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|−|<div id="wikinotes">Within the DNA Bank Network specimen data are recalled by the same wrappers which are used by GBIF. </ div> |+|
the data the GBIF . /
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|−|The data architecture of the DNA Bank Network is based on the GBIF infrastructure. The basic principle of GBIF as well as of the DNA Bank Network is to record all data sets only once. Stored at only one place they can be used as a linked reference for different applications. |+|
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|−|Since many institutions joined GBIF applying different database structures each, the installation of wrappers has become a standard to combine different sources and integrate data easily into networks. There are three main wrapper softwares available BioCASE, DiGIR and TAPIR. All of them use a xml schema for data transfer: BioCASE - ABCD, DiGIR and TAPIR - DarwinCore(DwC). |+|
the data ...
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data developed the DNA . is to .
|−|<div id="wikinotes">For DNA data management an open source software was developed at the BGBM the "DNA Module". Furthermore it is possible to use its own database system. </div> | |
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|−|The DNA Module is one of key components of the networks database system. To find related specimen data of a DNA sample the module sends a query to the respective specimen database via BioCASE or DiGIR. A copy including few specimen attributes is as well stored in the DNA cache ( speed up queries). By following the BioCASe and DiGIR protocol it is so possible to connect any GBIF compliant specimen database worldwide. |+|
DNA is the database. a the a the . in the (). .
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|−|The DNA Module is currently used by three of the four project partners associated with their own specimen databases . The DSMZ in Braunschweig applies its own system for DNA data input. |+|
system DNA data .
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DNA an for DNA and . . of .
|−|<div id="wikinotes">To transfer DNA data into the webportal of the DNA Bank Network an DNA extension for ABCD was developed. Thus BioCASE Provider Software is required.</div> | |
|−|Another BioCASE wrapper using the new DNA extension for ABCD has been installed on all three DNA Modules and the database in Braunschweig separately to offer all DNA samples and its related specimen data on the central webportal (www. dnabank-network. org). | |
|−|The source code of the DNA Bank Network's Webportal is available under Mozilla Public License Version 1.1 at | |
|−|http://ww2.biocase. org/svn/dnabank/DNA_Bank_Network/webportal/ | |
Latest revision as of 14:29, 1 March 2017
The data architecture of the GGBN Data Portal is based on the GBIF infrastructure. The basic principle of GBIF as well as of the GGBN is to record all data sets only once. Stored at only one place they can be used as a linked reference for different applications. The GGBN Data Portal bridges the gap between sequence portals and GBIF (see Figure). More information about the GGBN Data Portal can also be found in Droege et al. 2014 Nucl Acids Res.
Within GGBN specimen data are recalled by the same data pipelines which are used by GBIF
Since many institutions joined GBIF applying different database structures each, the installation of wrappers has become a standard to combine different sources and integrate data easily into networks. There are two main wrapper softwares available BioCASE, and IPT. GGBN has developed the GGBN Data Standard to share DNA and tissue data via GGBN. This standard is meant to be used together with ABCD or DarwinCore.
General data architecture of the GGBN Dta Portal. Specimen and DNA sample databases (on top left) are operated by the Network partners. Their data content is structured and provided by using BioCASe or IPT and the GGBN Data Standard extensions. The Berlin Harvesting and Indexing Toolkit (click to see documentation) is used to harvest GGBN data and store them in a MySQL database. In addition we use a SOLR instance to speed the query. After harvesting the data are cleaned and enriched by e.g. a match against certain datasets of the GBIF checklist bank. Finally the data are aggregated from multiple sources in the data portal (click to see documentation) to be displayed. GGBN offers a web service, documentation will follow soon.
DNA and Tissue Bank databases
You can use any database system to manage your DNA or tissue bank. IPT and BioCASe can handle most of them. Please check out which parameters are required to share data via GGBN.
The DNA Module has been developed as an open source solution for administer a DNA and tissue bank. A new version is currently planned. Some of our partners are already using it, but you can use any suitable software.