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marco-bolo / dataset-catalogue

The index for MBO datasets
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Use WoRMS LSIDs or URIs for taxonomic coverage #8

Open pieterprovoost opened 10 months ago

marc-portier commented 10 months ago

unclear what the actual context and suggestion is - please elaborate

upfront -- might be useful to know that within the MareGraph project there is an agreement to introduce stable http-uri for the marine-species. These will co-exist with the known LSID-URN, but are to be preferred in an linked-data (RDF) context.

current uri-pattern would be https://aphia.org/id/taxname/{aphiaid} - note: a w3id.org alternative has been suggested too, but currently has not been motivating / convincing widely

see also https://doi.org/10.5281/zenodo.10083478

kmexter commented 10 months ago

I have a question here: so for the first datasets I am describing based on VLIZ input, they are working with zooplankton and phytoplankton. I am no taxonomic expert, but apparently these are not taxa, but rather a grouping. It is not feasible to add all species that were observed here, I can go to genus or even further away, and for now I will do that But I was wondering if we we wanted to add another way to refer to organism groupings in this taxonomic coverage field, so that I could add "zooplankton" here in a way that is controlled? Or do we stick just to worms for taxonomy?

pieterprovoost commented 10 months ago

No, it doesn't make sense to list WoRMS taxa for these datasets. There are other vocabs such as https://vocab.nerc.ac.uk/collection/S25/current/BE004249/. WoRMS also has phytoplankton as a functional group but I'm not sure if they have a URI for that.

kmexter commented 10 months ago

In that case, do we have another column for this scenario, and what would we call it? I suspect other datasets will be similar? Or do we stick the taxonomy alltogether? there is no schema term for it anyway and perhaps we don't need this info?

pieterprovoost commented 10 months ago

There is, https://schema.org/BioChemEntity has taxonomicRange. I would stick it all in the taxonomy column.

kmexter commented 10 months ago

ok, grand. So we say to enter either a worms URL, an NBCI URL, another taxonomy URL, or another term that describes your group/class/ of organisms but as a full URL? That we, we just plonk whatever is in there in that column in that schema field, and voila? For WORMS URLs, yes @marc-portier we will need to change them later to the new ones, but I guess that will be a global-replace

kmexter commented 10 months ago

I have used BODC. So for me, this issue is solved, but will wait to see if @marc-portier has any comments regarding the WORMS URIs?

kmexter commented 1 month ago

I think it would be useful to wait to see how diverse the biology is that we get from the WPs, before we decide how to do this. Assigning to me meanwhile to keep an eye on this.