein interaction networks” John Wilbanks, Neurocommons It will open up scientific literature for data mining

14. HOW?

15. accessfor human ANDmachine

16. It is about digesting millions of pages: >>100 M pages taxonomic literature25M scientific publications / year25K journals>2K with zoological taxonomic descriptions18K descriptions of new species / year

17. PDF is not enough

18. data and information in context

19. semantic markup

20. context of content

21. XMLeXtended Markup Language

22. <tax:treatment> <tax:nomenclature> <tax:name> <tax:xid source="HNS" identifier="193329"/> <tax:xmldata> <dc:Genus>Mystrium</dc:Genus> <dc:Species>leonie</dc:Species> </tax:xmldata> Mystrium leonie Bihn & Verhaagh, new species </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, HL 1.02, HW 0.95, CI 93, SL 1.30, SI 137, PW 0.73, ML 0.38. Mandible outer margin strongly curving to a sharp apical tooth, the apex parallel to the anterior clypeal margin. (Holotype with material in mandibles, so mandibles and anterior clypeus described below from paratypes.) Median clypeus .... </treatment>

23. content in a complex e-environment

24. linking

25. Azteca instabilis Would then read like <tax:name> <tax:xid source=“LSID" identifier=“urn:lsid:biosci.ohio-state.edu.osuc_concetps:13452"/> Link to external database <tax:xmldata> Normalization of data <dc:Genus>Azteca</dc:Genus> <dc:Species>instabilis</dc:Species> </tax:xmldata> Azteca instabilis </tax:name>

26. definition of XML tags DTD schema

27. transformations from XML html print pdf archiving rdf database

28. legacyTaxonXTaxpubprospective

29. how to use XML?

30. legacy publications

32. CBOL

33. NCBI

34. specimen

35. images

36. .....- Get geographic long/lat from geonames.org Legacy publications

37. linked data

38. last resort

39. prospective publications

41. the future

42. dissemination - access

43. Plazi: access to treatments TAPIR, SPM, etc. You You human machine You

44. “protein-protein interaction networks” John Wilbanks, Neurocommons It will open up scientific literature for data mining and extraction

45. http://plazi.org Thank you very much! Donat Agosti, Terry Catapano, Lyubomir Penev & Guido Sautter agosti@plazi.org

46. JSTOR did not permit users:c. to make other than personal use of individually downloaded articles.Aaron Swartz indictment, July 14, 2011