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Toward verifiable science: iPython meets PROV-O (Semantics in Ecosystems Assessments).

Toward verifiable science: iPython meets PROV-O (Semantics in Ecosystems Assessments). April 16, 2014 ERRT. Peter Fox (RPI/ Tetherless World Constellation and WHOI/AOP&E) pfox@cs.rpi.edu (@taswegian) and collaborators on the

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Toward verifiable science: iPython meets PROV-O (Semantics in Ecosystems Assessments).

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  1. Toward verifiable science: iPython meets PROV-O(Semantics in Ecosystems Assessments). April 16, 2014 ERRT Peter Fox (RPI/ Tetherless World Constellation and WHOI/AOP&E) pfox@cs.rpi.edu (@taswegian) and collaborators on the NSF INTEROP ECO-OP project. http://tw.rpi.edu/web/project/ECOOP

  2. Stace Beaulieu

  3. Marine ecosystems

  4. Stace Beaulieu

  5. Stace Beaulieu

  6. Fish, science, decision

  7. Stace Beaulieu

  8. Why important? Stace Beaulieu

  9. Vision? • “Our vision is to develop, facilitate, and maintain sustained multi-way engagement of natural and social scientists and many practitioners in multi-scale local to global networks for LMEs”. • Goal: We want to perform routine assessments of LMEs involving all (or as many) stakeholders and we want robust science data presented in forms that various end-users can consume… and verify

  10. Environmental Assessment

  11. Northeast Status Report ?

  12. Generation Stace Beaulieu

  13. Tracing Stace Beaulieu

  14. W3C PROV Stace Beaulieu

  15. Past Experience with PROV Stace Beaulieu

  16. Extended Use Case Stace Beaulieu

  17. Stace Beaulieu

  18. Instrument a tool - iPython Stace Beaulieu

  19. Stace Beaulieu

  20. Stace Beaulieu

  21. Screenshot of IPython Notebook used to track both data and workflow provenance http://ipython.org/ Code in Python, Matlab, R, other Stace Beaulieu

  22. Screenshot of IPython Notebook used to track both data and workflow provenance http://ipython.org/ Notebook can be shared, or output as script, HTML, PDF, other Stace Beaulieu

  23. PDF output of IPython Notebook with clickable links to data and code Stace Beaulieu

  24. Screenshot of csv file at GitHub Access not only to the data that are plotted, but also to provenance metadata for reproducibility Stace Beaulieu

  25. Outcomes • Implemented PROV-O in iPython NoteBook* • Extended GCIS ontology for ECOOP to include dataset generation • Improved the practice of annotation and generation of report materials

  26. Beaulieu - Indicators Stace Beaulieu

  27. Indicators Stace Beaulieu

  28. Current (Proposal) Stace Beaulieu

  29. Indicators Explained Stace Beaulieu

  30. Next … iPython meets NCA NCA=National Climate Assessment Stace Beaulieu

  31. Thanks!

  32. If needed

  33. Informatics enables a new approach • Use cases • Stakeholders • Distributed authority • Access control • Ontologies • Maintaining Identity

  34. Framework - DPSIR

  35. Semantics of DPSIR?

  36. Drivers/ Pressures • Physical Drivers • North Atlantic Oscillation • Atlantic Multi-decadal Oscillation • Human Drivers • Population • Income • Human Pressures (Fishery Removals) • Number Groundfish Vessels • Landings, Principal Groundfish • Landings, Other Fish • Landings, Small Pelagics • Landings, Crustaceans • Landings, Molluscs • Temperature • Extended Reconstructed SST • Coastal Temperature, Virginia • Coastal Temperature, Woods Hole • Costal Temperature, Boothbay Harbor • Survey sea surface temperature • Survey bottom sea temperature • Thermal Habitat <4oC • Thermal Habitat >5oC and <15 oC • Thermal Habitat >16oC • River Discharge • River Flow-Gulf of Maine • River Flow-Middle Atlantic Bight • River Flow-Southern New England • Wind Fields • Wind Stress, Cape Hatteras • Wind Stress, New York • Wind Stress, Georges Bank • Wind Stress East-West, Cape Hatteras • Wind Stress East-West, New York • Wind Stress East-West, Georges Bank • Wind Stress North-South, Cape Hatteras • Wind Stress North-South, New York • Wind Stress North-South, Georges Bank • Other • Stratification • Survey surface salinity • Survey bottom salinity • Gulf Stream Location • %Labrador-Subarctic Slope Water in GoM

  37. Ecosystem State Variables • Demography/Trophic Level • Mean Trophic Level Catch • Mean Trophic Level Survey • Primary Production Required, Landings • Mean Length • Community Composition • Thermal Preference • Pelagic to Demersal Ratio • Elasmobranch to Demersal Groundfish Ratio • Impacts • Groundfish Fishery Revenue Plankton • Continuous Plankton Recorder Color Index. • Zooplankton Ecosystem Biovolume • Ratio of Small to Large Zooplankton Nekton/Benthos • Relative Abundance, Crustaceans • Relative Abundance, Elasmobranch • Relative Abundance, Ground Fish • Relative Abundance, Molluscs • Relative Abundance, Other Fish • Relative Abundance, Small Pelagics • Relative Abundance, All Species

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