Technical requirements - Revision history

WikiSysop at 12:08, 23 January 2025

2025-01-23T12:08:13Z

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	=Information technology requirements for Core and Associate Members=		=Information technology requirements for Core and Associate Members=

			==BioCASe and IPT==
			Similar to other infrastructures GGBN partner use BioCASe and IPT to provide their data to GGBN. Both are open source software and provide a mapping between your database or csv file and the two established data exchange standards DarwinCore and ABCD. You'll need a webserver to run this software, most of our partners already are GBIF providers and have a running BioCASe or IPT installation. You don't need both, either BioCASe or IPT is fine. But you'll need to use the GGBN Data Standard.

	==Voucher Specimen Data==		==Voucher Specimen Data==

WikiSysop: WikiSysop moved page IT requirements to Technical requirements: matching portal output

2025-01-23T12:00:39Z

WikiSysop moved page IT requirements to Technical requirements: matching portal output

← Older revision	Revision as of 14:00, 23 January 2025
(No difference)

WikiSysop at 14:21, 28 January 2021

2021-01-28T14:21:49Z

← Older revision		Revision as of 16:21, 28 January 2021
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	<div id="wikinote">~~This site is not yet up to date.~~ Please contact us via email (support@ggbn.org) if you have any questions related to sharing your data with GGBN~~. Please look back again in January for updates to this page~~.</div>		<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 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.		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 to share data with GGBN can be found [[Mandatory_and_recommended_fields_for_sharing_data_with_GGBN \| here]].</div>		<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=

WikiSysop: /* Technical support and features for Core Members */

2021-01-28T14:20:59Z

Technical support and features for Core Members

← Older revision		Revision as of 16:20, 28 January 2021
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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.		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 ~~Catalogue of Life in use~~)		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) ~~Shopping-System~~: Customers order samples via the GGBN data portal and the DNA banks will receive an email automatically		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]]

WikiSysop: /* DNA and Tissue Data */

2021-01-28T14:19:18Z

DNA and Tissue Data

← Older revision		Revision as of 16:19, 28 January 2021
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	==DNA and Tissue Data==		==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 BOLD and 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. 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. 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.		'''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.

	'''Requirement:''' Every DNA dataset has to be referenced to its respective specimen dataset ~~through GBIF~~.		'''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, and ~~InstitutionCode~~. These ABCD or DarwinCore elements together with the '''WrapperUrl''' unambiguously define a specimen 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.

	<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>
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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.		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~~.		If not: Please contact the technical support for help.

	==Technical support and features for Core Members==		==Technical support and features for Core Members==

WikiSysop: /* Voucher Specimen Data */

2021-01-28T14:17:46Z

Voucher Specimen Data

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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]).		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]] 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~~.		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 contact the GGBN technical staff~~.		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==

WikiSysop: /* Overview */

2021-01-28T14:11:16Z

Overview

← Older revision		Revision as of 16:11, 28 January 2021
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	=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 to share data with GGBN can be found [[Mandatory_and_recommended_fields_for_sharing_data_with_GGBN \| here]].</div>		<div id="wikinote">An overview about mandatory and highly recommend fields to share data with GGBN can be found [[Mandatory_and_recommended_fields_for_sharing_data_with_GGBN \| here]].</div>

WikiSysop: /* DNA and Tissue Data */

2020-04-30T08:51:16Z

DNA and Tissue Data

← Older revision		Revision as of 10:51, 30 April 2020
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	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 BOLD and publications. The software is optimized for PHP 5 and MySQL 5. Any GBIF compliant specimen database worldwide can be accessed by the DNA Module.		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 BOLD and 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. 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. 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.		'''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.

	'''Requirement:''' Every DNA dataset has to be referenced to its respective specimen dataset through GBIF.		'''Requirement:''' Every DNA dataset has to be referenced to its respective specimen dataset through GBIF.

WikiSysop at 16:04, 16 December 2015

2015-12-16T16:04:55Z

← Older revision		Revision as of 18:04, 16 December 2015
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	<div id="wikinote">This site is not yet up to date. Please contact us via email (support@ggbn.org) if you have any questions related to sharing your data with GGBN.</div>		<div id="wikinote">This site is not yet up to date. Please contact us via email (support@ggbn.org) if you have any questions related to sharing your data with GGBN. Please look back again in January for updates to this page.</div>

	=Overview=		=Overview=

WikiSysop at 14:26, 16 December 2015

2015-12-16T14:26:34Z

← Older revision		Revision as of 16:26, 16 December 2015
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	=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. 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 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=