DNA extension for ABCD - General information & installation
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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 (www.dnabank-network.org).
Although the
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
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: ‘MeasurementsOrFacts’
and ‘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
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
mapping example. |
Using ABCDDNA
The basic ABDC 2.06 version is remains unmodified. The new created DNA schema covers more than
35 elements such as “ExtractionDate”, “ExtractionMethod” for DNA
extraction as well as an “Amplification-Container” for
Sequences, GenBankNumbers, CloneStrain etc.
-> View ABCDDNA schema:
html or
xml.
-> View DNA part only:
html or
xml.
The following requirements have to be met to
use the schema:
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1. Installation of BioCASe Provider
Software (Download
section).
The installation is documented
here.
Note:
If the software package DiGIR is already implemented on your
specimen database it is possible to run both installations in
parallel!
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2. Installation of ABCDDNA-Template
The current BioCASe Provider Software package does not
include this template! It requires a cm file which can be
downloaded form the website of the DNA Bank Network –
Download section.
Please copy it into the template folder of your BioCASe
installation.Version 2.4.2:
your_biocase2.4.2_folder/configuration/templates/cmf/
Version 2.5.0: your_biocase2.5.0_folder/templates/cmf/
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Fig. 4. Copy the cm file into your BioCASe cmf folder.
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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 BioCASe
documentation for assistance or contact
Gabi Droege
(g.droege@bgbm.org).
After you have created a new datasource you have to declare the
database connection and the database structure.
Then you can select a schema (ABCDDNA) and click on “Create”.
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4. Mapping the DNA database
The first time you open the mapping page only few fields are
visible. Select “Show all concepts” and press “Refresh” to see
all available features.
Since the DNA sample means ABCD Unit the
Triple Identifier
(composed of UnitID, SourceInstitutionID and SourceID) has
to map as follows:
UnitID → DNA Bank Number (unique DNA Number in your database
but NOT the ID in the DNA table)
SourceInstitutionID → Code or abbreviation of the institution
the DNA bank is located, e.g. BGBM for Botanic Garden and
Botanical Museum Berlin-Dahlem
SourceID → Designation of the collection, e.g. DNA bank
Note:
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.
UnitAssociation
(Triple Identifier of the related specimen):
Fig. 5. UnitAssociation in ABCD schema. All attributes
are required, except 'Comment'. 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.
AssociatedUnitSourceName →
Designation of the collection the
specimen/voucher of the DNA sample is deposited.
AssociatedUnitID →
Unique identifier/number of the specimen/voucher of the DNA
sample within the specimen database.
These three listed attributes of the 'UnitAssociation' and
the Triple Identifier used in the original specimen database
should have the same values. They can than be used as GUIDs (Globally
Unique Identifier) since both values describe the same
specimen.
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Example:
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
AssociatedUnitSourceName → Herbarium
Berolinense
AssociatedUnitID → B 10 0140204
That Triple Identifier equals to the Triple Identifier used in
the original specimen database (verify
with BioCASE).
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Note:
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.
Note:
Please pay attention to special characters like µ, ä,
ö, ü, ß! They have to be translated into Unicode. E.g. a
common mistake is to complete the field Unit@Concentration with
“ng/µl” when “ng/ µl” should be used instead.
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
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.
Please save your mapping to finish the process!
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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:
<filter>
<like
path='/DataSets/DataSet/Units/Unit/Identifications/Identification/Result/TaxonIdentified/ScientificName/
FullScientificNameString'>A*</like>
</filter>
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. |
