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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
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Stace Beaulieu
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Marine ecosystems
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Stace Beaulieu
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Stace Beaulieu
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Fish, science, decision
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Stace Beaulieu
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Why important?
Stace Beaulieu
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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
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Environmental Assessment
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Northeast Status Report
?
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Generation
Stace Beaulieu
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Tracing
Stace Beaulieu
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W3C PROV
Stace Beaulieu
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Past Experience with PROV
Stace Beaulieu
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Extended Use Case
Stace Beaulieu
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Stace Beaulieu
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Instrument a tool - iPython
Stace Beaulieu
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Stace Beaulieu
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Stace Beaulieu
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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
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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
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PDF output of IPython Notebook with clickable links to data and code
Stace Beaulieu
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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
Stace Beaulieu
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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
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Beaulieu - Indicators
Stace Beaulieu
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Indicators
Stace Beaulieu
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Current (Proposal)
Stace Beaulieu
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Indicators Explained
Stace Beaulieu
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Next … iPython meets NCA
NCA=National Climate Assessment
Stace Beaulieu
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Thanks!
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If needed
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Informatics enables a new approach
• Use cases• Stakeholders• Distributed
authority• Access control• Ontologies• Maintaining
Identity
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Framework - DPSIR
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Semantics of DPSIR?
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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
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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