Transcript CU Museum of Natural History Web / Database

OBIS Data Scenarios:
Using Darwin Core
to bring data into OBIS
Philip Goldstein
May 5, 2014
OCEAN BIOGEOGRAPHIC INFORMATION SYSTEM
OBIS Uses Ratified Darwin Core
• Darwin Core (DwC) was ratified by
TDWG in 2009 incorporates
knowledge gained up to that point.
Ratified Darwin Core
OBIS Darwin Core terms
Today’s Scenarios
(2014-05-05)
• Ratified DwC continues to be updated
on a controlled basis.
• OBIS uses a subset of Ratified DwC
• Potentially all of DwC is usable by
OBIS nodes (discussions later this
week)
For Darwin Core definitions …
•Google “Darwin Core Terms” or …
•Go to http://rs.tdwg.org/dwc/terms/
TDWG is the
“Taxonomic
Databases
Working
Group”
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OBIS Data Scenario #1
Chesapeake Bay Fisheries Data
• Data provided to OBIS-USA in spreadsheet form
• Column names are in original form, not Darwin Core form
• See the sample worksheet approach to mapping data from
original contents to Darwin Core
OCEAN BIOGEOGRAPHIC INFORMATION SYSTEM
OBIS Data Scenario #2
Polar Bear Dens
• Locations of polar bear dens
• Is this biological occurrence data?
• Sources: historical, current, various methods
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OBIS Data Scenario #3
Texas Coastal Fisheries
• Data in spreadsheets
• Data are in matrix form (also known as “unpivoted form”)
• Must convert from matrix to rows as well as map to Darwin Core
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OBIS Data Scenarios: Various Forms of Original
Data Contain Occurrence Data
(estimated % of encountered datasets)
Data Sheet
70%
Matrix
(unpivoted)
8%
Relational
Database
Occurrence Data
Format
Get data into
Taxon-time-location
format; from data
originators’ various
original technologies.
20%
GIS
2%
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OBIS Data Scenario #4
Gulf of Mexico (Alabama) Trawl Samples
• Data in a relational database (MS Access / postgreSQL)
• Different database structure for each state
• OBIS format will make them all interoperable
• Use query language to extract from relational database
• Also use the worksheet to determine precise alignment of terms.
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OBIS Data Scenario #4
Gulf of Mexico (Alabama) Trawl Database – database diagram
OCEAN BIOGEOGRAPHIC INFORMATION SYSTEM
OBIS Data Scenario #4
Gulf of Mexico (Alabama) Trawl Database – table definitions
(table) Samples
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“SampleCode”
“YYYY”
“MM”
“DD”
“StationCode”
(table) Trawls
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"Sample Code”
“Species Code”
“Measured”
“Total Number”
(table) Species
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"Species Code”
"Phylum
"Class”
"Family”
"Scientific Name”
"Common Name"
(table) Lengths
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"Sample Code”
“Species Code”
“Length”
(table) Station
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"Station Code”
“Station”
“Description”
"Latitude”
”Longitude”
“Water Body"
(table) Lengths
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"Sample Code”
“Species Code”
“Length”
OCEAN BIOGEOGRAPHIC INFORMATION SYSTEM
OBIS Data Scenario #4
Gulf of Mexico (Alabama) Trawl Database – excerpt of database query
OCEAN BIOGEOGRAPHIC INFORMATION SYSTEM