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Genomic Biodiversity Interest Group
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Use Case: diatom eDNA from water sample with sequences #74

Open gdadade opened 2 years ago

gdadade commented 2 years ago

Use Case: diatom eDNA from water sample with sequences Parent water sample record has >100 children and >100 grandchilden, see image below Terms used according to current GGBN mapping recommendations ( 09/2021) Note: Test mapping done with ABCD, terms mapped to dwc to fit use case template. How to map sequences and the associated names will need to be discussed in the TG! Record in current GGBN Sandbox showing child/parent relationship: https://sandbox.ggbn.org/search/record?unitID=DB+e200000&collectioncode=DNA+Bank&institutioncode=B Taxa found in this sample are shown in the "Taxon list" tab. In addition a Krona file is available (also displayed in the "Visualization tab" in the portal): https://www.ggbn.org/ggbn_portal/documents/krona.html

Parent record: environmental sample (water sample without scientific names)

Standard Term Value
dwc decimalLatitude 53,035444
dwc decimalLongitude 14,311167
dwc recordedBy J. Zimmermann
dwc year/month/day 19.05.2011
dwc fieldNumber 20110519jz05
dwc locality Schwedt/Krajnik Dolny, Grenzbrücke, Oder
dwc stateProvince Brandenburg
dwc country Germany
dwc verbatimElevation 6 m
ggbn materialSampleType environmental sample
ggbn preparationType water sample
dwc catalogNumber 20110519jz05
dwc collectionCode Environmental Barcoding
dwc institutionCode B
dwc basisOfRecord MaterialSample
dwc occurrenceID not needed in ABCD
dwc samplingProtocol Scraped epilithic sample

Child record: eDNA sample with sequences and scientific names

Standard Term Value
dwc decimalLatitude 53,035444
dwc decimalLongitude 14,311167
dwc recordedBy J. Zimmermann
dwc year/month/day 19.05.2011
dwc fieldNumber 20110519jz05
dwc locality Schwedt/Krajnik Dolny, Grenzbrücke, Oder
dwc stateProvince Brandenburg
dwc country Germany
dwc verbatimElevation 6 m
ggbn materialSampleType DNA
ggbn preparationType eDNA
dwc catalogNumber DB e200000
dwc collectionCode DNA Bank
dwc institutionCode B
dwc basisOfRecord MaterialSample
dwc occurrenceID not needed in ABCD
(parentCalatogNumber) 20110519jz05 (parsed from relationshipOfResource)
dwc relatedResourceID institutionCode=Environmental Barcoding&collectionCode=B&catalogNumber=20110519jz05&accessPoint=http://ww3.bgbm.org/biocase/pywrapper.cgi?dsa=test_AlgaTerra_Occurrences
dwc relationshipOfResource from mixed water sample
ggbn marker 18S
ggbn markerSubfragment V4

in ABCD the GGBN extension is plugged into the identification container for this test case, which looks like this:

<?xml version='1.0' encoding='UTF-8'?>
<biocase:response xmlns:abcd="http://www.tdwg.org/schemas/abcd/2.1" xmlns:biocase="http://www.biocase.org/schemas/protocol/1.3" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.biocase.org/schemas/protocol/1.3 http://www.bgbm.org/biodivinf/schema/protocol_1_31.xsd">
<biocase:header>
…    <biocase:type>search</biocase:type></biocase:header>
<biocase:content recordCount="10" recordDropped="0" recordStart="0" totalSearchHits="11">    <abcd:DataSets><abcd:DataSet><abcd:Units>
<abcd:Unit>
…
<abcd:Identifications>
   <abcd:Identification>
    <abcd:Result>
     <abcd:Extension>
       <ggbn:GGBN>
       … Sequences and Names…
       </ggbn/GGBN>
     </abcd:Extension>
   </abcd:Result>
  </abcd:Identification>
</abcd:Identifications>
</abcd:Unit>
</abcd:Units> ></abcd:DataSet></abcd:DataSets>

See full ABCD document: https://sandbox.ggbn.org/search/downloadabcd?unitID=DB+e200000

Sequences and Scientific Names are provided as shown in this example csv: DB_e200000.csv grafik