Revision as of 13:10, 29 August 2011

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.

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 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”.

4. Mapping the DNA database

The first time you open the mapping page only few fields are visible. Select “Show all concepts” and press “Refresh” to see all available features.

Since the DNA sample means ABCD Unit the Triple Identifier (composed of UnitID, SourceInstitutionID and SourceID) has to map as follows:

UnitID → DNA Bank Number (unique DNA Number in your database but NOT the ID in the DNA table)

SourceInstitutionID → Code or abbreviation of the institution the DNA bank is located, e.g. BGBM for Botanic Garden and Botanical Museum Berlin-Dahlem

SourceID → Designation of the collection, e.g. DNA bank

UnitAssociation (Triple Identifier of the related specimen):

Fig. 4. UnitAssociation in ABCD schema. All attributes are required. It has to be mapped similar to the Triple Identifier of the DNA sample. AssociatedUnitSourceInstitutionCode → Code or abbreviation of the institution the specimen/voucher of the DNA sample is deposited.

AssociatedUnitSourceName → Designation of the collection the specimen/voucher of the DNA sample is deposited.

AssociatedUnitID → Unique identifier/number of the specimen/voucher of the DNA sample within the specimen database.

Comment → WrapperURL of the specimen database.

These three listed attributes of the "UnitAssociation" and the Triple Identifier used in the original specimen database should have the same values. They can than be used as GUIDs (Globally Unique Identifier) since both values describe the same specimen.