DNA barcode library / Database / Informatics

The database (developed within the Dutch FES project, 2006-2010) has been further developed during the QBOL project in this work package.

Objectives

  • To create a complex database structure including and interlinking the different organisms (fungi, arthropods, bacteria, nematodes, viruses and phytoplasmas) and associated data.
  • To develop a web based public Database system for correct taxonomic identification of relevant Quarantine plant pathogens. The internet based system will allow online deposit of any data related to the pathogens or the host plants and will be automatically linked to other database systems systems such as Genbank, EMBL, BOLD and GBIF. The online version will provide an unique identification system of the included organisms that could involve any scientific data considered of importance by the partners involved (morphological, physiological, molecular, etc). Polyphasic identifications will be possible for any Internet user.

Tasks

  • Task 9.1  Selection of fields to be included into the database for each group of organisms and associated functions and algorithms
  • Task 9.2  Training and data entry
  • Task 9.3  Testing databases, linking and the efficiency of identification tools
  • Task 9.4  Last modifications and release of the system
  • Task 9.5  Contingency plan

Deliverables

  • D 9.1 List of fields to be included into the Database for each group of organisms (Month 6)
  • D 9.2 Prototype of Internet accessible Database for barcode sequences and taxonomic characters of selected Q-organisms (Month 18)
  • D 9.3 Internet accessible Database for barcode sequences and taxonomic characters of selected Q-organisms (Month 30)
  • D 9.4 Regular contacts and data exchange with other Databases (Month 1-36)
  • D 9.5 Detailed contingency plan for WP9 (Month 6)
Results



Results

The database (developed within the Dutch FES project, 2006-2010) has been further developed during the QBOL project in this work package. Together with QBOL work package leaders and associated researchers, we have created six databases: for fungi, arthropods, bacteria, nematodes, viruses and phytoplasmas. All groups have access to their databases via Citrix XenApp. The total database Q-bank is freely accessible via www.q-bank.eu. Contacts with CBOL/BOLD, EDIT, QBOL work packages, GBIFStrainInfoGenBank and EMBL were taken at several occasions during the course of the project in order to import from and export data to the respective projects or databases. A software module to export to and import from Genbank (and therefore EMBL) has been implemented. In discussion with the curators of the database we continuously improved the Internet-based software to comply with the needs of the end-users during pairwise meetings. Additional training was provided during the meetings with QBOL work package leaders and associated researchers.

Filling of the Q-bank databases has been done during last stages of the QBOL project and will continue even beyond the end of the project. Publication of the created databases is now complete and internet visitors are regularly using the system. Websites are therefore not restricted to the users participating in the QBOL project anymore. Usage of the different databases are monitored by Google Analytics.