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SIOS-Svalbard / Nansen_Legacy_template_generator

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DNA derived data extension #60

Closed lhmarsden closed 10 months ago

lhmarsden commented 10 months ago

Elizabeth Lawrence, affiliated with the OBIS Secretariat, has suggested that this extension is added: http://rs.gbif.org/extension/gbif/1.0/dna_derived_data_2021-07-05.xml

She writes this:

For terms, I don't believe there are specific required terms, and the recommended can differ between the type of DNA data (eDNA vs qPCR for example). I don't imagine you will be able to make a distinction for data type, so I've listed below what I think are extremely important terms for DNA data, with some notes on type just in case.

Recommended for the Occurrence table (in addition to regularly required Occurrence table terms): Class Occurrence | DwC: organismQuantity Class Occurrence | DwC: OrganismQuantityType Class Event | DwC: sampleSizeValue Class Event | DwC: sampleSizeUnit Required for DNA derived data extension: DNA Derived | DwC: sop DNA Derived | DwC: target_gene DNA Derived | DwC: target_subfragment DNA Derived | DwC: pcr_primer_forward DNA Derived | DwC: pcr_primer_reverse DNA Derived | DwC: pcr_primer_name_forward DNA Derived | DwC: pcr_primer_name_reverse DNA Derived | DwC: pcr_primer_reference DNA Derived | DwC: Pcr_cond Recommended DNA terms: DNA Derived | DwC: DNA_sequence (for eDNA/barcoding data, not for qPCR) DNA Derived | DwC: annealingTemp DNA Derived | DwC: annealinTempUnit DNA Derived | DwC: ampliconSize DNA Derived | DwC: env_broad_scale DNA Derived | DwC: env_local_scale DNA Derived | DwC: env_medium DNA Derived | DwC: seq_meth DNA Derived | DwC: otu_class_appr DNA Derived | DwC: otu_seq_comp_appr DNA Derived | DwC: otu_db DNA Derived | DwC: baselineValue (for qPCR) DNA Derived | DwC: automaticThresholdQuantificationCycle (for qPCR) DNA Derived | DwC: quantificationCycle (for qPCR) DNA Derived | DwC: concentration (for qPCR) DNA Derived | DwC: concentrationUnit (for qPCR) DNA Derived | DwC: methodDeterminationConcentrationAndRatios (for qPCR) DNA Derived | DwC: ratioOfAbsorbance260_230 (for qPCR) DNA Derived | DwC: ratioOfAbsorbance260_280 (for qPCR) DNA Derived | DwC: probeQuencher (for qPCR) DNA Derived | DwC: probeReporter (for qPCR)

According to @dagendresen:

I would consider the source_mat_id as the identifier for each sample in the MIxS extension

https://w3id.org/gensc/terms/MIXS:0000026 http://rs.tdwg.org/dwc/terms/materialSampleID

materialampleID --> http://rs.tdwg.org/dwc/terms/materialEntityID

Each row would be a MaterialEntity in Darwin Core. (Often published as one-to-one with the Occurrence in the current simplified GBIF model).