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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 (see grey info box).

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).

An alternative solution is the DNA Module. This software for DNA data input and management has been developed by the DNA Bank Network. A dedicated specimen tool able to manage your specimen data is part of the DNA Module. The specimen tool can also be used to become a GBIF provider.

GBIF (Global Biodiversity Information Facility)

GBIF is a very powerful network and platform for specimen and observation data. Via the GBIF portal one can search for more than 180 million records worldwide. All required software packages are available for free. Please read the GBIF sites for more information. GBIF's most relevant tool in this context is the wrapper software. It enables the transformation of different database structures into standard formats.

- How to join the GBIF Network
- Informatics infrastructure

Wrappers/Provider Software

Three wrapper types are most often used:

- BioCASE (Biological Collection Access Service)
- DiGIR (Distributed Generic Information Retrieval)
- TAPIR (TWDG Access Protocol for Information Retrieval)

All provider softwares have pros and cons and use standard transfer schemes to exchange amongst others specimen and observation data stored in online accessible databases.

- BioCASE - ABCD Access to Biological Collection Data
- DiGIR and TAPIR - DarwinCore
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 via email: contact[at]dnabank-network.org

DNA Data
The DNA Module is 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 BioCASE Provider Software and ABCDDNA. Please note: The ABCDDNA is not part of the current version of the BioCASE Provider Software!

The ABCDDNA extension is available here. An installation guide and 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. A beta version is available to date. Please request it via email: contact[at]dnabank-network.org.