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gbif / doc-publishing-dna-derived-data

This guide shows how to publish DNA-derived spatiotemporal biodiversity data and make it discoverable through national and global biodiversity data discovery platforms. Based on experiences from Australia, Norway, Sweden, UNITE, and GBIF.
https://doi.org/10.35035/doc-vf1a-nr22
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Section 2.2 'basisOfRecord' in table 2 and 4 #131

Closed CecSve closed 3 years ago

CecSve commented 3 years ago

In the description fields of basisOfRecord, the links to the different categories is not up to date and need to match the revision. E.g. in Table 4: Recommended fields for Occurrence core for ddPCR/qPCR data, the text should be changed to (changes in bold):

The specific nature of the data record - a subtype of the dcterms:type. For DNA-derived occurrences (see Category I and Category III), use MaterialSample. For enriched occurrences (see Category II), use PreservedSpecimen or LivingSpecimen as appropriate.

In Table 2. Recommended fields for Occurrence core for Metabarcoding data:

The specific nature of the data record - a subtype of the dcterms:type. For DNA-derived occurrences, (see Category I and Category III) use MaterialSample. For enriched occurrences (Category II) use PreservedSpecimen or LivingSpecimen as appropriate.

Maybe someone with qPCR/PCR experience would double check it fits for Table 4? @FFossoy?

dschigel commented 3 years ago

It is a pity that he have no chance to review bOR before v1 of the guide is out. Would it be more honest to use Unknown for the time being? DNA related evidence categorization is not adequate yet, and even though I agree we sort of have nearest-working terms for I-III, but for qPCR detection the nearest I can imagine is human or machine observation, as PCR detection is fundamentally not so different from a camera trap, with only difference that you need to process your "DNA negative" of species presence in a lab. But it feels very wrong to use this term for qPCR detection. I recently captured my unfinished thoughts on the evidence / record / dataset categorization matters here https://github.com/gbif/registry/issues/247#issuecomment-726101099. I suspect this is not a helpful comment.

CecSve commented 3 years ago

It looks like I accidentally stumbled upon a 'basisOfRecords' issue - my edit was just to make sure the numbering was correct, but I do see the point in having a more fitting 'basisOfRecord' or 'category'. For example, my data doesn't fit well in this categorization either since it is based on non-destructive extraction of bulk samples where sample vouchers will be integrated into the museum collection, so even though it is an 'enriched occurrence' it is not a 'preservedSpecimen', since it is bulk samples. Now the museum does not generally like to have unsorted/bulk samples, but I know some environmental surveys (in Aarhus) also keeps the bulk samples. Also, besides the bulk samples, there is also often leftover DNA that can be integrated into collections and re-analyzed at a later stage and even to target other taxa.

dschigel commented 3 years ago

Thanks for clarification. Let's separate two things

  1. Fix the numbers, could please clarify in a "change from: to:" way and tag it do & close?
  2. Please take a look on the list of thoughts linked above re: bOR
dschigel commented 3 years ago

Let's only review numeration and references, and not enter bOR swamps for v1