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DNA extension for ABCD - Mapping Example

The following boxws should lead you through important or required ABCDDNA attributes in mapping. If you have further questions please contact Gabi Droege (g.droege@bgbm.org).
To see all available attributes select 'Show all concepts' and press 'Refresh'.

Note: Please don't select 'Add new concepts'! Otherwise only the basic ABCD 2.06 version will appear but not the entire ABCDDNA schema.
 

Fig. 6. Mapping with ABCDDNA - Metadata. The root and static table alias should be defined at first. The root table should include the UnitIDs which are unique 'DNA Bank Numbers' in that case. Static table alias applies for all data and is mostly defined as the Metadata table. It is very important to define contact persons as well as legal rights for using the DNA data. Finally, it is impossible to see the data via wrapper if the Metadata has not been mapped.
 

Related Specimen data:
Fig. 7. Mapping with ABCDDNA - UnitAssociation. The actual Unit data including all DNA data and some rudimental specimen information are listed following the Metadata. It is absolutely essential to map both the Triple Identifier for the related voucher/specimen (UnitAssociation) and the mandatory feature 'AssociationType'. All UnitAssociation data won't be visible otherwise.
For further information please click here.
 
Fig. 8. Mapping with ABCDDNA - Gathering and Identification. The 'Gathering' and 'Identification' part has to be mapped that these data can be loaded into the web index of the DNA Bank Network's web portal. If such data, e.g. 'Taxon Name' or 'Country', are not in the web index searches for them won't be succesful. For that matter it would be as well advantageous to map specimen images as 'MultiMediaObject'. Search results in the web portal can than be limited to samples only if a  digital image to the related voucher/specimen of a DNA sample exists.

Note: There is another attribute for an image URL within the part 'DNA Sample'. Please pay attention to correctly map the image URL for the specimen images and for the DNA such as gel images by applying the appropriate ABCD attribute!
 

DNA data:

Some attributes of the basic ABCD 2.06 schema such as 'KindOfUnit', 'RecordBasis', 'UnitID', 'SourceID', 'SourceInstitutionID' and the Metadata (see Fig. 6) have to be mapped in the DNA context.
Fig. 9. Mapping with ABCDDNA - Kind of Unit, Record Basis, SourceID, SourceInstitutionID, UnitID. 'Kind of Unit' indicates the type of DNA isolated, e.g. mitochondrial or genomic DNA. 'RecordBasis' has to be mapped as 'OtherSpecimen', because no other option for 'DNA sample' is provided in the ABCD 2.06 vocabulary (details).
Since ABCD Unit is synonymous to DNA sample as a certain sample type the UnitID has to be mapped as the (unique) 'DNA Bank Number'. Furthermore 'SourceID' could, for example, be mapped as 'DNA Bank' and 'SourceInstitutionID' as the institution holding the collection.
 
Fig. 10. Mapping with ABCDDNA - Detail of the DNA extension. The lately created DNA part of the mapping schema covers more than 35 elements such as 'ExtractionDate', 'ExtractionMethod' for DNA extraction as well as an 'Amplification Container'  for sequences, GenBank Numbers, clone strains etc. Note that 'Amplification Container' subsumes data of more than one amplification if necessary. Most of the other ABCDDNA attributes (DNA part) have a one-to-one relation to the UnitID that is every Unit (every UnitID) has, for example, only one 'ExtractionDate'.