Difference between revisions of "Input DNA Data"
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* amplified sequence fragments | * amplified sequence fragments | ||
* respective Genbank No. and/or BOLD IDs | * respective Genbank No. and/or BOLD IDs | ||
| − | can be | + | can be linked to specimen data, previously integrated in an GBIF database.<br> |
| − | Before entering DNA data you have to load the relevant specimen data. There is no possibility to save DNA data without specimen information! 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. If the respective databases are not yet integrated into the DNA Bank Network, these can either be [[#Add new specimen provider|newly added]] or alternatively, if the specimen data are not | + | Before entering DNA data you have to load the relevant specimen data. There is no possibility to save DNA data without specimen information! 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. If the respective databases are not yet integrated into the DNA Bank Network, these can either be [[#Add new specimen provider|newly added]] or alternatively, if the specimen data are not available in an online database, these can be set up offline with the [[Specimen Tool]].<br> |
Once you have successfully logged in, click “Input Tool” to add DNA details.<div style="clear:both;"></div> | Once you have successfully logged in, click “Input Tool” to add DNA details.<div style="clear:both;"></div> | ||
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====Specimen number/UnitID==== | ====Specimen number/UnitID==== | ||
| − | The UnitID is a unique identifier applied to a specimen in an electronic database | + | The UnitID is a unique identifier applied to a specimen in an electronic database. It is necessary to conduct a successful wrapper query. In an ideal world, the collection uses a definite voucher ID, which is also used for the electronic database (e.g. the herbarium at the BGBM uses the barcodes for the herbarium vouchers as UnitIDs for the electronic database). However, in other collections, the original voucher ID might differ from the UnitID in the electronic database. In this case, a wrapper query for the voucher ID would fail and the user has to investigate for the accordant UnitID. |
====Collection databases==== | ====Collection databases==== | ||
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There are several cases, why a specimen number might currently not be available:<br> | There are several cases, why a specimen number might currently not be available:<br> | ||
* The respective collection has no electronic database | * The respective collection has no electronic database | ||
| − | * The respective collection has an electronic database, but is not accessible online via Wrapper. | + | * The respective collection has an electronic database, but it is not accessible online via Wrapper. |
* The electronic collection database is accessible online, but the wanted specimen data is not online yet. | * The electronic collection database is accessible online, but the wanted specimen data is not online yet. | ||
* The wanted specimen is in private ownership and thus not accessible online. | * The wanted specimen is in private ownership and thus not accessible online. | ||
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===Add new specimen provider=== | ===Add new specimen provider=== | ||
| − | New specimen databases can be integrated with the 'New specimen provider' menu. Specimen databases are generally hosted by provider (institutes, museums, collections etc.). The | + | New specimen databases can be integrated with the 'New specimen provider' menu. Specimen databases are generally hosted by a provider (institutes, museums, collections etc.). The provider url for each specific specimen database is generally available via GBIF (or alternatively from the respective institute). |
[[File:Add_new_1.jpg|thumb|200px|Add new specimen provider]] | [[File:Add_new_1.jpg|thumb|200px|Add new specimen provider]] | ||
[[File:Add_new_2.jpg|thumb|200px|Add new specimen provider]] | [[File:Add_new_2.jpg|thumb|200px|Add new specimen provider]] | ||
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=HerbariumImages<br> | + | Example 1: http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=HerbariumImages Anm: Adresse zeigt Fehlermeldung!!!<br> |
Example 2: http://aadc-maps.aad.gov.au/digir/digir.php<br> | Example 2: http://aadc-maps.aad.gov.au/digir/digir.php<br> | ||
Example 3: http://www.biologie.uni-ulm.de/cgi-bin/biocase_new/www/pywrapper.cgi?dsa=zoological | Example 3: http://www.biologie.uni-ulm.de/cgi-bin/biocase_new/www/pywrapper.cgi?dsa=zoological | ||
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The database scheme is mandatory and can be selected from a rolldown menu list (ABCD 1.2, ABCD 2.05, ABCD 2.06, DarwinCore/Digir). This information can either be found directly in the Url (in the case of Digir databases) or retrieved by accessing the Url. The latter will display a xml-scheme, where 'Supportedschemas' provides the correct scheme information.<br> | The database scheme is mandatory and can be selected from a rolldown menu list (ABCD 1.2, ABCD 2.05, ABCD 2.06, DarwinCore/Digir). This information can either be found directly in the Url (in the case of Digir databases) or retrieved by accessing the Url. The latter will display a xml-scheme, where 'Supportedschemas' provides the correct scheme information.<br> | ||
| − | Example | + | Example 3: |
<SupportedSchemas request="true" namespace="http://www.tdwg.org/schemas/abcd/1.2" response="true"> | <SupportedSchemas request="true" namespace="http://www.tdwg.org/schemas/abcd/1.2" response="true"> | ||
Here, the ABCD 1.2 scheme is used. | Here, the ABCD 1.2 scheme is used. | ||
| − | If using Digir databases, the 'Resource' and 'Source' information | + | 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 refering to 'source' and 'resource'.<br> |
| − | Example | + | Example 2: |
<response> | <response> | ||
<header> | <header> | ||
| Line 87: | Line 87: | ||
<destination>192.38.28.101</destination> | <destination>192.38.28.101</destination> | ||
</header></response><br> | </header></response><br> | ||
| − | Here, 'seabirds' refers to the resource and the url refers to the 'source'. | + | Here, 'seabirds' refers to the resource and the url refers to the 'source'. Please paste these information into the respective fields. The 'source' information are mostly similar or identical to the provider url. |
==DNA Details== | ==DNA Details== | ||
| − | In this section DNA extraction details can be linked with the respective voucher specimen. Furthermore, associated information like amplified fragments and | + | In this section, the DNA extraction details can be linked with the respective voucher specimen. Furthermore, associated information, like amplified fragments and Genbank Acc. No. or BOLD Process IDs can be added. |
The following table provides explanations and an example to all DNA details. | The following table provides explanations and an example to all DNA details. | ||
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|- valign="bottom" | |- valign="bottom" | ||
| height="13" | Blocked Until | | height="13" | Blocked Until | ||
| − | | Sample data will be visible via web portal but can not be ordered until | + | | Sample data will be visible via web portal but can not be ordered until the given date; YYYY-MM-DD |
| - | | - | ||
| No | | No | ||
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The DNA numbers are sorted in ascending order. 'Last DNA No.' displays the highest assigned DNA number, which generally (but not always) refers to the last entered number. | The DNA numbers are sorted in ascending order. 'Last DNA No.' displays the highest assigned DNA number, which generally (but not always) refers to the last entered number. | ||
| − | + | '''Extraction Number'''<br> | |
The extraction code provided here should be exclusively numerical. Institutional codes might be added later for all provided data sets. | The extraction code provided here should be exclusively numerical. Institutional codes might be added later for all provided data sets. | ||
| − | + | '''Relation to voucher'''<br> | |
'No voucher available (voucher->observation)' should be selected, if only parts of an organism (blood, feathers or leaves) have been collected. | 'No voucher available (voucher->observation)' should be selected, if only parts of an organism (blood, feathers or leaves) have been collected. | ||
| − | + | '''Tissue'''<br> | |
'Tissue material gone': Please select this box, if the tissue used for DNA extraction has been used up. | 'Tissue material gone': Please select this box, if the tissue used for DNA extraction has been used up. | ||
| − | + | '''Extraction date'''<br> | |
'Extraction Date not available': Please select this box, if the extraction date cannot be determined any more. | 'Extraction Date not available': Please select this box, if the extraction date cannot be determined any more. | ||
| − | + | '''Ratio of Absorbance'''<br> | |
The ratio OD<sub>260nm/OD280nm</sub> provides an estimation of the purity of the sample. The measured value should range from 1.8 to 2.1. The ratio OD<sub>260nm/OD230nm</sub> provides an estimation of the purity against polysaccharides and polyphenol (important for some plants). The measured value should range above 2.0. | The ratio OD<sub>260nm/OD280nm</sub> provides an estimation of the purity of the sample. The measured value should range from 1.8 to 2.1. The ratio OD<sub>260nm/OD230nm</sub> provides an estimation of the purity against polysaccharides and polyphenol (important for some plants). The measured value should range above 2.0. | ||
| − | + | '''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???? | |
=='Save' and 'Save + Carry Forward'== | =='Save' and 'Save + Carry Forward'== | ||
| − | After succesfully filling out all fields for which you | + | After succesfully filling out all fields for which you can provide information, please select 'save' to add the DNA details to the respective specimen voucher, or click on 'save and carry forward' if you wish to add DNA details to more than one specimen voucher, so that you do not have to fill out all fields again. |
If you chose 'Save + Carry Forward' a new consecutively 'Extraction No.' will automatically be generated and all fields previously filled will contain the same information as the voucher you entered before. | If you chose 'Save + Carry Forward' a new consecutively 'Extraction No.' will automatically be generated and all fields previously filled will contain the same information as the voucher you entered before. | ||
Revision as of 11:42, 18 May 2011
Input Tool
This feature enables to set up references between DNA and specimen data. Here, specific DNA information like:
- DNA extraction (e.g. extraction process, DNA quality and long-term storage)
- amplified sequence fragments
- respective Genbank No. and/or BOLD IDs
can be linked to specimen data, previously integrated in an GBIF database.
Before entering DNA data you have to load the relevant specimen data. There is no possibility to save DNA data without specimen information! 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. If the respective databases are not yet integrated into the DNA Bank Network, these can either be newly added or alternatively, if the specimen data are not available in an online database, these can be set up offline with the Specimen Tool.
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.
The GBIF world
GBIF technologies are basis and backbone of the DNA Module and the DNA Bank Network. Many institutions are GBIF providers, more than 213 millions of specimen and observation records are available via GBIF.
But how to find out if the required specimen data is available via GBIF? For that you should check the following facts:
- Where is the DNA voucher deposited?
- Is the relevant institution already a GBIF provider? Ask administrators or curators for help.
- If so: The requirement related to specimen data is fulfilled.
- If not: Is the relevant 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?
Integration of Specimen data
To integrate specimen data, the following information are necessary:
- The unique specimen number/UnitID.
- The respective collection database, where the specimen (data) is stored.
Specimen number/UnitID
The UnitID is a unique identifier applied to a specimen in an electronic database. It is necessary to conduct a successful wrapper query. In an ideal world, the collection uses a definite voucher ID, which is also used for the electronic database (e.g. the herbarium at the BGBM uses the barcodes for the herbarium vouchers as UnitIDs for the electronic database). However, in other collections, the original voucher ID might differ from the UnitID in the electronic database. In this case, a wrapper query for the voucher ID would fail and the user has to investigate for the accordant UnitID.
Collection databases
The respective collection database can be selected from either the 'internal' or the 'external' rolldown menu, which include all databases currently integrated in (associated with?) the DNA-Bank Network. If the respective database is not yet integrated, it is possible to add a new specimen provider.
There are several cases, why a specimen number might currently not be available:
- The respective collection has no electronic database
- The respective collection has an electronic database, but it is not accessible online via Wrapper.
- The electronic collection database is accessible online, but the wanted specimen data is not online yet.
- The wanted specimen is in private ownership and thus not accessible online.
In these cases, please use the Specimen Tool to add offline specimen data. These offline data can later be replaced by eventually now online available collection database.
Add new specimen provider
New specimen databases can be integrated with the 'New specimen provider' menu. Specimen databases are generally hosted by a provider (institutes, museums, collections etc.). The provider url for each specific specimen database is generally available via GBIF (or alternatively from the respective institute).
This list shows three different examples of provider urls:
Example 1: http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=HerbariumImages Anm: Adresse zeigt Fehlermeldung!!!
Example 2: http://aadc-maps.aad.gov.au/digir/digir.php
Example 3: http://www.biologie.uni-ulm.de/cgi-bin/biocase_new/www/pywrapper.cgi?dsa=zoological
In following, the standard procedure to add a new speceimen database via GBIF is described.
- Enter: http://data.gbif.org/welcome.htm
- Search for taxon name of the specimen -> 'Explore' -> 'Occurences'
- Add search filter: 'Catalogue Number' -> Enter Specimen No. -> Check 'Add filter' -> Check 'Search'
- In table 'Sample results' check 'View'
- Check 'Data set'
- Copy Provider Url ('Access Point Url') and paste into the 'Wrapper Url'-Field -> Check 'Verify'
If the Url does not exist yet, you can now set up a new provider/dataset. The following informations must be provided:
- Database scheme ('Schema')
- Digir Resource/Source (if using a Digir database)
- View ('Bezeichnung')
- Internal or external database
The database scheme is mandatory and can be selected from a rolldown menu list (ABCD 1.2, ABCD 2.05, ABCD 2.06, DarwinCore/Digir). This information can either be found directly in the Url (in the case of Digir databases) or retrieved by accessing the Url. The latter will display a xml-scheme, where 'Supportedschemas' provides the correct scheme information.
Example 3:
<SupportedSchemas request="true" namespace="http://www.tdwg.org/schemas/abcd/1.2" response="true">
Here, the ABCD 1.2 scheme is used.
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 refering to 'source' and 'resource'.
Example 2:
<response> <header> <version>$Revision: 1.10 $</version> <sendTime>01-12-2007 01:28:09+1100<sendTime>
http://aadc-maps.aad.gov.au:80/digir/digir.php<destination>192.38.28.101</destination> </header></response>
Here, 'seabirds' refers to the resource and the url refers to the 'source'. Please paste these information into the respective fields. The 'source' information are mostly similar or identical to the provider url.
DNA Details
In this section, the DNA extraction details can be linked with the respective voucher specimen. Furthermore, associated information, like amplified fragments and Genbank Acc. No. or BOLD Process IDs can be added.
The following table provides explanations and an example to all DNA details.
| DNA and Tissue Data | Explanation | Pre-defined | Mandatory? | Example |
| General Details: | ||||
| DNA Extraction Number | A unique identifier or code for this individual DNA sample. | No | Yes | ZFMK-DNA ColCar 0399 |
| Relation to Voucher | Relation between DNA/Tissue and voucher specimen. | Yes | Yes | DNA from specimen (voucher) |
| Tissue | Type of tissue | No | Yes | leg |
| Preservation | Method of preservation | Yes | Yes | in alcohol (ethanol, 96%) |
| DNA Type | Origin of DNA | Yes | No | gDNA |
| Extraction Details: | ||||
| DNA Extraktion Date | Date of DNA extraction;YYYY-MM-DD | Yes | Yes | |
| DNA Extraktion Method: | DNA isolation kit (company/product name) or extraction protocol. | No | Yes; if unknown = "Unknown" | Unknown |
| DNA Extraktion Staff | Person who extraced DNA | No | Yes; if unknown = "Unknown" | C.Blume/C.Etzbauer |
| Quality Details: | ||||
| DNA Purification Method | DNA purification kit (company/product name) or protocol. | Yes; if unknown = "Unknown" | QIAquick PCR Purification Kit Qiagen | |
| Ratio of Absorbance | Assessment of DNA optical density | No | No | 1,99 OD260nm/OD280nm |
| Concentration in ng/µl | Concentration of DNA | No | No | 26,64ng/µl |
| DNA Quality | Rating of DNA quality | Yes | No | high |
| Quality Check Date | Date of DNA quality check;YYYY-MM-DD | Yes | No | - |
| GenBank or BOLD Entries: | ||||
| Genetic Locus | Yes | No | COI | |
| GenBank Acc.No / Bold Process ID | No | No | - | |
| Link | No | No | - | |
| Notes: | ||||
| DNA Sample Provided by | Person who provided the DNA | Yes | Yes; if unknown = "Unknown" | Zoological Research Museum Alexander Koenig |
| Blocked Until | Sample data will be visible via web portal but can not be ordered until the given date; YYYY-MM-DD | - | No | - |
| Remarks for Customers | - | - | No | - |
| Internal Remarks | - | - | No | - |
| Stock/Aliquots: 1) | ||||
| Fridge/Rack/Box | - | No | - | |
| Barcode | - | No | - | |
| Position | Positon in fridge | - | No | - |
| Source volume (µl) | Original volume of aliquot | - | No | - |
| Remaining volume (µl) | Volume of aliquot left | - | No | - |
| Price per Aliqout | - | - | No | - |
1) Not shown in the DNA-Bank-Network webportal.
Comments on the DNA details
The DNA numbers are sorted in ascending order. 'Last DNA No.' displays the highest assigned DNA number, which generally (but not always) refers to the last entered number.
Extraction Number
The extraction code provided here should be exclusively numerical. Institutional codes might be added later for all provided data sets.
Relation to voucher
'No voucher available (voucher->observation)' should be selected, if only parts of an organism (blood, feathers or leaves) have been collected.
Tissue
'Tissue material gone': Please select this box, if the tissue used for DNA extraction has been used up.
Extraction date
'Extraction Date not available': Please select this box, if the extraction date cannot be determined any more.
Ratio of Absorbance
The ratio OD260nm/OD280nm provides an estimation of the purity of the sample. The measured value should range from 1.8 to 2.1. The ratio OD260nm/OD230nm provides an estimation of the purity against polysaccharides and polyphenol (important for some plants). The measured value should range above 2.0.
Blocking specimen data
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????
'Save' and 'Save + Carry Forward'
After succesfully filling out all fields for which you can provide information, please select 'save' to add the DNA details to the respective specimen voucher, or click on 'save and carry forward' if you wish to add DNA details to more than one specimen voucher, so that you do not have to fill out all fields again.
If you chose 'Save + Carry Forward' a new consecutively 'Extraction No.' will automatically be generated and all fields previously filled will contain the same information as the voucher you entered before.
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.
