search

gbif / edna-tool-ui

Frontend for the eDNA tool
2 stars 1 forks source link

Is it possible to map abiotic measurements in this tool? #54

Closed EstebanMH-SiB closed 5 months ago

EstebanMH-SiB commented 8 months ago

I was wondering if it is possible to map abiotic measurements, most of our eDNA datasets have at least some abiotic measurements (pH, conductivity, temperature, etc). In the mapping section I couldn't find measurementType/measurementValue fields, I think that would be really valuable to include.

From the publishing guide and the slides about the tool (where you can see pH as a column) I understand that abiotic measurements are encouraged in eDNA datasets, but maybe I am wrong.

If those elements will not be available in the tool, perhaps it can be explained in the FAQ section.

Thanks in advance and sorry if this was addressed before, but I could find information about it.

thomasstjerne commented 8 months ago

Hi @EstebanMH-SiB You can actually have any column in the sample file, and it will be stores in the BIOM files. However, we are so far only mapping to fields from dwc:occurrence and DNA Derived Data. This means that currently, the fields you mention will not make it to the DWC archive. How ever, we are thinking about the possibility to also produce extended measurements and facts at a later stage

tobiasgf commented 7 months ago

Consider just converting unmapped fields from the sample-sheet to eMoF. A quick start could be by simply "melting" the remaining unmapped fields in the sample-sheet (broad to tall format): using the field name/header as measurementType and the cell value as measurementValue. A next step could then be to allow the user to manually add measurementUnit afterwards.

Links the to relevant occurrences/events should be added in the processing. Look at e.g. https://www.gbif.org/occurrence/4422934732

tobiasgf commented 5 months ago

We should prioritize developing a way to add extended measurements/facts