work on the omics terms

[isanti]

check the Darwin core list (from Katrina) to the MIxS checklist to the list Ioulia has to the info Genoscope is senting us decide on what we keep

[kmexter]

The list of terms to add to the CSV files that make up the DwCA for DNA-based occurrances (with or without actual species detections) are

• DNA extension part: https://rs.gbif.org/extension/gbif/1.0/dna_derived_data_2021-07-05.xml. Most of these are linked to MIXS terms
• Occurrance file part: http://rs.gbif.org/core/dwc_occurrence_2015-07-02.xml. Most (all) are DwCA terms BUT there are some terms that I really do think are missing, in particular wrt how to reference species names. However, as (for now) there will be no species names for EMO BON, we do not need to worry about this.
• EMOF part: http://rs.gbif.org/extension/obis/extended_measurement_or_fact.xml.
• Event part (some terms of which are in the DNA extension part so this is a useful additional reference): http://rs.gbif.org/core/dwc_event_2015_05_29.xml

See also https://docs.gbif.org/publishing-dna-derived-data/1.0/en/ for more on mandatory and some easier to understand explanations and examples See also https://manual.obis.org/examples.html#edna-dna-derived-data for the OBIS view.

ENA: the MIXS terms

• The various ENA checklists (https://www.gensc.org/pages/standards/checklists.html). There is not one for ARMS units and today I emailed Christina to ask her if we can finally do this, before Sept.
• We could consider making our own checklists IF the existing ones (water, sediment, and eventually ARMS) are not good enough for us? I don't know how easy it is to get a checklist into ENA, I think Christina will tell me since I said in my email that "it surely can't be that difficult or take that long"

[kmexter]

I think the next step is for Ioulia and Katrina to go thru these lists - row by row - and decide which ones are relevant to EMO BON water, sediment, and ARMS; who provides them and where the values for each term can be found; for which destination (ENA or OBIS or GBIF) they are for; and which vocab link each term has (MIXS, DwCA, etc). We can turn that into a CSV file that can be turned into something better by the rest of the OpSci team, to use in GitHub.

[isanti]

Here is the list of terms with explanations that I created a while back: https://docs.google.com/spreadsheets/d/1zRlazR0jx15SfmczgxZ6v4MxUUUuxCxS/edit#gid=394038639 Most terms come from the MIxS list. We don't have to go through the MiXS list again since all the other lists (including the list above) derive from this (MIxS). There are some additional terms that I created but we should look at those again.

For the ENA checklists, all the terms I have seen come from the MIxS list and they haven't updated them for a long while. The mandatory terms for ENA are very few. We can go beyond that and include a lot more when we submit to ENA. We should pay special attention to the ARMS relevant terms because 1) they are not in ENA at all and 2) I also didn't have it in mind while creating the list above. However, the DNA terms for ARMS should be the same as the ones for sediment and seawater. It is the sampling and handling part that is different.

[isanti]

Ioulia will go through the DwC DNA, Occurence, Measurement, Event and check 1) if there are extra terms we might need, 2) map in which spreadsheet the metadata is, 3) if it has a different term name.

[isanti]

Ioulia will go through the DwC DNA, Occurence, Measurement, Event and check 1) if there are extra terms we might need, 2) map in which spreadsheet the metadata is, 3) if it has a different term name.