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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) [email protected] (@taswegian) and collaborators on the NSF INTEROP ECO-OP project. http://tw.rpi.edu/web/project/ECOOP
Stace Beaulieu
Marine ecosystems
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Fish, science, decision
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Why important?
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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
Environmental Assessment
Northeast Status Report
?
Generation
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Tracing
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W3C PROV
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Past Experience with PROV
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Extended Use Case
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Instrument a tool - iPython
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http://ipython.org/Screenshot of IPython Notebook used to track both data and workflow
provenance
Code inPython,Matlab,R, other Stace Beaulieu
http://ipython.org/Screenshot of IPython Notebook used to track both data and workflow
provenance
Notebook can be shared, or output as script, HTML, PDF,other Stace Beaulieu
PDF output of IPython Notebook with clickable links to data and code
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Screenshot of csv file at GitHub
Access not only to the data that are plotted, but also to provenance metadata for reproducibility
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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
Beaulieu - Indicators
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Indicators
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Current (Proposal)
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Indicators Explained
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Next … iPython meets NCA
NCA=National Climate Assessment
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Thanks!
If needed
Informatics enables a new approach
• Use cases• Stakeholders• Distributed
authority• Access control• Ontologies• Maintaining
Identity
Framework - DPSIR
Semantics of DPSIR?
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
Ecosystem State Variables
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
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