Missouri Botanical Garden Open Conference Systems, TDWG 2014 ANNUAL CONFERENCE

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Biocode Field Information Management System
John Deck

Building: Elmia Congress Centre, Jönköping
Room: Rum 10
Date: 2014-10-30 02:10 PM – 02:15 PM
Last modified: 2014-10-03


The Biocode Field Information Management Systems (Biocode FIMS https://code.google.com/p/biocode-fims/) takes spreadsheet data that is generated in the field, validates it, aligns it with global metadata standards, assigns unique identifiers, and publishes it. While the publishing step can be optionally private, the public version can be referenced by other applications such as collections management systems, Genbank, data harvesters, and laboratory information management systems.  Biocode FIMS is designed by building on principles of good data linking: creating persistent identifiers where samples are created and aligning with standardized vocabularies and ontologies.   This presentation will show how the Biocode FIMS can be used to process spreadsheet data that is generated in the field.

The technical details: Biocode FIMS is an open source app­­­lication, using XML configuration files to define validation rules and to structure logical relationships between sets of columns.  A client-server interface, built on Java and REST services is used to control all interactions.  Upon upload, data is stored in an Apache Fuseki TDB triplestore (http://jena.apache.org/documentation/serving_data/) with identifier keys and dataset metadata stored in a Mysql database (http://dev.mysql.com/).   The Biocode FIMS identifier solution is based on EZID (http://n2t.net/ezid), from the California Digital Library.  All code is available under the Berkeley Standard Distribution 3-Clause license (http://opensource.org/licenses/BSD-3-Clause).