IT requirements

From DNA Bank Network Wiki

Revision as of 08:45, 13 September 2011 by WikiSysop (Talk | contribs)

Jump to: navigation, search

Joining the Network - IT Requirements

Summary

1. Specimen data in GBIF compliant database

2. DNA sample data in database (separate DNA database or combined DNA and specimen database)

3. Reference DNA sample to specimen/voucher data in terms of GBIF

4. BioCASE Provider Software and ABCDDNA

Specimen Data

To guarantee both the safeguarding and long-term availability of referenced DNA samples these should be deposited in research collections. Corresponding data including voucher information have to be stored in suitable collections databases.

Requirement: Applied collections databases have to be GBIF compliant so that they can be accessed via the web portal. This can be accomplished by setting up the wrapper software on the collections database ( find out more).

Please check if the relevant institution is already a GBIF provider. Ask administrators or curators for help.

If so: The requirement related to specimen data is fulfilled.

If not: Is the relevant institution planning or willing to become a GBIF provider?

If so: The requirement will be met if the relevant database is GBIF accessible. (The grey info box contains information about GBIF.)

If not: Relevant institution has no specimen database or no possibility of becoming a GBIF provider any time soon?

There are several software solutions to administer specimen and observation data (e.g. Specify, Diversity Workbench with DiversityCollection).

An alternative solution is the Specimen Tool. This software is part of the DNA Module. The Specimen Tool can also be used to manage your specimen and observation data and furthermore to become a GBIF provider yourself.

External vouchers

Often tissue or DNA and the respective voucher with its documentation might not be held at the same institutional locality (= external vouchers). The DNA Module can link to unlimited numbers of specimen databases worldwide if they are GBIF compliant. For further information please contact the DNA Bank Network administrators.

DNA Data

The DNA Module is an open source software to manage DNA specific data such as DNA sample number, extraction method, DNA quality, storage documentation, etc. Furthermore it is possible to administer customer requests and set links to GenBank entries as well as to publications. The software is optimised for PHP 5 and MySQL 5. Any GBIF compliant specimen database worldwide can be accessed by the DNA Module.

DNA sample data have to be transferred to the portal using the principle applied for specimen data. An international database standard for DNA documentation was established, called ABCDDNA, which is an extension for the database collection standard ABCD as both DarwinCore and ABCD lack necessary features for DNA data.

To run ABCDDNA requires the current version of BioCASE Provider Software!

A mapping example with metadata can be found on our website. If DIGIR/DarwinCore is used for the specimen database it is also possible to run BioCASE/ABCDDNA alongside it.

Requirement: DNA metadata (contact details, terms of use, database description) and the ABCDDNA extension are needed for mapping DNA databases.

Requirement: Every DNA dataset has to be referenced to its respective specimen dataset through GBIF.

That reference consists of the record identifiers UnitID, CollectionCode, and InstitutionCode. These ABCD or DarwinCore elements together with the WrapperUrl unambiguously define a specimen dataset.

Please check if a DNA sample database is available where references to specimen datasets can be put in place. Is it possible to install the BioCASE Provider Software?

If so: The required references to specimen datasets have to be defined and BioCASE as well as the ABCDDNA schema must be set up. If this is accomplished the DNA data related requirements are fulfilled.

If not: The DNA Module might be suitable for your purposes. All the required data flows can be realised using this software. Please contact us for further details or browse this Wiki.

Personal tools
DNA Bank Network
Downloads
Sample Deposition
More Information
feedback