Environment Institute Science Seminar Series 2009 A virtual co-laboratory for large scale taxonomic research Presented by:...
A virtual co-laboratory for large-scale taxonomic research Norman F. Johnson The Ohio State University urn:lsid:zoobank.or...
Planetary Biodiversity Inventory Goals & Focus <ul><li>new collections of specimens </li></ul><ul><li>phylogenetic analysi...
Focal taxon: Platygastroidea (Hymenoptera) <ul><li>Biology </li></ul><ul><ul><li>egg parasitoids of insects, spiders </li>...
Project participants <ul><li>Australia : A. Austin, M. Dowton, J. Jennings, S. Thompson </li></ul><ul><li>Brazil : A.P. Ag...
Project goals: Collecting <ul><li>Brazil: A.P. Aguiar </li></ul><ul><li>South Africa: S. van Noort </li></ul><ul><li>south...
 
Project goals: Phylogenetics <ul><li>~250 genera considered valid </li></ul><ul><ul><li>add/subtract about equal numbers f...
 
Project goals: Taxonomy <ul><li>Scelionini  s. lato </li></ul><ul><ul><li>extrusible, telescoping ovipositor </li></ul></ul>
Infrastructure Canadian National Collection, Ottawa
Infrastructure <ul><li>Taxonomic catalogs </li></ul><ul><ul><li>Johnson 1992, Vlug 1995 </li></ul></ul><ul><li>Electronic ...
Inaugural workshop <ul><li>Workshop: 5-9 Feb., 2007 </li></ul>
Specimen Acquisition Museums Published Literature Science Taxa Characters Description Publication New Collections Taxonomi...
Published Literature <ul><li>PDF library of taxonomic publications </li></ul><ul><ul><li>1,177 articles </li></ul></ul><ul...
Taxon-Character Loop <ul><li>specimen documentation </li></ul><ul><ul><li>bar-code added </li></ul></ul><ul><ul><li>label ...
Taxon-Character Loop <ul><li>specimen documentation </li></ul><ul><ul><li>extended-focus imaging </li></ul></ul>
 
 
 
 
 
Taxon-Character Loop
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Software Components <ul><li>Database: Oracle </li></ul><ul><ul><li>custom applications to handle data </li></ul></ul><ul><...
Data/Protocol standards <ul><li>specimen data: DarwinCore </li></ul><ul><li>specimen queries: DiGIR </li></ul><ul><li>char...
Life Sciences Identifiers (LSIDs) <ul><li>Globally unique identifiers for </li></ul><ul><ul><li>taxonomic concepts, taxono...
 
 
Heptascelio lugens  Kieffer: urn:lsid:biosci.ohio-state.edu:osuc_concepts:4542
Acknowledgments <ul><ul><li>PBI team: A. Austin, A. Aguiar, B. Coelho, H. Clebsch, J. Cora, C. Darling, M. Dowton, J. Earl...
Environment Institute Science Seminar Series 2009 Next Seminar – 4 May A tale of three rivers: The Nile, the Darling and t...
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Science Seminar Series 4 Norman Johnson

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Professor Norm Johnson from Ohio State University will present the topic ‘A virtual co-laboratory for large scale taxonomic research’.

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Science Seminar Series 4 Norman Johnson

  1. 1. Environment Institute Science Seminar Series 2009 A virtual co-laboratory for large scale taxonomic research Presented by: Professor Norm Johnson Ohio State University
  2. 2. A virtual co-laboratory for large-scale taxonomic research Norman F. Johnson The Ohio State University urn:lsid:zoobank.org:author:3508C4FF-F027-445F-8417-90AB4AB8FE0D
  3. 3. Planetary Biodiversity Inventory Goals & Focus <ul><li>new collections of specimens </li></ul><ul><li>phylogenetic analysis </li></ul><ul><li>species description of a “major” taxonomic group </li></ul>
  4. 4. Focal taxon: Platygastroidea (Hymenoptera) <ul><li>Biology </li></ul><ul><ul><li>egg parasitoids of insects, spiders </li></ul></ul><ul><ul><li>egg-larval parasitoids of gall flies </li></ul></ul><ul><li>1 family, 4840 “known” species </li></ul>
  5. 5. Project participants <ul><li>Australia : A. Austin, M. Dowton, J. Jennings, S. Thompson </li></ul><ul><li>Brazil : A.P. Aguiar, B. Coelho </li></ul><ul><li>Canada : L. Masner, C. Darling, M. Yoder, A. Guidotti </li></ul><ul><li>Costa Rica : A. Valerio </li></ul><ul><li>Hungary : I. Mikó </li></ul><ul><li>India : Rajmohana K. </li></ul><ul><li>Italy: F. Bin, G. Salerno, R. Conti </li></ul><ul><li>New Zealand : J. Early </li></ul><ul><li>South Africa : S. van Noort </li></ul><ul><li>Taiwan: Chen S.-P. </li></ul><ul><li>UK : A. Polaszek </li></ul><ul><li>USA : L. Musetti, H. Klompen, J. Cora, S. Hemly, E. Talamas, C. Taekul, M. Buffington </li></ul>
  6. 6. Project goals: Collecting <ul><li>Brazil: A.P. Aguiar </li></ul><ul><li>South Africa: S. van Noort </li></ul><ul><li>southeast Asia: D.C. Darling </li></ul>
  7. 8. Project goals: Phylogenetics <ul><li>~250 genera considered valid </li></ul><ul><ul><li>add/subtract about equal numbers for new genera & synonyms </li></ul></ul><ul><li>preliminary work: > 70 in-group taxa, 3 genes (18S, 28S, COI) </li></ul><ul><li>goal: 200 in-group, 5 genes </li></ul>
  8. 10. Project goals: Taxonomy <ul><li>Scelionini s. lato </li></ul><ul><ul><li>extrusible, telescoping ovipositor </li></ul></ul>
  9. 11. Infrastructure Canadian National Collection, Ottawa
  10. 12. Infrastructure <ul><li>Taxonomic catalogs </li></ul><ul><ul><li>Johnson 1992, Vlug 1995 </li></ul></ul><ul><li>Electronic version </li></ul><ul><ul><li>Hymenoptera Name </li></ul></ul><ul><ul><li>Server </li></ul></ul><ul><ul><li>10,725 platygastroid names </li></ul></ul><ul><ul><li>218,013 hymenopteran </li></ul></ul><ul><ul><li>names </li></ul></ul>
  11. 13. Inaugural workshop <ul><li>Workshop: 5-9 Feb., 2007 </li></ul>
  12. 14. Specimen Acquisition Museums Published Literature Science Taxa Characters Description Publication New Collections Taxonomic Workflow Model Taxonomic History Keys Material Examined Images Maps
  13. 15. Published Literature <ul><li>PDF library of taxonomic publications </li></ul><ul><ul><li>1,177 articles </li></ul></ul><ul><ul><li>28,213 pages </li></ul></ul><ul><ul><li>93% of total </li></ul></ul><ul><ul><li>linked to catalog </li></ul></ul><ul><ul><li>annotations </li></ul></ul>
  14. 16. Taxon-Character Loop <ul><li>specimen documentation </li></ul><ul><ul><li>bar-code added </li></ul></ul><ul><ul><li>label data recorded </li></ul></ul><ul><ul><li>parsed </li></ul></ul><ul><ul><li>verbatim </li></ul></ul>
  15. 17. Taxon-Character Loop <ul><li>specimen documentation </li></ul><ul><ul><li>extended-focus imaging </li></ul></ul>
  16. 23. Taxon-Character Loop
  17. 43. Software Components <ul><li>Database: Oracle </li></ul><ul><ul><li>custom applications to handle data </li></ul></ul><ul><li>Images </li></ul><ul><ul><li>Cartograph/Archimed, Automontage </li></ul></ul><ul><ul><li>Specimage </li></ul></ul><ul><li>Web servers: Apache </li></ul><ul><li>Scripting: Perl, JavaScript </li></ul>
  18. 44. Data/Protocol standards <ul><li>specimen data: DarwinCore </li></ul><ul><li>specimen queries: DiGIR </li></ul><ul><li>character data: SDD </li></ul><ul><li>literature data: MODS </li></ul><ul><li>taxonomic concepts: TCS </li></ul><ul><li>taxonomic treatments: TaxonX </li></ul><ul><li>unique identifiers: LSIDs </li></ul>
  19. 45. Life Sciences Identifiers (LSIDs) <ul><li>Globally unique identifiers for </li></ul><ul><ul><li>taxonomic concepts, taxonomic names, people, publications, specimens, etc. </li></ul></ul><ul><li>Retrieve data about object </li></ul><ul><li>Mechanism to establish identity between objects </li></ul>
  20. 48. Heptascelio lugens Kieffer: urn:lsid:biosci.ohio-state.edu:osuc_concepts:4542
  21. 49. Acknowledgments <ul><ul><li>PBI team: A. Austin, A. Aguiar, B. Coelho, H. Clebsch, J. Cora, C. Darling, M. Dowton, J. Early, A. Guidotti, J. Jennings, H. Klompen, L. Masner, I. Mikó, L. Musetti, A. Polaszek, Rajmohana K., C. Taekul, E. Talamas, S. Thompson, A. Valerio, S. van Noort, M. Yoder </li></ul></ul><ul><ul><li>National Science Foundation (Grant DEB-0614764) </li></ul></ul>
  22. 50. Environment Institute Science Seminar Series 2009 Next Seminar – 4 May A tale of three rivers: The Nile, the Darling and the Son Presented by: Emeritus Professor Martin Williams

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