OBIS Data Scenarios: Using Darwin Core to bring data into OBIS Philip Goldstein O CEAN B IOGEOGRAPHIC I NFORMATION S YSTEM May 5, 2014

OBIS Uses Ratified Darwin Core O CEAN B IOGEOGRAPHIC I NFORMATION S YSTEM Ratified Darwin Core OBIS Darwin Core terms Darwin Core (DwC) was ratified by TDWG in 2009 incorporates knowledge gained up to that point. 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) Today’s Scenarios ( ) For Darwin Core definitions … Google “Darwin Core Terms” or … Go to TDWG is the “Taxonomic Databases Working Group”

OBIS Data Scenario #1 O CEAN B IOGEOGRAPHIC I NFORMATION S YSTEM 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

OBIS Data Scenario #2 O CEAN B IOGEOGRAPHIC I NFORMATION S YSTEM Polar Bear Dens Locations of polar bear dens Is this biological occurrence data? Sources: historical, current, various methods

OBIS Data Scenario #3 O CEAN B IOGEOGRAPHIC I NFORMATION S YSTEM 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

OBIS Data Scenarios: Various Forms of Original Data Contain Occurrence Data O CEAN B IOGEOGRAPHIC I NFORMATION S YSTEM Occurrence Data Format Get data into Taxon-time-location format; from data originators’ various original technologies. Data Sheet 70% Matrix (unpivoted) 8% Relational Database 20% GIS 2% (estimated % of encountered datasets)

OBIS Data Scenario #4 O CEAN B IOGEOGRAPHIC I NFORMATION S YSTEM 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.

OBIS Data Scenario #4 O CEAN B IOGEOGRAPHIC I NFORMATION S YSTEM Gulf of Mexico (Alabama) Trawl Database – database diagram

OBIS Data Scenario #4 O CEAN B IOGEOGRAPHIC I NFORMATION S YSTEM Gulf of Mexico (Alabama) Trawl Database – table definitions (table) Samples “SampleCode” “YYYY” “MM” “DD” “StationCode” (table) Species "Species Code” "Phylum "Class” "Family” "Scientific Name” "Common Name" (table) Station "Station Code” “Station” “Description” "Latitude” ”Longitude” “Water Body" (table) Trawls "Sample Code” “Species Code” “Measured” “Total Number” (table) Lengths "Sample Code” “Species Code” “Length” (table) Lengths "Sample Code” “Species Code” “Length”

OBIS Data Scenario #4 O CEAN B IOGEOGRAPHIC I NFORMATION S YSTEM Gulf of Mexico (Alabama) Trawl Database – excerpt of database query