Open sformel-usgs opened 7 months ago
@sformel-usgs @EliLawrence Good point, we'll update the OBIS manual. I think the example in the guide is pretty clear as it is.
Good, point. I'll make sure to make this more precise in our guidance material, including "the guide".
To clarify what you're suggesting @sformel-usgs, are you recommending that associatedSequences should include reference to the namespace, or that it does not have to? All the examples for associatedSequences you linked to are in the https://www.ncbi.... kind of format. Perhaps I am not entirely clear on what you mean by namespace in this context...
So if we updated the OBIS Manual documentation to
associatedSequences
should contain a link, identifier, or list (concatenated and separated) of identifiers of genetic sequence information associated with the Occurrence. Can be used for linking to archived raw barcode reads and/or associated genome sequences, like in a public repository. Example: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA887898/. The actual sequence of the occurrence will be documented in the DNA Derived Data extension.
would this be sufficient?
@EliLawrence Yes, associatedSequences
should include reference to the URL domain (what I'm calling namespace. Apologies if that isn't quite correct), to give meaning to the identifier. It's analogous to AphiaID
vs LSID
from WoRMS. Does that make sense?
Yes that makes sense, thanks Steve! I've updated the OBIS Manual guidelines for this accordingly:
associatedSequences
should contain a reference to the URL domain where genetic sequence information associated with the Occurrence can be found, e.g. a link, identifier, or list (concatenated and separated) of identifiers. Can link to archived raw barcode reads and/or associated genome sequences, like a public repository. It is recommended that links contain the domain name (e.g. NCBI) in the URL, for example: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA887898/. The actual sequence of the occurrence will be documented in the DNA Derived Data extension.
Opening again to keep it on my to-do list for the GBIF docs.
A conversation with some other folks made me realize that in the gomecc data [1][2], we used
aasociatedSequences
to provide the NCBI identifiers (e.g. PRJNA887898) without an indication of the namespace, e.g. "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA887898/", to make it easy for non-experts (and future experts) to know what this identifier refers to. This was probably due to bad advice from me, because when I see PRJNA, SAMN, SRR, etc., I think NCBI. If you look at the Darwin Core examples, they include the NCBI namespace in the URI.Because of this faux pas, I'm wondering if this could be made for explicit in the DNA publishing guides. The OBIS manual describes it as:
and then gives and example of
NCBI BioProject acc. nr. PRJNA433203
in a table further on.The GBIF guide more or less uses the DwC definition, which includes the namespace example:
I don't think these are bad definitions, but I think the way 'identifier' is used, leaves it open for interpretation of what an identifier is. I'm not losing sleep over this one, but I'm curious if anyone else has an opinion on it? @tobiasgf @pieterprovoost @saarasuominen @ksil91?