Difference between revisions of "IT requirements"

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=Joining the Network - IT Requirements=
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<div id="wikinote">Please contact us via email (support@ggbn.org) if you have any questions related to sharing your data with GGBN.</div>
==Summary==
 
1. Specimen data in GBIF compliant database
 
  
2. DNA sample data in database (separate DNA database or combined DNA and specimen database)
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=Overview=
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The purpose of this document is to outline the technical requirements for GGBN Members to publish data through the GGBN Data Portal. These requirements must be met in order for GGBN’s technical staff to assist GGBN Members in making their DNA and Tissue data discoverable through the GGBN Data Portal. Please contact us for specific questions on the GGBN requirements outlined below.
  
3. Reference DNA sample to specimen/voucher data in terms of GBIF
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<div id="wikinote">An overview about mandatory and highly recommend fields and mapping principles to share data with GGBN can be found [[Mandatory_and_recommended_fields_for_sharing_data_with_GGBN | here]].</div>
  
4. BioCASE Provider Software and ABCDDNA
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=Information technology requirements for Core and Associate Members=
  
==Specimen Data==
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==Voucher 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.
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To guarantee both the safeguarding and long-term availability of referenced DNA and Tissue samples, these should be deposited in research collections. If voucher specimens exist these should be deposited in research collections too to enable verification of results. If no voucher exists ideally an e-voucher should be made available instead. Corresponding data 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 ([[GBIF | find out more]]).
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'''Requirement:''' Applied specimen databases have to be GBIF compliant so that they can be accessed via GBIF and the GGBN Data Portal. This can be accomplished by setting up a wrapper software on the collections database([[GBIF | find out more]]).
  
 
<div id="wikinote">'''Please check if the relevant institution is already a GBIF provider. Ask administrators or curators for help.'''</div>
 
<div id="wikinote">'''Please check if the relevant institution is already a GBIF provider. Ask administrators or curators for help.'''</div>
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If so: The requirement related to specimen data is fulfilled.
 
If so: The requirement related to specimen data is fulfilled.
  
If not: '''Is the relevant institution planning or willing to become a GBIF provider?'''
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If not: '''Is the 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.)
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If so: The requirement will be met if the relevant database is GBIF accessible.
  
 
If not: '''Relevant institution has no specimen database or no possibility of becoming a GBIF provider any time soon?'''
 
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. [http://www.specifysoftware.org/ Specify], [http://www.diversityworkbench.net/ Diversity Workbench with DiversityCollection]).
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There are several open source software solutions to administer specimen and observation data (e.g. [http://www.specifysoftware.org/ Specify], [http://www.diversityworkbench.net/ 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.
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As an interim solution you can provide your tissue and sample data without an associated voucher record. Often tissues are not accompanied by a deposited specimen records for certain reasons. This is fine with GGBN, whenever possible the deposition of a voucher specimen is recommended though.
  
 
===External vouchers===
 
===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 [[Special:Contact | contact]] the DNA Bank Network administrators.
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Often tissue or DNA and the respective voucher with its documentation might not be held at the same institutional locality (= external vouchers).
  
==DNA Data==
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==DNA and Tissue 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.
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DNA sample data have to be transferred to the portal using the principle applied for specimen data. GGBN has developed the [http://terms.tdwg.org/wiki/GGBN_Data_Standard GGBN Data Standard] to ensure both BioCASe/ABCD and IPT/DarwinCore can be used to share data with GGBN. '''To run the GGBN extensions with ABCD and DwC requires BioCASe v3.5.3 or higher and IPT v2.2 or higher.'''
  
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 | ABCDDNA]], which is an extension for the database collection standard ABCD as both DarwinCore and ABCD lack necessary features for DNA data.
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'''Requirement:''' An appropriate webserver must be in place (e.g., Linux, Microsoft).  Once the webserver is in place, [http://www.biocase.org BioCASe] or [http://www.gbif.org/ipt IPT] must be installed.
  
To run ABCDDNA requires the current version of BioCASE Provider Software!
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'''Requirement:''' Every DNA dataset has to be referenced to its respective specimen or tissue dataset.
  
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.
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That reference consists of the record identifiers UnitID/CatalogueNumber, CollectionCode, InstitutionCode and GUID. These ABCD or DarwinCore elements together with the '''WrapperUrl''' unambiguously define a specimen dataset.
  
'''Requirement:''' DNA metadata (contact details, terms of use, database description) and the ABCDDNA extension are needed for mapping DNA databases.
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<div id="wikinote">'''Please check if a DNA and Tissue sample database is available where references to specimen datasets can be put in place. Is it possible to install the BioCASE Provider Software?'''</div>
  
'''Requirement:''' Every DNA dataset has to be referenced to its respective specimen dataset through GBIF.
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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.
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If not: Please contact the technical support for help.
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==Technical support and features for Core Members==
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Core Members will receive the following support from GGBN technical staff:
  
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.
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1) Assistance with setting up BioCASe and IPT as well as mapping of the GGBN Data Standard
  
<div id="wikinote">'''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?'''</div>
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2) Assistance with a Member institution’s DNA and Tissue Data updates to the GGBN Data Portal every month. It is possible to re-index provider data on-demand if required.
  
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.
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3) Support if problems or errors appear with BioCASe. The GGBN Technical Secretariat also runs the BioCASe helpdesk. The IPT helpdesk is maintainted by GBIF.
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4) Data quality checks, matching with taxonomic backbone (currently four backbones used (GBIF, CoL, NCBI, Prokarya)
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5) Easy access to DNA, tissue and voucher data; catalogue of possible on-demand extractions can be provided
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6) Sample reqeust system: Customers order samples via the GGBN data portal and the DNA banks will receive an email automatically
  
If not: '''The DNA Module might be suitable for your purposes. All the required data flows can be realised using this software.''' Please [[Special:Contact | contact]] us for further details or browse this Wiki.
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7) Data privacy: detailed information about data privacy at GGBN can be found [[Data_Privacy | here]]

Latest revision as of 15:21, 28 January 2021

Please contact us via email (support@ggbn.org) if you have any questions related to sharing your data with GGBN.

Overview

The purpose of this document is to outline the technical requirements for GGBN Members to publish data through the GGBN Data Portal. These requirements must be met in order for GGBN’s technical staff to assist GGBN Members in making their DNA and Tissue data discoverable through the GGBN Data Portal. Please contact us for specific questions on the GGBN requirements outlined below.

An overview about mandatory and highly recommend fields and mapping principles to share data with GGBN can be found here.

Information technology requirements for Core and Associate Members

Voucher Specimen Data

To guarantee both the safeguarding and long-term availability of referenced DNA and Tissue samples, these should be deposited in research collections. If voucher specimens exist these should be deposited in research collections too to enable verification of results. If no voucher exists ideally an e-voucher should be made available instead. Corresponding data have to be stored in suitable collections databases.

Requirement: Applied specimen databases have to be GBIF compliant so that they can be accessed via GBIF and the GGBN Data Portal. This can be accomplished by setting up a 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 institution planning or willing to become a GBIF provider?

If so: The requirement will be met if the relevant database is GBIF accessible.

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

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

As an interim solution you can provide your tissue and sample data without an associated voucher record. Often tissues are not accompanied by a deposited specimen records for certain reasons. This is fine with GGBN, whenever possible the deposition of a voucher specimen is recommended though.

External vouchers

Often tissue or DNA and the respective voucher with its documentation might not be held at the same institutional locality (= external vouchers).

DNA and Tissue Data

DNA sample data have to be transferred to the portal using the principle applied for specimen data. GGBN has developed the GGBN Data Standard to ensure both BioCASe/ABCD and IPT/DarwinCore can be used to share data with GGBN. To run the GGBN extensions with ABCD and DwC requires BioCASe v3.5.3 or higher and IPT v2.2 or higher.

Requirement: An appropriate webserver must be in place (e.g., Linux, Microsoft). Once the webserver is in place, BioCASe or IPT must be installed.

Requirement: Every DNA dataset has to be referenced to its respective specimen or tissue dataset.

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

Please check if a DNA and Tissue 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: Please contact the technical support for help.

Technical support and features for Core Members

Core Members will receive the following support from GGBN technical staff:

1) Assistance with setting up BioCASe and IPT as well as mapping of the GGBN Data Standard

2) Assistance with a Member institution’s DNA and Tissue Data updates to the GGBN Data Portal every month. It is possible to re-index provider data on-demand if required.

3) Support if problems or errors appear with BioCASe. The GGBN Technical Secretariat also runs the BioCASe helpdesk. The IPT helpdesk is maintainted by GBIF.

4) Data quality checks, matching with taxonomic backbone (currently four backbones used (GBIF, CoL, NCBI, Prokarya)

5) Easy access to DNA, tissue and voucher data; catalogue of possible on-demand extractions can be provided

6) Sample reqeust system: Customers order samples via the GGBN data portal and the DNA banks will receive an email automatically

7) Data privacy: detailed information about data privacy at GGBN can be found here