Input DNA Data - Revision history

A.Plank: fix (syntaxhighlighting error) →

2023-01-09T10:39:09Z

fix <source> (syntaxhighlighting error) → <pre>

← Older revision		Revision as of 12:39, 9 January 2023
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	Example 2:		Example 2:
	<~~code~~><response>		<pre>
			<response>
	<header>		<header>
	<version>$Revision: 1.21 $</version>		<version>$Revision: 1.21 $</version>
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	<...>		<...>
	<resource><name>Herp Specimens</name>		<resource><name>Herp Specimens</name>
	<code>HerpSpecimensDwC2~~</code>~~</code>		<code>HerpSpecimensDwC2</code>
	<relatedInformation/>		<relatedInformation/>
	</resource>		</resource>
			</pre>

	Here, 'HerpSpecimensDwC2' refers to the resource and http://herpnet.ua.edu:80/DiGIRprov/DiGIR.php refers to the 'source'. Please paste these information into the respective fields. The 'source' information is mostly similar or identical to the provider url.		Here, 'HerpSpecimensDwC2' refers to the resource and http://herpnet.ua.edu:80/DiGIRprov/DiGIR.php refers to the 'source'. Please paste these information into the respective fields. The 'source' information is mostly similar or identical to the provider url.
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	# Check 'Retrieve' -> 'Retrieve original record from data publisher'		# Check 'Retrieve' -> 'Retrieve original record from data publisher'

	<~~code~~>		<pre>
	<record>		<record>
	<darwin:InstitutionCode>UAHC</darwin:InstitutionCode>		<darwin:InstitutionCode>UAHC</darwin:InstitutionCode>
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	<...>		<...>
	</record>		</record>
	</~~code~~>		</pre>

	Here, the provider uses CatalogNumberText, so you should select 'DWC (digir, CatalogNumberText)'. If both CatalogNumber and CatalogNumberText is used please select 'DWC (digir, CatalogNumber)'.		Here, the provider uses CatalogNumberText, so you should select 'DWC (digir, CatalogNumberText)'. If both CatalogNumber and CatalogNumberText is used please select 'DWC (digir, CatalogNumber)'.

WikiSysop: /* Input Tool */

2012-02-20T17:00:59Z

Input Tool

← Older revision		Revision as of 19:00, 20 February 2012
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	<div id="wikinote">There is no possibility to save DNA data without specimen information! The DNA Module makes use of GBIF technology to reference to the underlying specimen. It is absolutely essential that voucher/specimen data are available via a GBIF compliant database! if the specimen data are not available in a GBIF compliant database, these can be set up offline with the [[Specimen Tool]].</div>		<div id="wikinote">There is no possibility to save DNA data without specimen information! The DNA Module makes use of GBIF technology to reference to the underlying specimen. It is absolutely essential that voucher/specimen data are available via a GBIF compliant database! if the specimen data are not available in a GBIF compliant database, these can be set up offline with the [[Specimen Tool]].</div>
	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.		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 collection databases.
	==Specimen Details==		==Specimen Details==
	Each DNA sample is extracted from a specimen. This specimen can be a tissue sample, a complete individual, a living plant or animal or a culture (algae, microorganisms). By defining a reference between DNA sample and the DNA voucher you should keep in mind what exactly the DNA voucher is. In terms of the DNA Bank Network the ideal DNA voucher means a complete individual, from which the tissue and DNA sample was taken from. This DNA voucher should be deposited in a natural history collection and the voucher data are available via GBIF. In many cases it is not possible to deposit such an ideal voucher, because it is for example a threatend species. Than you should reference to the most applicable DNA voucher.		Each DNA sample is extracted from a specimen. This specimen can be a tissue sample, a complete individual, a living plant or animal or a culture (algae, microorganisms). By defining a reference between DNA sample and the DNA voucher you should keep in mind what exactly the DNA voucher is. In terms of the DNA Bank Network the ideal DNA voucher means a complete individual, from which the tissue and DNA sample was taken from. This DNA voucher should be deposited in a natural history collection and the voucher data are available via GBIF. In many cases it is not possible to deposit such an ideal voucher, because it is for example a threatend species. Than you should reference to the most applicable DNA voucher.

WikiSysop: /* Input Tool */

2012-02-20T17:00:30Z

Input Tool

← Older revision		Revision as of 19:00, 20 February 2012
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	=Input Tool=		=Input Tool=
	[[File:Main_menu_input.jpg\|thumb\|200px\|Main menu with symbol of input new DNA data]]		[[File:Main_menu_input.jpg\|thumb\|200px\|Main menu with symbol of input new DNA data]]
	This feature enables to set up references between DNA and specimen data. Once you have successfully logged in, click “Input Tool”. Here, specific DNA information ~~like~~:		This feature enables to set up references between DNA and specimen data. Once you have successfully logged in, click “Input Tool”. Here, specific DNA information such as:
	* DNA extraction (e.g. extraction process, DNA quality and long-term storage)		* DNA extraction (e.g. extraction process, DNA quality and long-term storage)
	* amplified sequence fragments		* amplified sequence fragments

WikiSysop: /* Input Tool */

2012-02-19T15:16:21Z

Input Tool

← Older revision		Revision as of 17:16, 19 February 2012
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	=Input Tool=		=Input Tool=
	[[File:Main_menu_input.jpg\|thumb\|200px\|Main menu]]		[[File:Main_menu_input.jpg\|thumb\|200px\|Main menu with symbol of input new DNA data]]
	This feature enables to set up references between DNA and specimen data. Once you have successfully logged in, click “Input Tool”. Here, specific DNA information like:		This feature enables to set up references between DNA and specimen data. Once you have successfully logged in, click “Input Tool”. Here, specific DNA information like:
	* DNA extraction (e.g. extraction process, DNA quality and long-term storage)		* DNA extraction (e.g. extraction process, DNA quality and long-term storage)

WikiSysop: /* Comments on the DNA details */

2012-02-10T13:19:51Z

Comments on the DNA details

← Older revision		Revision as of 15:19, 10 February 2012
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	'''Genbank and BOLD entries'''<br>		'''Genbank and BOLD entries'''<br>
	If available, respective Genbank No. and BOLD Process IDs can be provided here. Beside these accession numbers, the 'Link' field can be used to provide a direct link to the Genbank or BOLD entries. If you want to enter more than one entry, check the 'add Genbank Entries' box.		If available, respective Genbank No. and BOLD Process IDs can be provided here. Beside these accession numbers, the 'Link' field can be used to provide a direct link to the Genbank or BOLD entries. If you want to enter more than one entry, check the 'add Genbank Entries' box. Please don't forget to enter the '''Genetic Locus'''!

	'''Blocking specimen data'''<br>		'''Blocking specimen data'''<br>

WikiSysop: /* Comments on the DNA details */

2012-02-10T13:19:12Z

Comments on the DNA details

← Older revision		Revision as of 15:19, 10 February 2012
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	'''Blocking specimen data'''<br>		'''Blocking specimen data'''<br>
	The DNA Bank offers the possibility to block the DNA details for a limited period of time. For this purpose, you can enter a date in the 'block until' field. The DNA data will be visible via web portal but cannot be ordered until the given date. Alternatively, if the DNA data should GENERALLY not be searchable or available via the DNA Bank Network's webportal, please check the box 'Block in General'. ~~Anm: Stimmt das so????~~		The DNA Bank offers the possibility to block the DNA details for a limited period of time or in general. For this purpose, you can enter a date in the 'block until' field. The DNA data will be visible via web portal but cannot be ordered until the given date. Alternatively, if the DNA data should GENERALLY not be searchable or available via the DNA Bank Network's webportal, please check the box 'Block in General'.

	'''Stock/Aliquots'''<br>		'''Stock/Aliquots'''<br>

WikiSysop: /* Input Tool */

2012-02-09T15:31:35Z

Input Tool

← Older revision		Revision as of 17:31, 9 February 2012
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	=Input Tool=		=Input Tool=
	[[File:Main_menu_input.jpg\|thumb\|200px\|Main menu]]		[[File:Main_menu_input.jpg\|thumb\|200px\|Main menu]]
	This feature enables to set up references between DNA and specimen data. Once you have successfully logged in, click “Input Tool” ~~to add DNA details~~. Here, specific DNA information like:		This feature enables to set up references between DNA and specimen data. Once you have successfully logged in, click “Input Tool”. Here, specific DNA information like:
	* DNA extraction (e.g. extraction process, DNA quality and long-term storage)		* DNA extraction (e.g. extraction process, DNA quality and long-term storage)
	* amplified sequence fragments		* amplified sequence fragments

WikiSysop: /* Search/Edit */

2012-01-17T13:11:22Z

Search/Edit

← Older revision		Revision as of 15:11, 17 January 2012
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	If you just click on 'save new specimen', the DNA details will be saved to the database and you can start with a new, empty input-sheet.		If you just click on 'save new specimen', the DNA details will be saved to the database and you can start with a new, empty input-sheet.

	~~=Search/Edit=~~


	[[Category:DNA_Module]]		[[Category:DNA_Module]]

WikiSysop: /* Add new specimen provider */

2012-01-17T13:10:54Z

Add new specimen provider

← Older revision		Revision as of 15:10, 17 January 2012
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	</record>		</record>
	</code>		</code>

			Here, the provider uses CatalogNumberText, so you should select 'DWC (digir, CatalogNumberText)'. If both CatalogNumber and CatalogNumberText is used please select 'DWC (digir, CatalogNumber)'.

	==DNA Details==		==DNA Details==

WikiSysop: /* Add new specimen provider */

2012-01-17T13:09:02Z

Add new specimen provider

← Older revision		Revision as of 15:09, 17 January 2012
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	This list shows three different examples of provider urls:<br>		This list shows three different examples of provider urls:<br>
	Example 1: http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=Herbar<br>		Example 1: http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=Herbar<br>
	Example 2: http://~~nhb-acsmith2~~.si.edu/~~emuwebvzbirdsweb~~/~~webservices/digir~~.php<br>		Example 2: http://herpnet.ua.edu/DiGIRprov/DiGIR.php<br>

	In following, the standard procedure to add a new specimen database via GBIF is described. Follow steps 1 to 4 for checking if an institution is a GBIF provider already. Every dataset/data provider has an overview page where you find the provider URL at the bottom.		In following, the standard procedure to add a new specimen database via GBIF is described. Follow steps 1 to 4 for checking if an institution is a GBIF provider already. Every dataset/data provider has an overview page where you find the provider URL at the bottom.
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	response="true">		response="true">
	Here, the ABCD 2.06 scheme is used.		Here, the ABCD 2.06 scheme is used.

			'''DiGIR specials:'''

	If using Digir databases, the ''''Resource' and 'Source'''' information are mandatory. These can also be retrieved by accessing the url. In the header, you will find a line referring to 'source' and 'resource'.<br>		1. If using Digir databases, the ''''Resource' and 'Source'''' information are mandatory. These can also be retrieved by accessing the url. In the header, you will find a line referring to 'source' and 'resource'.<br>

	Example 2:		Example 2:
	<code><response>		<code><response>
	<header>		<header>
	<version>~~KE EMu DiGIR Provider 3~~.0</version>		<version>$Revision: 1.21 $</version>
	<sendTime>2012-01-17 07:46:18.00Z</sendTime>		<sendTime>2012-01-17 07:46:18.00Z</sendTime>
	<source>http://~~nhb-acsmith2~~.si.edu/~~emuwebvzbirdsweb~~/~~webservices/digir~~.php</source>		<source>http://herpnet.ua.edu:80/DiGIRprov/DiGIR.php</source>
	<type>metadata</type>		<type>metadata</type>
	~~<...>~~
	</header>		</header>
	</response>		</response>
	<...>		<...>
	<resource><name>~~NMNH Vertebrate Zoology Birds Collections~~</name>		<resource><name>Herp Specimens</name>
	<code>~~NMNH-VZBirds~~</code></code>		<code>HerpSpecimensDwC2</code></code>
	<relatedInformation~~>http://www.nmnh.si.edu/vert<~~/~~relatedInformation~~>		<relatedInformation/>
	</resource>		</resource>

	Here, '~~NMNH-VZBirds~~' refers to the resource and http://~~nhb-acsmith2~~.si.edu/~~emuwebvzbirdsweb/webservices~~/~~digir~~.php refers to the 'source'. Please paste these information into the respective fields. The 'source' information is mostly similar or identical to the provider url.		Here, 'HerpSpecimensDwC2' refers to the resource and http://herpnet.ua.edu:80/DiGIRprov/DiGIR.php refers to the 'source'. Please paste these information into the respective fields. The 'source' information is mostly similar or identical to the provider url.

	'''CatalogNumber/CatalogNumberText''':		2. '''CatalogNumber/CatalogNumberText''':

	Unfortunately DarwinCore/DiGIR has two alternative elements for the CatalogNumber and you will have to check which one is used prior to save new dataset.		Unfortunately DarwinCore/DiGIR has two alternative elements for the CatalogNumber and you will have to check which one is used prior to save new dataset.

			# Go to a single record of required dataset at GBIF portal
			# Check 'Retrieve' -> 'Retrieve original record from data publisher'

			<code>
			<record>
			<darwin:InstitutionCode>UAHC</darwin:InstitutionCode>
			<darwin:CollectionCode>Main</darwin:CollectionCode>
			<darwin:CatalogNumberText>871</darwin:CatalogNumberText>
			<darwin:ScientificName>Acris gryllus</darwin:ScientificName>
			<...>
			</record>
			</code>

	==DNA Details==		==DNA Details==