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emo-bon / emobon-ontology

Space where we collaborate on assembling the ontology and shape files
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tax_id needs to go into ttl as URL #12

Open kmexter opened 1 month ago

kmexter commented 1 month ago

the tax_id in the sampling column should be expanded to its URL or an NBCI-style id so that would be either https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1874687 (@marc-portier may have something to say about this one) or NCBI:txid1874687

I am open to this happening anywhere in the chain e.g. in the logsheets QC/transforming stage. Let's discuss

marc-portier commented 1 month ago

Well, this format with multiple parameters tends to be not canonical (and thus confusing: many format variants will appear to work and thus be equivalent - but for rdf references they should be exactly matching)

It might be wise to connect with ncbi on this issue.

kmexter commented 1 month ago

yeh..I can look at raising an issue, but it will not be solved until next year. As far as I can see, that is the only URL to use ...well no, it can be trimmed down to https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1874687

laurianvm commented 1 month ago

@marc-portier given the fact that URL is what it is, do you have an opinion on whether to use URL or PID?

@kmexter to change the logsheet_schema_extended accordingly @laurianvm to check datatype in templates accordingly

cpavloud commented 1 month ago

Just to comment, for the ENA submission the tax_id should be just a number.

So neither this https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1874687 nor this NCBI:txid1874687 would work

This is needed 1874687