biocode field information management system (fims) john deck, uc berkeley tdwg, 2014
TRANSCRIPT
Biocode Field Information Management System (FIMS)
John
Dec
k, U
C Be
rkel
ey
TDWG, 2014
Biocode Field Information System -- Biocode,LLC
Collecting
Tissue Sub-sampling
Manage data on the following field-based activities and data
Specimen Preparation
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Offline data entry
Robust
Data validation
GUIDs at the source
System Requirements
Retain and archive all versions
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FIMS Workflow
Create Project
Create Project• Validation rules for data• Lookup lists• Identifier policies
Spreadsheet Template
Generate Spreadsheet Template• User sets what columns they want to see• Creates an Excel Spreadsheet for use
Enter Data
Enter Data on Spreadsheet• Spreadsheet data entry happens off-line.• Drop-down lists available for defined lists
Validation
Validation• Iterative process• Provides user with feedback for improving their data
Upload
Upload• Each dataset is given a persistent identifier• Stored natively as RDF triples• No need to define unique schema for each project
Query
Query• Each project defines whether it is public or not.• Query capabilities via web interface or API
Biocode Field Information System -- Biocode,LLC
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Generate Template
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Enter Data (Data Fields Tab)
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Enter Data (Lists Tab)
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Enter Data (Samples Tab)
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Validate Data (Response w/ Errors)
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User Fixes Data
jd2
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Validate Data Take 2 (Proceed with Warnings)
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Finish Validation and Publish to Archive
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Data stored as RDF:Queryable in triple-store; offers semantic integration; archivable;
portable to any other format
<ark:/21547/MY2jd1> a <dwc:MaterialSample> ; <dwc:decimalLatitude> "46" ; <dwc:decimalLongitude> "-122" ; <dwc:materialSampleID> "jd1" ; <dwc:phylum> "Chordata" ; <urn:principalInvestigator> "Jdeck" .
<ark:/21547/MY2jd2> a <dwc:MaterialSample> ; <dwc:decimalLatitude> "46" ; <dwc:decimalLongitude> "-122" ; <dwc:materialSampleID> "jd2" ; <dwc:phylum> "Chordata" ; <urn:principalInvestigator> "Jdeck" .
GUID Assignment Native DwC Term Reference
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Data Query and Visualization
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Thank YouAcknowledgements:Moorea Biocode Project, Gordon and Betty Moore FoundationBiSciCol, National Science Foundation (DBI-0956426)Berkeley Natural History Museums, UC BerkeleySmithsonian Institution
Continued Development and Support:Biocode, LLC, building software in support of sample-based data collection. Contact [email protected] for more information
For more Information:http://biscicol.org/biocode-fims/