Difference between revisions of "IT requirements"
(→Technical support and features for Core Members) |
|||
| (9 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| + | <div id="wikinote">Please contact us via email (support@ggbn.org) if you have any questions related to sharing your data with GGBN.</div> | ||
| + | |||
=Overview= | =Overview= | ||
| − | 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. | + | 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. |
| + | |||
| + | <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> | ||
=Information technology requirements for Core and Associate Members= | =Information technology requirements for Core and Associate Members= | ||
| Line 21: | Line 25: | ||
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]). | 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]). | ||
| − | + | 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) | + | 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 and Tissue Data== | ||
| − | + | 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.''' | |
| + | '''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. | ||
| − | DNA | + | '''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. | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | That reference consists of the record identifiers UnitID, CollectionCode, and | ||
<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> | <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> | ||
| Line 50: | Line 44: | ||
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: | + | If not: Please contact the technical support for help. |
| − | |||
| − | |||
==Technical support and features for Core Members== | ==Technical support and features for Core Members== | ||
| Line 61: | Line 53: | ||
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. | 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. | + | 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 | + | 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 | 5) Easy access to DNA, tissue and voucher data; catalogue of possible on-demand extractions can be provided | ||
| − | 6) | + | 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 [[Data_Privacy | here]] | 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
Contents
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.
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).
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.
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
