ABCDDNA

DNA extension for ABCD - General information & installation manual

Another BioCASE wrapper on all connected databases had to be installed mandatory to offer DNA samples and its related specimen data on the central webportal (http://www.dnabank-network.org). Although the ABCD 2.06 schema (part of the BioCASE wrapper) is currently preferred its existing part for DNA ‘Sequences’ lacks important features. So, it shouldn’t be used any longer. The whole ABCD 2.06 schema is available here. If you want to learn more about the meaning of BioCASe and ABCD please follow the links.

ABCD offers two options to add supplementary contents: ‘MeasurementsOrFacts’ and ‘UnitExtensions’. Since the hierarchical structure of DNA specific features is too complex for ‘MeasurementsOrFacts’ we decided to use ‘UnitExtensions’ to integrate an xml schema definition for DNA data similar to the ABCDEFG extension for geosciences. That new DNA extension for ABCD 2.06 is called ABCDDNA.

The DNA Sample means ABCD Unit and the identifier (Triple ID) for the related specimen is defined by ‘UnitAssociation’. Please read the following manual for using the schema within the BioCASe provider software and have a look at a mapping example.

Using ABCDDNA

The basic ABDC 2.06 version is remains unmodified. The new created DNA schema covers more than 76 elements such as “ExtractionDate”, “ExtractionMethod” for DNA extraction as well as an “Amplification-Container” for Sequences, GenBankNumbers, CloneStrain etc.

-> View ABCDDNA schema: html or xml. -> View DNA part only: html or xml.

The following requirements have to be met to use the schema:

1. Installation of BioCASe Provider Software (BPS)

The installation is documented at the BPS Wiki: http://wiki.bgbm.org/bps/index.php/Main_Page.

Note: If the software package DiGIR is already implemented on your specimen database it is possible to run both installations in parallel!

2. ABCDDNA-Template

The current BioCASe Provider Software package (version 2.6.1, see BPS download section) includes the ABCDDNA template! If you are using an older version please upgrade your BPS!

3. Creating a new datasource

If you want to use the ABCDDNA schema for mapping you have to create a new datasource connection. You can use the BioCASe documentation for assistance or [Special:Contact contact the DNA Bank Network team].

After you have created a new datasource you have to declare the database connection and the database structure. Then you can select a schema (ABCDDNA) and click on “Create”.