Revision as of 12:44, 21 November 2011

Input Tool

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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 302 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? Please go ahead at this point: Specimen databases

Defining reference to Specimen data

To reference specimen data, the following information are required:

• The unique specimen number (UnitID, CatalogueNumber).
  
• The respective collection database, where the specimen (data) is stored.

Specimen number/UnitID/CatalogueNumber

The UnitID (CatalogueNumber) is a unique identifier applied to a specimen in an database that is connected to GBIF. 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 database (e.g. the herbarium at the BGBM uses the barcodes for the herbarium vouchers as UnitIDs for the database). However, in other collections, the original voucher ID might differ from the UnitID in the database. In this case, a wrapper query for the voucher ID would fail and the user has to investigate for the accordant UnitID.

Specimen databases

The respective collection database can be selected from either the 'internal' or the 'external' dropdown menu, which include all databases currently integrated in your DNA Module. 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 database
• The respective collection has an database, but it is not accessible online via Wrapper.
• The 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 (placed at input mask. 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).

Add new specimen provider

This list shows three different examples of provider urls:
Example 1: http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=Herbar
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.

1. Enter: http://data.gbif.org/welcome.htm
2. Search for taxon name of the specimen -> 'Explore' -> 'Occurences'
3. Add search filter: 'Catalogue Number' -> Enter Specimen No. -> Check 'Add filter' -> Check 'Search'
4. In table 'Sample results' check 'View'
5. Check 'Data set'
6. 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)
• Display
• Internal or external database

Add new specimen provider

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.

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
With the configuration tool, institutional codes might can be defined 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 OD_{260nm/OD280nm} provides an estimation of the purity of the sample. The measured value should range from 1.8 to 2.1. The ratio OD_{260nm/OD230nm} provides an estimation of the purity against polysaccharides and polyphenol (important for some plants). The measured value should range above 2.0.

Genbank and BOLD entries
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.

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????

Stock/Aliquots
Here specific information on the storage of stocks and aliquots of the extracted DNA can be provided. 'Fridge/Rack/Box' and 'Position in fridge' allow a detailed information on the storage placement. If a 'Barcode' is used, this can be entered in the respective field. The 'Price' for an aliquot depends on the institute, which stores the specimen/DNA and/or provides the respective database. Please refer to DNA Bank administrator of the respective institute.

'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.

Search/Edit

GenBank and BOLD entries