Use Case: diatom eDNA from water sample with sequences

[gdadade]

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