Biocode Field Information Management System (FIMS) John Deck, UC Berkeley TDWG, 2014

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

Biocode Field Information System Biocode,LLC

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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 jdeck88@gmail.com for more information

For more Information:http://biscicol.org/biocode-fims/