Difference between revisions of "Configuration Tool"

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(→‎Workflow for Mapping Specimen Tool database)
(→‎Workflow for Mapping DNA database)
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# Set up BioCASe provider Software (BPS) on a web server
 
# Set up BioCASe provider Software (BPS) on a web server
 
# Create a new datasource with '''empty template''' (default password for BPS is ACDC)
 
# Create a new datasource with '''empty template''' (default password for BPS is ACDC)
−
# Copy/overwrite "provider_setup_file.xml" and "cmf_ABCDDNA_2.06" from "YOUR_DNA_MODULE_FOLDER\wrapper\DNA_Mapping\" to "YOUR_BIOCASE_FOLDER\config\datasources\YOUR_DATASOURCE\"; '''If you copy these files into the bps folder you don't have to do the mapping manually'''
+
# Copy/overwrite "provider_setup_file.xml" and "cmf_ABCDDNA_2.06" from "YOUR_DNA_MODULE_FOLDER\wrapper\DNA_Mapping\" to "YOUR_BIOCASE_FOLDER\config\datasources\YOUR_DNA_DATASOURCE\"; '''If you copy these files into the bps folder you don't have to do the mapping manually'''
 
# Edit database connection (DBMS = mysql, encoding = utf_8)
 
# Edit database connection (DBMS = mysql, encoding = utf_8)
 
# Test mapping using BPS query forms
 
# Test mapping using BPS query forms

Revision as of 13:51, 9 February 2012

Overview

Config-Tool-Administrator.jpg

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.

Workflow for Mapping DNA database

mapping screen after copying DNA Module templates (see step 5)
  1. Make sure your DNA Module (or a copy) is on a web server
  2. Define the Metadata for your DNA collection using the Configuration Tool (s.b.)
  3. Set up BioCASe provider Software (BPS) on a web server
  4. Create a new datasource with empty template (default password for BPS is ACDC)
  5. Copy/overwrite "provider_setup_file.xml" and "cmf_ABCDDNA_2.06" from "YOUR_DNA_MODULE_FOLDER\wrapper\DNA_Mapping\" to "YOUR_BIOCASE_FOLDER\config\datasources\YOUR_DNA_DATASOURCE\"; If you copy these files into the bps folder you don't have to do the mapping manually
  6. Edit database connection (DBMS = mysql, encoding = utf_8)
  7. Test mapping using BPS query forms

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:

Metadata DNA.jpg

edit metadata of your DNA bank records via the Configuration Tool
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 must be "OtherSpecimen"
SourceID short description of relevant collection should be "DNA Bank"
SourceInstitutionID short name/abbreviation of relevant institution BGBM

Wrapper url for DNA data

The Wrapper url is required if you want to share your DNA data via the central Web portal of the DNA Bank Network. You can find this url in your BPS settings. Please contact the DNA Bank Network for further assistance. In opposite to the Specimen Tool it's not required to record the url in the Configuration Tool.

Workflow for Mapping Specimen Tool database

BILDCHEN

  1. Make sure your Specimen Tool/DNA Module (or a copy) is on a web server
  2. Define the Metadata for your Specimen Tool using the Configuration Tool (s.b.)
  3. Set up BioCASe provider Software (BPS) on a web server
  4. Create a new datasource with empty template (default password for BPS is ACDC)
  5. Copy/overwrite "provider_setup_file.xml" and "cmf_ABCD_2.06" from "YOUR_DNA_MODULE_FOLDER\wrapper\SpecimenTool_Mapping\" to "YOUR_BIOCASE_FOLDER\config\datasources\YOUR_SPECIMEN_DATASOURCE\"; If you copy these files into the bps folder you don't have to do the mapping manually
  6. Note that you should use ABCD2.06 instead of ABCDDNA for your specimen records.
  7. Edit database connection (DBMS = mysql, encoding = utf_8)
  8. Test mapping using BPS query forms

Providing Specimen Tool records to GBIF?

Of course you can provide the Specimen Tool records to GBIF if you want! All what you need is the wrapper url, a working mapping and the Metadata (s.b.). Than go to the GBIF portal and register your database. Please don't hesitate to contact the DNA Bank Network if you have any further questions.

Metadata for Specimen Tool

Please keep in mind that the Specimen Tool should only be used for DNA vouchers that are not available via GBIF!

Be careful with Metadata information, since you might not be the owner in every case!
You can use the Specimen Tool as your main specimen collection management tool if you don't have one yet. In that case the terms of Metadata information might be easier to find. Please don't hesitate to contact the DNA Bank Network if you have any questions!

Group Element Remarks Example
ContentContact Address Complete Address of the responsible person
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 specimen data
Description/Representation Details
Description/Representation Title Short title that describes your collection
IPRStatements/Citation Text
IPRStatements/Copyright Text
IPRStatements/TermsOfUse Text
IconURI complete url path to the logo of your institution/organisation
Owner Address Complete Address of the institution/organisation that owns the data
Owner/Representation Text name of your institution/organisation
Owner URL path to website of your institution/organisation
RevisionData DateModified date of last modification of your data
TechnicalContact Address Complete Address of the responsible person
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
RecordBasis this value must be part of the ABCD vocabulary dynamically generated from Table: cachecollection, is defined during entering new record
SourceID short description of relevant collection dynamically generated from Table: cachecollection, is defined during entering new record
SourceInstitutionID short name/abbreviation of relevant institution dynamically generated from Table: cachecollection, is defined during entering new record

Wrapper url for Specimen Tool

The Wrapper url is required for sharing data with GBIF or the DNA Bank Network. All specimen databases that are relevant for your DNA samples are recorded in two tables (provider and dataset). When setting up the DNA Module and the Specimen Tool the Specimen Tool is listed without a wrapper url. After you have finished the ABCD2.06 mapping for your Specimen Tool you should record this wrapper url also in the Wrapper Configuration Tool of the DNA Module.

At first enter the wrapper url and check the provider availability. If the provider is available save the entry. Once you have saved you can edit the url later if you want.

Example: http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=ZSM_DNAModule_Specimens

Note: After entering the wrapper url of the Specimen Tool into the Configuration Tool the display of Specimen Tool records in combination with DNA data might change a bit because now they are coming via wrapper and no longer directly from the database. Entering and editing data in your Specimen Tool won't change!

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

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