Missouri Botanical Garden Open Conference Systems, TDWG 2014 ANNUAL CONFERENCE

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Standards-based management of specimen-derived DNA sequences
James A Macklin, Satpal Bilkhu, Nazir El-Kayssi, Chris T Lewis

Building: Elmia Congress Centre, Jönköping
Room: Rydbergsalen
Date: 2014-10-28 02:10 PM – 02:30 PM
Last modified: 2014-10-03


Agriculture and Agri-Food Canada (AAFC) Ottawa is home to a world-class taxonomy program based on Canada’s national agricultural collections for Botany (DAO), Mycology (DAOM & CCFC) and Entomology (CNC).  These collections are valuable resources for authoritative identification material in DNA barcoding, metagenomic sequence identification and whole genome sequencing applications.  AAFC’s internally developed Sequence and Specimen management web application, SeqDB, manages source specimen information, DNA extractions, PCR reactions, and sequence reactions leading to DNA sequences.  The database adheres to the Biodiversity Information Standards (TDWG) Darwin Core standard, as well as the Genome Standards Consortium (GSC) Minimum Information about any (X) Sequences (MIxS) specification.  The database will be updated to reflect the Global Genome Biodiversity Network (GGBN) data standard and other standards as they are finalized.

SeqDB is built on top of a Java stack consisting of Hibernate, Spring, and Struts 2.  The next iteration of SeqDB will see an increased focus on the management of metagenomics data in the context of specimen-based reference sequences and seamless integration with the Galaxy workflow system for analysis of SeqDB-managed data.  We are also developing a web services API to SeqDB, which will permit SeqDB to provide a DNA module to the DINA web-based information management system for natural history data.  We are actively exploring options within the Government of Canada context to make the full source code for the database available to the public.