20110725 ibc xml
- 1. A Schema for Description and Exchange of TaxonomicPublication's ContentDonat Agosti, Terry Catapano, Lyubomir Penev & Guido SautterPlazi, Bern, Switzerland25. July 2011, IBC, Melbourne
- 2. WHY?
- 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. OpenAccess
- 7. An example from the Neurocommons text mining pilot: PubMed abstracts: > 16,000,000
- 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 papers128,437 papers41,985 papers4,563 papers10,365 papersIn 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, NeurocommonsIt will open up scientific literature for data mining
- 14. HOW?
- 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
- 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 clypeusdescribed below from paratypes.) Median clypeus....</treatment>
- 23. content in a complex e-environment
- 24. linking
- 25. Azteca instabilisWould 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 tagsDTDschema
- 29. how to use XML?
- 31. Plazi workflow: GoldenGate editor based mark up and linking- Get LSID from Hymenoptera Name Server for names; ZooBank?Add new names - Get bibliographic Guids from bioguid (or EDIT?)- Get bibliographic Metadata from HNS (MODS)Get Guids for
- 32. CBOL
- 33. NCBI
- 34. specimen
- 35. images
- 36. .....- Get geographic long/lat from geonames.orgLegacy publications
- 37. linked data
- 38. last resort
- 41. the future
- 43. Plazi: access to treatmentsTAPIR, SPM, etc.YouYouhumanmachineYou
- 44. “protein-protein interaction networks”John Wilbanks, NeurocommonsIt will open up scientific literature for data mining and extraction
- 45. http://plazi.orgThank you very much!Donat Agosti, Terry Catapano, Lyubomir Penev & Guido Sautteragosti@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