Using Specimen Data in Scientific Workflow Environments to Connect to Metadata Archive and Discovery...
Download
1 / 22

CJ Grady, J.H. Beach, A. Stewart, J. Cavner University of Kansas Biodiversity Institute - PowerPoint PPT Presentation


  • 114 Views
  • Uploaded on

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

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' CJ Grady, J.H. Beach, A. Stewart, J. Cavner University of Kansas Biodiversity Institute' - moe


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

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
Geospatial Metadata Connect to Metadata Archive and Discovery Services in Environmental Biology

  • Describes

    • What it is

    • What it looks like

    • Who assembled it

    • When it was collected

    • Etc

1960 - 1990


EML Connect to Metadata Archive and Discovery Services in Environmental Biology

  • Ecological Metadata Language

    • XML Schema

    • Open Source

    • Community Driven

    • Describes ecological data

      • Occurrence Data

      • Climate Layers

      • Species Ranges


Narratives
Narratives Connect to Metadata Archive and Discovery Services in Environmental Biology

  • 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


Narrative example
Narrative Example Connect to Metadata Archive and Discovery Services in Environmental Biology


  • DataONE Connect to Metadata Archive and Discovery Services in Environmental Biology

    • Distributed system for:

      • Queries

      • Data replication

    • Initially supports EML


Study of experiment reproducibility
Study of Experiment Connect to Metadata Archive and Discovery Services in Environmental BiologyReproducibility

Ellison, Aaron. 2010. Repeatability and transparency in ecological research. Ecology 90.


There is a solution
There is a Solution! Connect to Metadata Archive and Discovery Services in Environmental Biology


Process metadata
Process Metadata Connect to Metadata Archive and Discovery Services in Environmental Biology

  • Data about the process used

  • Descriptive and prescriptive

  • Documents process used to generate data / metadata

    • Quality control

    • SDM experiments

    • RAD experiments


Capabilities
Capabilities Connect to Metadata Archive and Discovery Services in Environmental Biology

  • Reproducibility

    • Actions are documented

  • Transparency

    • Experiments can be evaluated and validated

  • Publishing

    • Metadata can be published along with results


What we have done
What we have done Connect to Metadata Archive and Discovery Services in Environmental Biology

  • 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


What we have done1
What we have done Connect to Metadata Archive and Discovery Services in Environmental Biology

  • Clients

    • Python library

    • VisTrails

    • QGIS


What we are doing
What we are doing Connect to Metadata Archive and Discovery Services in Environmental Biology

  • Publishing EML to a repository

  • Client extensions

  • Extending process metadata

    • HTTP message

    • XPath


Process metadata extensions
Process Metadata Connect to Metadata Archive and Discovery Services in Environmental BiologyExtensions

  • HTTP Message

    • Documents any web resource call over HTTP

  • XPath processing


What we will do next
What we will do next Connect to Metadata Archive and Discovery Services in Environmental Biology

  • 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)


Reproducibility
Reproducibility Connect to Metadata Archive and Discovery Services in Environmental Biology

  • Simple process metadata

  • EML process metadata extensions

  • Lifemapper client EML reader


Transparency
Transparency Connect to Metadata Archive and Discovery Services in Environmental Biology

  • EML for all service objects

  • Descriptive process metadata


Publishing aid
Publishing Aid Connect to Metadata Archive and Discovery Services in Environmental Biology

  • Client access to public data / metadata catalogs

  • Publish buttons


Lessons learned
Lessons Learned Connect to Metadata Archive and Discovery Services in Environmental Biology

  • 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


Lifemapper funded by
Lifemapper funded by: Connect to Metadata Archive and Discovery Services in Environmental Biology

U.S. National Science Foundation NSF EPSCoR 0553722

NSF EPSCoR 0919443

EHR/DRL 0918590

BIO/DBI 0851290

OCI/CI-TEAM 0753336

http://www.lifemapper.org

[email protected]


ad