Difference between revisions of "IT requirements"
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| − | + | The purpose of this document is to outline the technical requirements for GGBN Members. 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. | |
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| − | + | =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. ([[GBIF | find out more]]). | |
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| − | '''Requirement:''' Applied | ||
<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 | + | 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 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]). | + | 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. | + | An alternative solution is the Specimen Tool. This software is part of the [[DNA Module]] which is an open source software to manage DNA data. The Specimen Tool can also be used to manage your specimen and observation data and furthermore to become a GBIF provider yourself. |
===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 | + | 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 GGBN technical staff. |
| + | |||
| + | ==DNA and Tissue Data== | ||
| + | The DNA Module is an open source software to manage DNA and Tissue specific data such as tissue sample number, tissue quality, DNA extraction method, DNA quality, storage documentation, etc. Furthermore it is possible to administer customer requests and set links to GenBank/EMBL/DDBJ entries as well as to publications. The software is optimized 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. | + | DNA sample data have to be transferred to the portal using the principle applied for specimen data. Currently one database standards for DNA and Tissue documentation was established, called ABCDDNA (add link here). A DNA and Tissue Extension for DwC-A is currently in the developing process (add link here). ABCDDNA is an extension for the data collection standard ABCD and DwC-A DNA and Tissue Extension is an extension to Darwincore-Archive, as both DarwinCore and ABCD lack necessary features for DNA and Tissue data. |
| − | To run ABCDDNA requires the current version of BioCASE Provider Software! | + | ''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. | 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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| + | '''Requirement:''' An appropriate webserver must be in place (e.g., Linux, Microsoft). Once the webserver is in place, Python 2.5, Java, Apache/Tomcat must be installed and the BioCase publisher must be set up. | ||
'''Requirement:''' DNA metadata (contact details, terms of use, database description) and the ABCDDNA extension are needed for mapping DNA databases. | '''Requirement:''' DNA metadata (contact details, terms of use, database description) and the ABCDDNA extension are needed for mapping DNA databases. | ||
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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. | 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. | ||
| − | <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> | + | <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> |
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 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 | + | If not: '''The DNA Module might be suitable for your purposes. All the required data flows can be realized using this software.''' Please contact us for further details. |
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| + | <div id="wikinote">We are currently working on a solution to enable the use of '''DarwinCore-Archive''' in parallel to ABCDDNA. To reach this goal we are working together with the GBIF developer team on a DNA and Tissue extension for DarwinCore-Archive.</div> | ||
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| + | ==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 mapping ABCD/ABCDDNA | ||
| + | |||
| + | 2) Assistance with a Member institution’s DNA and Tissue Data updates to the GGBN Data Portal every three months. It is expected that each update will take GGBN technical staff one day. It is possible to re-index provider data on-demand if required. | ||
| + | |||
| + | 3) Support if problems or errors appear with the BioCASe Provider Software. | ||
| + | |||
| + | 4) Data quality checks, matching with taxonomic backbone (currently Catalogue of Life in use) | ||
| + | |||
| + | 5) Easy access to DNA, tissue and voucher data; catalogue of possible on-demand extractions can be provided | ||
| + | |||
| + | 6) Shop-System: Customers order samples via the GGBN data portal and the DNA banks will receive an email automatically | ||
| + | |||
| + | 7) Data privacy: Webstatistics are stored using Piwik software, order history is not stored | ||
Revision as of 14:09, 25 July 2013
Contents
0verview
The purpose of this document is to outline the technical requirements for GGBN Members. 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.
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).
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).
An alternative solution is the Specimen Tool. This software is part of the DNA Module which is an open source software to manage DNA data. 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 GGBN technical staff.
DNA and Tissue Data
The DNA Module is an open source software to manage DNA and Tissue specific data such as tissue sample number, tissue quality, DNA extraction method, DNA quality, storage documentation, etc. Furthermore it is possible to administer customer requests and set links to GenBank/EMBL/DDBJ entries as well as to publications. The software is optimized 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. Currently one database standards for DNA and Tissue documentation was established, called ABCDDNA (add link here). A DNA and Tissue Extension for DwC-A is currently in the developing process (add link here). ABCDDNA is an extension for the data collection standard ABCD and DwC-A DNA and Tissue Extension is an extension to Darwincore-Archive, as both DarwinCore and ABCD lack necessary features for DNA and Tissue 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: An appropriate webserver must be in place (e.g., Linux, Microsoft). Once the webserver is in place, Python 2.5, Java, Apache/Tomcat must be installed and the BioCase publisher must be set up.
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.
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 realized using this software. Please contact us for further details.
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 mapping ABCD/ABCDDNA
2) Assistance with a Member institution’s DNA and Tissue Data updates to the GGBN Data Portal every three months. It is expected that each update will take GGBN technical staff one day. It is possible to re-index provider data on-demand if required.
3) Support if problems or errors appear with the BioCASe Provider Software.
4) Data quality checks, matching with taxonomic backbone (currently Catalogue of Life in use)
5) Easy access to DNA, tissue and voucher data; catalogue of possible on-demand extractions can be provided
6) Shop-System: Customers order samples via the GGBN data portal and the DNA banks will receive an email automatically
7) Data privacy: Webstatistics are stored using Piwik software, order history is not stored
