cj grady, j.h. beach, a. stewart, j. cavner university of kansas biodiversity institute
DESCRIPTION
Using Specimen Data in Scientific Workflow Environments to Connect to Metadata Archive and Discovery Services in Environmental Biology. CJ Grady, J.H. Beach, A. Stewart, J. Cavner University of Kansas Biodiversity Institute. Geospatial Metadata. Describes What it is What it looks like - PowerPoint PPT PresentationTRANSCRIPT
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Using Specimen Data in Scientific Workflow Environments to Connect to Metadata Archive
and Discovery Services in Environmental Biology
CJ Grady,J.H. Beach, A. Stewart, J. Cavner
University of Kansas Biodiversity Institute
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Geospatial Metadata
• Describes– What it is– What it looks like– Who assembled it– When it was collected– Etc
1960 - 1990
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EML
• Ecological Metadata Language– XML Schema– Open Source– Community Driven– Describes ecological data• Occurrence Data• Climate Layers• Species Ranges
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Narratives
• Transformation of metadata into a story that is appropriate for the intended audience
• Same metadata can be used to create narrative for:– Scientists– Undergrads– K-12 students
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Narrative Example
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• DataONE– Distributed system for:• Queries• Data replication
– Initially supports EML
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Study of Experiment Reproducibility
Ellison, Aaron. 2010. Repeatability and transparency in ecological research. Ecology 90.
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There is a Solution!
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Process Metadata
• Data about the process used• Descriptive and prescriptive• Documents process used to generate data /
metadata– Quality control– SDM experiments– RAD experiments
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Capabilities
• Reproducibility– Actions are documented
• Transparency– Experiments can be evaluated and validated
• Publishing– Metadata can be published along with results
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What we have done
• EML for all of our Species Distribution Modeling services
• Simple process metadata– Documents how an experiment is ran through our
cluster including what versions of software– Also describes what web services would be called
to execute the experiment again
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What we have done
• Clients– Python library– VisTrails– QGIS
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What we are doing
• Publishing EML to a repository• Client extensions• Extending process metadata– HTTP message– XPath
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Process Metadata Extensions
• HTTP Message– Documents any web resource call over HTTP
• XPath processing
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What we will do next
• Use standard APIs to communicate with DataONE
• Continue to search for standard process metadata and include it whenever possible
• Contribute process metadata extensions back to the community
• Add additional conditional analysis elements to the schema (JSON, etc)
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Reproducibility
• Simple process metadata• EML process metadata extensions• Lifemapper client EML reader
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Transparency
• EML for all service objects• Descriptive process metadata
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Publishing Aid
• Client access to public data / metadata catalogs
• Publish buttons
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Lessons Learned
• Had success starting with narrow, specific, process steps and generalizing them– Calls to our web services expanding to any HTTP
call• Easy to get carried away with all of the
possibilities
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Lifemapper funded by:
U.S. National Science Foundation
NSF EPSCoR 0553722
NSF EPSCoR 0919443
EHR/DRL 0918590
BIO/DBI 0851290
OCI/CI-TEAM 0753336
http://[email protected]