Configuration Tool

Overview

Only members of group "Administrator" have full access to the Configuration Tool.

Feature	Access
Database connection	Administrator
User Management	Administrator, Team
General settings	Administrator, Team
User defined settings	Administrator, Team, Project, Guest
Change own password	Administrator, Team, Project, Guest
Wrapper Configuration	Administrator

Connection to DNA database

edit database connection

Only administrators are allowed to edit the database connection. The DNA Module can be used currently with MySQL only. Password of database user can be left empty if not assigned.

User Management

user management

Members of group "Administrator" and "Team" are allowed to add or delete users and to edit user details. Furthermore the tool gives an overview how many DNA and specimen records a individual user has created .

An user can not be deleted if he/her has created records! You should change his/her group membership instead.

Add new user

For creating a new user please select "Add User" (see screenshot). You have to enter the email address of the new user, his/her real and login name and define his/her group membership. After creating the user will receive an email with an automatically generated password. Please make sure you have define SMTP parameters first!

Group overview

Tool	Feature	Administrator	DNA Bank Team	Projects	Guest
All tools	Add new records	Yes	Yes	Yes	No
All tools	Delete records	Yes	Yes	No	No
All tools	Read blocked records created by other users	Yes	Yes	No	No
All tools	Edit blocked records created by other users	Yes	Yes	No	No
All tools	Read unblocked records created by other users	Yes	Yes	Yes	Yes
All tools	Edit unblocked records created by other users	Yes	Yes	No	No
All tools	Read internal notes of records created by other users	Yes	Yes	No	No
All tools	Edit internal notes of records created by other users	Yes	Yes	No	No
All tools	Read/Edit records created by themself	Yes	Yes	Yes	No
All tools	Read/Edit internal notes of records created by themself	Yes	Yes	Yes	No
All tools	Unblock/verify records created by other users	Yes	Yes	No	No
All tools	Unblock/verify records created by themself	Yes	Yes	Yes	No
Configuration Tool	Access to Database configuration and mapping settings	Yes	No	No	No
Configuration Tool	Edit/Delete/Add Users	Yes	Yes	No	No
Configuration Tool	Change passwort	Yes	Yes	Yes	Yes
Configuration Tool	Define user settings	Yes	Yes	Yes	Yes
Data cleaning Tool	Access to data cleaning	Yes	Yes	Yes	No
Customer Requests	Access to customer requests in general	Yes	Yes	No	No

General Settings

general settings

Members of groups "Administrator" and "DNA Bank Management" define the following general settings:

• Customer requests:

Feature	Remarks
Price and currency of aliquots
Standard aliquot volume for shipping	These settings will be displayed when entering new DNA data and requests, but changes can be made for individual DNA samples if needed.

• Input & search:

Feature	Remarks
Prefix DNA extraction number	Please note, that you might add a space character after prefix if needed!
Backup aliquot made	One of the standards of the DNA Bank Network partners is to make sure there is a copy of the samples. This can be the stock aliquot stored in a different freezer, ideally it should be a backup aliquot stored in a different institution. Please select this option only if you store a backup aliquot.

• General - Please note that you should define these specific settings during First steps

Feature	Remarks
Logo path	You can add your own logo to be displayed at top right corner. Please enter image path from root, e.g. for YOUR_DNA_MODULE_FOLDER/images/logo.png type "images/logo.png"
SMTP path and port	of your email server, please ask your administrator for help
Administrator email	Enter email of local administrator that works as sender of any information or error reporting emails related to the DNA Module.

User defined Settings

user defined settings

All users can define the following settings:

• Search for DNA samples:
  • Records per page (hitlist)
  • Sorting
• Search for specimens (Specimen Tool):
  • Records per page (hitlist)
  • Sorting

Change Password

change password

Every user can change his/her password after first login. When creating a new user, a password will be generated automatically and will be send via email to the new user. The first user will be created during First steps.

Wrapper Configuration

The wrapper configuration is required for sharing DNA and specimen data with GBIF and the DNA Bank Network. If you don't want to share your data via these platforms you don't have to configure the wrapper.

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.

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 an xml schema for data transfer: BioCASE - ABCD, DiGIR and TAPIR - DarwinCore (DwC).

To transfer DNA data into the webportal of the DNA Bank Network a DNA extension for ABCD, called ABCDDNA has been developed. Thus BioCASE Provider Software is required. If your institution don't make use of BioCASe yet please follow the installation guide of BioCASe first. If your institution is using BioCASe already you can just add a further mapping. BioCASe can be used in parallel with other systems like DiGIR or TAPIR.

Metadata for DNA data

ABCD contains a lot of elements. Some are mandatory. Further information about ABCDDNA and a complete Mapping example can be found here in the Wiki. The curator of the DNA Bank has to define the Metadata of the DNA Bank data first.

Example of the Metadata of a DNA Bank, published with every single record via the DNA Bank Network's web portal.

We have to differ between elements that are required to build a valid xml file, elements that are required for the DNA Bank Network, and further elements that are not essential. The following table contains only those elements required for providing your DNA data via the web portal of the DNA Bank Network. Red labelling means required for building a valid xml file.
All metadata information should be in English!

Group	Element	Remarks	Example
ContentContact	Address	Complete Address of the responsible person	Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Koenigin-Luise-Str. 6-8, 14195 Berlin, Germany
ContentContact	Email	valid email address; will be used by the web portal for sending you annotations etc.	please use @ instead of masquerades like "[at]"
ContentContact	Name	Person, person team responsible for curation of your DNA Bank	Dr. Birgit Gemeinholzer
Description/Representation	Details	Short text to describe the focus and number of samples in your DNA collection. It must include the following phrase: The DNA bank is part of the DNA Bank Network which was established in spring 2007. The network was initiated by GBIF Germany and provides a technically optimized DNA collection service facility for all biological research accessible via one central web portal. The network promotes deposition of well documented reference DNA samples after project completion or data publication from scientists of other universities and institutions.	The DNA bank of the Botanic Garden and Botanical Museum Berlin-Dahlem holds currently a collection of 8200 plant DNA and tissue samples growing constantly. Its core collection focuses on the flora of the Berlin and Brandenburg but it also preserves DNA from the Alps, the Mediterranean and the Altai Mountains.
Description/Representation	Title	Short title that describes your DNA collection	DNA Bank of the Herbarium Berolinense
IPRStatements/Citation	Text		Droege, G., Zetzsche, H. & Gemeinholzer, B. (Ed.) 2008 - (continuously updated): DNA samples of the DNA bank at the BGBM (Botanic Garden and Botanical Museum Berlin-Dahlem).
IPRStatements/Copyright	Text		The copyright for any material created by the DNA bank of the BGBM is reserved. The duplication or use of information and data such as texts or images is only permitted with the indication of the source or with prior approval by the BGBM.
IPRStatements/TermsOfUse	Text		The use of the data is allowed only for non-profit scientific use and for non-profit nature conservation purpose. The data bases or part of it may only be used or copied by the written permission from the legal owner.
	IconURI	complete url path to the logo of your institution
Owner	Address	Complete Address of the institution that owns the DNA bank samples and data
Owner/Representation	Text	name of your institution	Botanic Garden an Botanical Museum Berlin-Dahlem (Freie Universität Berlin)
Owner	URL	path to website of your institution	http://www.bgbm.org
RevisionData	DateModified	date of last modification of your data
TechnicalContact	Address	Complete Address of the responsible person	Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Koenigin-Luise-Str. 6-8, 14195 Berlin, Germany
TechnichalContact	Email	valid email address; will be used by the web portal for sending you annotations etc.	please use @ instead of masquerades like "[at]"
TechnicalContact	Name	Person, person team responsible for technical issues of your database	Gabriele Droege
	RecordBasis	this value must be part of the ABCD vocabulary	please use only this: "OtherSpecimen"
	SourceID	short description of relevant collection	should be "DNA Bank"
	SourceInstitutionID	short name/abbreviation of relevant institution	BGBM

Wrapper url for Specimen Tool

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http://www.dnabank-network.org Webpage of the DNA Bank Network
http://www.gbif.org Webpage of the Global Biodiversity Information Facility (GBIF)
http://www.biocase.org Webpage of the Biological Collection Access Service (BioCASe)
http://www.biocase.org/products/provider_software/index.shtml Download BioCASe Provider Software
http://wiki.bgbm.org/bps/index.php/Main_Page BioCASe Provider Software - Wiki, Installation guide
http://www.bgbm.org/tdwg/codata/schema/ Access to Biological Collection Data (ABCD)
http://digir.net/prov/prov_manual.html Distributed Generic Information System (DiGIR)
http://wiki.tdwg.org/TAPIR/ TDWG Access Protocol for Information Retrieval (TAPIR)
http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome DarwinCore