ABCDDNA - Revision history

A.Plank: Category:Terms documentations

2023-01-09T11:21:32Z

← Older revision		Revision as of 13:21, 9 January 2023
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	-> View ABCDDNA schema: [http://www.dnabank-network.org/schemas/ABCDDNA/ABCDDNA.html html] or [http://www.dnabank-network.org/schemas/ABCDDNA/ABCDDNA.xml xml].		→ View ABCDDNA schema: [http://www.dnabank-network.org/schemas/ABCDDNA/ABCDDNA.html html] or [http://www.dnabank-network.org/schemas/ABCDDNA/ABCDDNA.xml xml].
	-> View DNA part only: [http://www.dnabank-network.org/schemas/ABCDDNA/DNA.html html] or [http://www.dnabank-network.org/schemas/ABCDDNA/DNA.xml xml].
			→ View DNA part only: [http://www.dnabank-network.org/schemas/ABCDDNA/DNA.html html] or [http://www.dnabank-network.org/schemas/ABCDDNA/DNA.xml xml].

	The following requirements have to be met to use the schema:		The following requirements have to be met to use the schema:
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	Please press "Submit" (on the top of the page) to send the query to your database. You will hopefully see some results in xml. Otherwise you should check the search key (A* searches for taxa beginning with A.) or change the debugging level for more detailed error messages.		Please press "Submit" (on the top of the page) to send the query to your database. You will hopefully see some results in xml. Otherwise you should check the search key (A* searches for taxa beginning with A.) or change the debugging level for more detailed error messages.


			[[Category:Terms documentations]]

WikiSysop at 12:52, 25 July 2013

2013-07-25T12:52:37Z

← Older revision		Revision as of 14:52, 25 July 2013
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	=DNA extension for ABCD - General information & installation manual=		=DNA extension for ABCD - General information & installation manual=
	~~Another~~ mapping with the BioCASE Provider Software (wrapper) on all connected databases had to be set up mandatory to offer DNA samples and its related specimen data on the central webportal (http://www.dnabank-network.org). Although the [http://wiki.tdwg.org/twiki/bin/view/ABCD/ ABCD 2.06 schema] (part of the BioCASE wrapper) is currently preferred its existing part for DNA ‘Sequences’ lacks important features. So, it shouldn’t be used any longer. The whole ABCD 2.06 schema is available [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/ABCD_2.06.XSD here]. If you want to learn more about the meaning of BioCASE and ABCD please follow the links.		Currently only BioCASe and ABCD can be used to provide data via the DNA Bank Network.
			Additionally to the mapping of the specimens a second mapping with the BioCASE Provider Software (wrapper) on all connected databases had to be set up mandatory to offer DNA samples and its related specimen data on the central webportal (http://www.dnabank-network.org). Although the [http://wiki.tdwg.org/twiki/bin/view/ABCD/ ABCD 2.06 schema] (part of the BioCASE wrapper) is currently preferred its existing part for DNA ‘Sequences’ lacks important features. So, it shouldn’t be used any longer. The whole ABCD 2.06 schema is available [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/ABCD_2.06.XSD here]. If you want to learn more about the meaning of BioCASE and ABCD please follow the links.

	ABCD offers two options to add supplementary contents: [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#complexType_MeasurementOrFact_Link03076C80 ‘MeasurementsOrFacts’] and [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#element_UnitExtension_Link031A1C90 ‘UnitExtensions’]. Since the hierarchical structure of DNA specific features is too complex for ‘MeasurementsOrFacts’ we decided to use ‘UnitExtensions’ to integrate an xml schema definition for DNA data similar to the [http://www.geocase.eu/ ABCDEFG extension] for geosciences. That new DNA extension for ABCD 2.06 is called ABCDDNA.		ABCD offers two options to add supplementary contents: [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#complexType_MeasurementOrFact_Link03076C80 ‘MeasurementsOrFacts’] and [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#element_UnitExtension_Link031A1C90 ‘UnitExtensions’]. Since the hierarchical structure of DNA specific features is too complex for ‘MeasurementsOrFacts’ we decided to use ‘UnitExtensions’ to integrate an xml schema definition for DNA data similar to the [http://www.geocase.eu/ ABCDEFG extension] for geosciences. That new DNA extension for ABCD 2.06 is called ABCDDNA.

WikiSysop at 11:24, 10 February 2012

2012-02-10T11:24:56Z

WikiSysop: /* UnitAssociation (Triple Identifier of the related specimen): */

2012-01-19T13:59:58Z

UnitAssociation (Triple Identifier of the related specimen):

← Older revision		Revision as of 15:59, 19 January 2012
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	<div id="wikinote"><span style="color:red;">'''Note:'''</span> Please don’t map DNA data only. To verify the related specimen it is absolutely '''essential''' to map both the '''identification part''' (Taxon Name) and the '''UnitAssociation'''. It is furthermore advantageous to map few gathering attributes such as CountryName or ISO-Code.</div>		<div id="wikinote"><span style="color:red;">'''Note:'''</span> Please don’t map DNA data only. To verify the related specimen it is absolutely '''essential''' to map both the '''identification part''' (Taxon Name) and the '''UnitAssociation'''. It is furthermore advantageous to map few gathering attributes such as CountryName or ISO-Code.</div>

	===UnitAssociation (Triple Identifier of the related specimen):===		===UnitAssociation (Triple Identifier of the related specimen)===
	[[File:UnitAssociation.png]]		[[File:UnitAssociation.png]]

WikiSysop: /* UnitAssociation (Triple Identifier of the related specimen): */

2012-01-19T13:59:05Z

UnitAssociation (Triple Identifier of the related specimen):

← Older revision		Revision as of 15:59, 19 January 2012
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	It is no problem if special characters are used in your database. But applied in the mapping scheme these characters constantly produce “fatal python errors”! To fix such a fatal mapping mistake you have to close the browser window and open it again. So, you will loose your changes if they are not saved. There’s no way to annul that error by going backwards in your browser!		It is no problem if special characters are used in your database. But applied in the mapping scheme these characters constantly produce “fatal python errors”! To fix such a fatal mapping mistake you have to close the browser window and open it again. So, you will loose your changes if they are not saved. There’s no way to annul that error by going backwards in your browser!

	'''Please have a look at a [~~http://www.dnabank-network.org/~~Mapping~~.php mapping~~ example].'''		'''Please have a look at a [[Mapping example]].'''

	Don't forget to set the '''"Root table alias"''' and the '''"Static table alias"'''. The static table mostly equals the table for metadata and contains only one row.		Don't forget to set the '''"Root table alias"''' and the '''"Static table alias"'''. The static table mostly equals the table for metadata and contains only one row.

WikiSysop: /* 4. Mapping the DNA database */

2012-01-19T13:58:39Z

4. Mapping the DNA database

← Older revision		Revision as of 15:58, 19 January 2012
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	<div id="wikinote"><span style="color:red;">'''Note:'''</span> Please don’t map DNA data only. To verify the related specimen it is absolutely '''essential''' to map both the '''identification part''' (Taxon Name) and the '''UnitAssociation'''. It is furthermore advantageous to map few gathering attributes such as CountryName or ISO-Code.</div>		<div id="wikinote"><span style="color:red;">'''Note:'''</span> Please don’t map DNA data only. To verify the related specimen it is absolutely '''essential''' to map both the '''identification part''' (Taxon Name) and the '''UnitAssociation'''. It is furthermore advantageous to map few gathering attributes such as CountryName or ISO-Code.</div>

	~~'''~~UnitAssociation (Triple Identifier of the related specimen):~~'''~~		===UnitAssociation (Triple Identifier of the related specimen):===
	[[File:UnitAssociation.png]]		[[File:UnitAssociation.png]]

WikiSysop: /* 4. Mapping the DNA database */

2012-01-19T12:58:01Z

4. Mapping the DNA database

← Older revision		Revision as of 14:58, 19 January 2012
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	DNA sample taken from Ballota itegrifolia deposited in the "Herbarium Berolinense" at the Botanic Garden and Botanical Museum Berlin-Dahlem with Barcode number "B 10 0140204".		DNA sample taken from Ballota itegrifolia deposited in the "Herbarium Berolinense" at the Botanic Garden and Botanical Museum Berlin-Dahlem with Barcode number "B 10 0140204".

	AssociatedUnitSourceInstitutionCode →> BGBM		AssociatedUnitSourceInstitutionCode → BGBM

	AssociatedUnitSourceName → Herbarium Berolinense		AssociatedUnitSourceName → Herbarium Berolinense

	AssociatedUnitID → B 10 0140204		AssociatedUnitID → B 10 0140204

	Comment → http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=Herbar		Comment → http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=Herbar

WikiSysop: /* 4. Mapping the DNA database */

2012-01-19T12:57:25Z

4. Mapping the DNA database

← Older revision		Revision as of 14:57, 19 January 2012
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	'''Fig. 4. UnitAssociation in ABCD schema. All attributes are required. It has to be mapped similar to the Triple Identifier of the DNA sample.		'''Fig. 4. UnitAssociation in ABCD schema. All attributes are required. It has to be mapped similar to the Triple Identifier of the DNA sample.
	'''		'''

	'''AssociatedUnitSourceInstitutionCode''' → Code or abbreviation of the institution the specimen/voucher of the DNA sample is deposited.		'''AssociatedUnitSourceInstitutionCode''' → Code or abbreviation of the institution the specimen/voucher of the DNA sample is deposited.

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	Please save your mapping to finish the process!		Please save your mapping to finish the process!


	==5. Test Mapping==		==5. Test Mapping==
	Please press "Test Mapping!" to execute a capability test as well as a scan and search test for ABCD 2.06. If you get the message. You can start a test search if you receive the message "No errors found!" during all three tests. Therefore, click on "QueryForms" and select "ABCD2 search". The following code should than be visible:		Please press "Test Mapping!" to execute a capability test as well as a scan and search test for ABCD 2.06. If you get the message. You can start a test search if you receive the message "No errors found!" during all three tests. Therefore, click on "QueryForms" and select "ABCD2 search". The following code should than be visible:

WikiSysop: /* DNA extension for ABCD - General information & installation manual */

2012-01-19T12:56:51Z

DNA extension for ABCD - General information & installation manual

← Older revision		Revision as of 14:56, 19 January 2012
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	=DNA extension for ABCD - General information & installation manual=		=DNA extension for ABCD - General information & installation manual=
	Another BioCASE wrapper on all connected databases had to be ~~installed~~ mandatory to offer DNA samples and its related specimen data on the central webportal (http://www.dnabank-network.org). Although the [http://wiki.tdwg.org/twiki/bin/view/ABCD/ ABCD 2.06 schema] (part of the BioCASE wrapper) is currently preferred its existing part for DNA ‘Sequences’ lacks important features. So, it shouldn’t be used any longer. The whole ABCD 2.06 schema is available [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/ABCD_2.06.XSD here]. If you want to learn more about the meaning of BioCASe and ABCD please follow the links.		Another mapping with the BioCASE Provider Software (wrapper) on all connected databases had to be set up mandatory to offer DNA samples and its related specimen data on the central webportal (http://www.dnabank-network.org). Although the [http://wiki.tdwg.org/twiki/bin/view/ABCD/ ABCD 2.06 schema] (part of the BioCASE wrapper) is currently preferred its existing part for DNA ‘Sequences’ lacks important features. So, it shouldn’t be used any longer. The whole ABCD 2.06 schema is available [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/ABCD_2.06.XSD here]. If you want to learn more about the meaning of BioCASe and ABCD please follow the links.

	ABCD offers two options to add supplementary contents: [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#complexType_MeasurementOrFact_Link03076C80 ‘MeasurementsOrFacts’] and [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#element_UnitExtension_Link031A1C90 ‘UnitExtensions’]. Since the hierarchical structure of DNA specific features is too complex for ‘MeasurementsOrFacts’ we decided to use ‘UnitExtensions’ to integrate an xml schema definition for DNA data similar to the [http://www.geocase.eu/ ABCDEFG extension] for geosciences. That new DNA extension for ABCD 2.06 is called ABCDDNA.		ABCD offers two options to add supplementary contents: [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#complexType_MeasurementOrFact_Link03076C80 ‘MeasurementsOrFacts’] and [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#element_UnitExtension_Link031A1C90 ‘UnitExtensions’]. Since the hierarchical structure of DNA specific features is too complex for ‘MeasurementsOrFacts’ we decided to use ‘UnitExtensions’ to integrate an xml schema definition for DNA data similar to the [http://www.geocase.eu/ ABCDEFG extension] for geosciences. That new DNA extension for ABCD 2.06 is called ABCDDNA.

WikiSysop: /* DNA extension for ABCD - General information & installation manual */

2011-10-10T08:43:32Z

DNA extension for ABCD - General information & installation manual

← Older revision		Revision as of 10:43, 10 October 2011
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	The DNA Sample means ABCD Unit and the identifier (Triple ID) for the related specimen is defined by ‘UnitAssociation’. Please read the following manual for using the schema within the BioCASe provider software and have a look at a [http://www.dnabank-network.org/Mapping.php mapping example].		The DNA Sample means ABCD Unit and the identifier (Triple ID) for the related specimen is defined by ‘UnitAssociation’. Please read the following manual for using the schema within the BioCASe provider software and have a look at a [http://www.dnabank-network.org/Mapping.php mapping example].

			=TDWG standard=
			ABCDDNA has been proposed as a new standard to the TDWG committee (09/01/2010): http://www.tdwg.org/standards/640/

	=Using ABCDDNA=		=Using ABCDDNA=

← Older revision		Revision as of 13:24, 10 February 2012
Line 1:		Line 1:
	=DNA extension for ABCD - General information & installation manual=		=DNA extension for ABCD - General information & installation manual=
	Another mapping with the BioCASE Provider Software (wrapper) on all connected databases had to be set up mandatory to offer DNA samples and its related specimen data on the central webportal (http://www.dnabank-network.org). Although the [http://wiki.tdwg.org/twiki/bin/view/ABCD/ ABCD 2.06 schema] (part of the BioCASE wrapper) is currently preferred its existing part for DNA ‘Sequences’ lacks important features. So, it shouldn’t be used any longer. The whole ABCD 2.06 schema is available [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/ABCD_2.06.XSD here]. If you want to learn more about the meaning of ~~BioCASe~~ and ABCD please follow the links.		Another mapping with the BioCASE Provider Software (wrapper) on all connected databases had to be set up mandatory to offer DNA samples and its related specimen data on the central webportal (http://www.dnabank-network.org). Although the [http://wiki.tdwg.org/twiki/bin/view/ABCD/ ABCD 2.06 schema] (part of the BioCASE wrapper) is currently preferred its existing part for DNA ‘Sequences’ lacks important features. So, it shouldn’t be used any longer. The whole ABCD 2.06 schema is available [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/ABCD_2.06.XSD here]. If you want to learn more about the meaning of BioCASE and ABCD please follow the links.

	ABCD offers two options to add supplementary contents: [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#complexType_MeasurementOrFact_Link03076C80 ‘MeasurementsOrFacts’] and [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#element_UnitExtension_Link031A1C90 ‘UnitExtensions’]. Since the hierarchical structure of DNA specific features is too complex for ‘MeasurementsOrFacts’ we decided to use ‘UnitExtensions’ to integrate an xml schema definition for DNA data similar to the [http://www.geocase.eu/ ABCDEFG extension] for geosciences. That new DNA extension for ABCD 2.06 is called ABCDDNA.		ABCD offers two options to add supplementary contents: [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#complexType_MeasurementOrFact_Link03076C80 ‘MeasurementsOrFacts’] and [http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#element_UnitExtension_Link031A1C90 ‘UnitExtensions’]. Since the hierarchical structure of DNA specific features is too complex for ‘MeasurementsOrFacts’ we decided to use ‘UnitExtensions’ to integrate an xml schema definition for DNA data similar to the [http://www.geocase.eu/ ABCDEFG extension] for geosciences. That new DNA extension for ABCD 2.06 is called ABCDDNA.

	The DNA Sample means ABCD Unit and the identifier (Triple ID) for the related specimen is defined by ‘UnitAssociation’. Please read the following manual for using the schema within the ~~BioCASe~~ provider software and have a look at a [http://www.dnabank-network.org/Mapping.php mapping example].		The DNA Sample means ABCD Unit and the identifier (Triple ID) for the related specimen is defined by ‘UnitAssociation’. Please read the following manual for using the schema within the BioCASE provider software and have a look at a [http://www.dnabank-network.org/Mapping.php mapping example].

	=TDWG standard=		=TDWG standard=
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	The following requirements have to be met to use the schema:		The following requirements have to be met to use the schema:

	==1. Installation of ~~BioCASe~~ Provider Software (BPS)==		==1. Installation of BioCASE Provider Software (BPS)==
	The installation is documented at the BPS Wiki: http://wiki.bgbm.org/bps/index.php/Main_Page.		The installation is documented at the BPS Wiki: http://wiki.bgbm.org/bps/index.php/Main_Page.
	<div id="wikinote><span style="color:red;">'''Note:'''</span> ''If the software package DiGIR is already implemented on your specimen database it is possible to run both installations in parallel!''</div>		<div id="wikinote><span style="color:red;">'''Note:'''</span> ''If the software package DiGIR is already implemented on your specimen database it is possible to run both installations in parallel!''</div>

	==2. ABCDDNA-Template==		==2. ABCDDNA-Template==
	The current ~~BioCASe~~ Provider Software package (version 2.6.1, see [http://www.biocase.org/products/provider_software BPS download section]) includes the ABCDDNA template! If you are using an older version please upgrade your BPS!		The current BioCASE Provider Software package (version 2.6.1, see [http://www.biocase.org/products/provider_software BPS download section]) includes the ABCDDNA template! If you are using an older version please upgrade your BPS!

	==3. Creating a new datasource==		==3. Creating a new datasource==
	If you want to use the ABCDDNA schema for mapping you have to create a new datasource connection. You can use the [http://wiki.bgbm.org/bps/index.php/Main_Page ~~BioCASe~~ documentation] for assistance or [[Special:Contact \| contact the DNA Bank Network team]].		If you want to use the ABCDDNA schema for mapping you have to create a new datasource connection. You can use the [http://wiki.bgbm.org/bps/index.php/Main_Page BioCASE documentation] for assistance or [[Special:Contact \| contact the DNA Bank Network team]].

	After you have created a new datasource you have to declare the database connection and the database structure.		After you have created a new datasource you have to declare the database connection and the database structure.
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	Comment → http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=Herbar		Comment → http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=Herbar

	That Triple Identifier equals to the Triple Identifier used in the original specimen database ([http://search.biocase.org/europe/search/units/details/getDetails?institutionID=BGBM&collectionID=Herbarium+Berolinense&unitID=B+10+0140204&resourceKey=1095&bioKey=144840874 verify with ~~BioCASe~~ portal]).</div>		That Triple Identifier equals to the Triple Identifier used in the original specimen database ([http://search.biocase.org/europe/search/units/details/getDetails?institutionID=BGBM&collectionID=Herbarium+Berolinense&unitID=B+10+0140204&resourceKey=1095&bioKey=144840874 verify with BioCASE portal]).</div>

	<div id="wikinote"><span style="color:red;">'''Note:'''</span> It is essential to map '''"AssociationType"''' describing the relation between a DNA sample and its voucher/specimen, e.g. "DNA from specimen", "DNA and specimen from the same population", "DNA from cultivated offspring of the specimen" or the like.</div>		<div id="wikinote"><span style="color:red;">'''Note:'''</span> It is essential to map '''"AssociationType"''' describing the relation between a DNA sample and its voucher/specimen, e.g. "DNA from specimen", "DNA and specimen from the same population", "DNA from cultivated offspring of the specimen" or the like.</div>