Open cpavloud opened 1 month ago
@cpavloud @kmexter questions: alot of this terms definitions are quite specific on emobon. example scientific name we look at NCBI. Do we want an URl correspondant within NERC voc terms for this also if is not that specific?
yes, a lot of the terms are specific to us. for example, a "person" can be defined not via BODC but schema.org as Person (see https://schema.org/Person), however a "sampling person" will never have a defintion as it is so specific, so for that one we do not expect a URL (if there is one, great, if not, that is fine). accession numbers: if you can find a term for "accession number" that is sufficient.
-- find terms in the BODC vocabulary
biomass: http://vocab.nerc.ac.uk/collection/P02/current/FIBM/ it is specific to fish but is possible to make it more general: Parameters quantifying the mass in total or by species per unit area or per unit volume in any body of fresh or salt water expressed in any form (e.g. wet weight, dry weight, carbon, nitrogen, etc.) Other option: the one proposed in ENA vocabulary
n_alkanes http://vocab.nerc.ac.uk/collection/P02/current/DALK/
organism_count: no in the BODC but there is in the ENA voc and GSC MIXS:0000103
samp_collect_device no found
samp_size_mass no found
Thanks a lot for the URI's of those terms! :)
Not sure if following 100% with the definition-example check; does the definition of 'scientific_name' need to be changed? or will the example be changed?
Hi, I think the example should be changed :)
The scientific name definition is correct and the example is correct. It is just missing from the sediment logsheets. And a Y should be added in columns MiXSmandatory(Y/N) and ENA_water_checklistmandatory(Y/N)
* biomass: http://vocab.nerc.ac.uk/collection/P02/current/FIBM/ it is specific to fish but is possible to make it more general: Parameters quantifying the mass in total or by species per unit area or per unit volume in any body of fresh or salt water expressed in any form (e.g. wet weight, dry weight, carbon, nitrogen, etc.) Other option: the one proposed in ENA vocabulary
--> the BODC one does not work, @09012000-tosca can you give me the link to the ENA one?
So as for the recommended changes to the definitions/examples - see comments from Tosca at the very top - that is for EMOBON HQ to do in the logsheets.
@09012000-tosca Check the logsheet_schema_extended.csv
-- review the definitions tab of the spreadsheets (water, sediment, ARMS) because sometimes the example does not follow the definition. all definition tabs for Wa and all for So are the same (for each observatory), so you can review one Wa and one So, but if any corrections are necessary, they have to be done manually in all of them.
-- check the official checklists in the GSC website for the water and the sediment, as well as in the ENA website for the water and sediment for the definition of those terms comm_samp scientific_name time_fi tidal_stage store_person size_frac ship_date sampl_person samp_mat_process samp_size_mass sample_collect_device sample accession number project accession number or just accession number project name organization all the loc_XX_XX in the logsheets
-- fetch the URL of the terms. E.g. the term "env_local_scale" has the URL https://genomicsstandardsconsortium.github.io/mixs/0000013/
-- find terms in the BODC vocabulary biomass n_alkanes organism_count samp_collect_device samp_size_mass
-- find ENVO or BODC or similar terms for phytoplankton diatoms dinoflagellates coccolitrophores other flagellates