michener workshop montpellier
TRANSCRIPT
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DataONEData Life Cycle:
Tools and Tips
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The DataONE Data Life Cycle
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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Field Research
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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Monitoring Project
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Publish
Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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Synthesis Project
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
Publish
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Develop Solutions for Research
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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The DataONE Data Life Cycle
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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1. Plan:Create and Follow a Data Management Plan
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Michener WK (2015) Ten Simple Rules
for Creating a Good Data Management Plan.
PLoS Comput Biol 11(10): e1004525.
doi:10.1371/journal.pcbi.1004525
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The DataONE Data Life Cycle
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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2. Collect and Organize:Logically Structure the Data to Support Use
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CC
im
ag
e b
y J
ustin
Se
e o
n F
lickr
Jones et al. 2007
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2. Collect and Organize
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• Columns of data are consistent:
only numbers, dates, or text
• Consistent Names, Codes, Formats (date) used in each column
• Data are all in one table, which is much easier for a statistical program to work with than multiple small tables which each require human intervention
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2. Collect and Organize
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• Columns of data are consistent:
only numbers, dates, or text
• Consistent Names, Codes, Formats (date) used in each column
• Data are all in one table, which is much easier for a statistical program to work with than multiple small tables which each require human intervention
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Googledocs Forms
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Googledocs Forms
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Data Entry Tools: Excel
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Data Entry Tools: Excel
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Excel: Data Validation
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Excel: Data Validation
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Excel: Data Validation
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The DataONE Data Life Cycle
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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3. Assure:Incorporate Quality Assurance & Quality
Control
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0
10
20
30
40
50
60
0 10 20 30 40
Quality Engine
MetaDIG DIBBs
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3. Assure
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3. Assure
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3. Assure
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3. Assure
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3. Assure
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3. Assure
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3. Assure
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3. Assure
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3. Assure
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3. Assure
• JMP
• R
• MATLAB
• many others
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The DataONE Data Life Cycle
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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4. Describe:Develop Comprehensive, Standardized
Metadata
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Darwin Core – species and biodiversity
collections
EML – Ecological Metadata Language
ISO 19115 – geospatial data
http://rs.tdwg.org/dwc/
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4. Describe
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Tools Specify
Morpho
https://knb.ecoinformatics.org/#tools/morpho
http://specifyx.specifysoftware.org
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The DataONE Data Life Cycle
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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5. Preserve:Protect and Preserve Data for Long-term
Use
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Catalog of 1,500+ Data Repositories
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Exercise• Search for repositories that host particular
types of data (e.g., biodoversity, trait)
• Visit one of the repositories and identify the
services that they offer
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The DataONE Data Life Cycle
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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6. Discover Search a Domain Portal
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Dryad links to journals
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Provides citation instructions
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6. Discover Search a Data Aggregator
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Data Federations (DataONE,
GBIF)
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Data Federations (DataONE,
GBIF)carbon cycling
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Data Federations (DataONE,
GBIF)carbon cycling
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Data Federations (DataONE,
GBIF)carbon cycling plant biomass
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Data Federations (DataONE,
GBIF)carbon cycling plant biomass
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Data Federations (DataONE,
GBIF)carbon cycling plant biomass
ocean nitrogen avian distribution
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Exercise• Search datadryad.org for plant trait
• Search DataONE.org for plant trait
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6. Discover:Support Discovery of Relevant Data
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Dryad DataONE google
plant trait 2,137 26,300,000
plant trait datadryad 803 1,908 17,400
• Differential content searched
• Automated annotation via ontologies and other
approaches
• Differential filtering
• Different definitions of data sets (e.g., entire
package vs individual data sets)
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The DataONE Data Life Cycle
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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7. Integrate:Enable Data Integration from Different
Sources
81 Jones et al. 2007
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7. Integrate:DataONE Provenance Tracking System
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The DataONE Data Life Cycle
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Plan
Collect
Assure
Describe
Preserve
Discover
Integrate
Analyze
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8. Analyze:https://www.vistrails.org
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8. Analyze:http://kepler-project.org
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8. Analyze:http://kepler-project.org
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8. Analyze:https://taverna.incubator.apache.org
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8. Analyze:https://www.myexperiment.org/
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Best PracticesWebinar series Lessons and
Exercises
DataONE.orgEducation Resources
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DataONE Vision and Mission
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dataone.org