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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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2.2.1. Mapping metabarcoding (eDNA) and barcoding data - Table 3 #133

Closed pragermh closed 3 years ago

pragermh commented 3 years ago

Specifying ref db:s and algorithms is a good idea, but:

1) the terms UViGs and vOTU in field names _votu_classappr, _votu_seq_compappr, _votudb refer to Uncultivated Virus Genome (MIUViG) and virus Operational Taxonomic Units, so perhaps a bit weird to recommend for describing sequence clustering in general? At least without commenting on this.

2) makes identificationRemarks (as defined in Table 2, same section) redundant.

dschigel commented 3 years ago

for TDWG, perhaps get rid of "v" in the three fields in the end of Table 3. To discuss with MIxS group. We need terms that works for all life @thomasstjerne

thomasstjerne commented 3 years ago

We discussed this on the meeting on Dec 9th 2020 an suspect the field names may be a legacy from early MIxS (when it was targeted Vira) However, the example values given for votu_db are "NCBI Viral RefSeq;83", "UNITE;8.2" This seems to indicate the field is also used for non-viral OTUs as well (as UNITE 8.2 is mainly for Fungi and Plants).

thomasstjerne commented 3 years ago

I have opened an issue for the GSC asking to remove taxonomic scope for votu_class_appr, votu_seq_comp_appr and votu_db.