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EMODnet / esas2obis

Darwin Core mapping of ESAS data for publication to OBIS
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Get taxonomic information #27

Closed peterdesmet closed 2 years ago

peterdesmet commented 2 years ago

@pieterprovoost @rubenpp7 how should I populate scientificName: with the scientific name as found in the source database (not always valid, sometimes even empty) or the one that matches the AphiaID? Note that I will always add a scientificNameID with an AphiaID that is the closest match in WoRMS.

Examples:

Source scientific name common name (not mapped) AphiaID WoRMS scientific name
Bulweria fallax Jouanin's Petrel 212650 Bulweria fallax
Calonectris diomedea / borealis  Scopoli's / Cory's Shearwater 137062 Calonectris
- unidentified petrel  136998 Procellariidae
- unidentified fish 11676 Pisces (unaccepted taxon in WoRMS)

See all possible values at: https://esas-docs.ices.dk/species/

pieterprovoost commented 2 years ago

@peterdesmet Current OBIS guidelines are to populate scientificName with the exact name as found in the source. But I'll discuss with our taxonomy task team because verbatimIdentification may be more appropriate for that. Also, please use the full LSID for scientificNameID. LSIDs can be for unaccepted names, we resolve to accepted names during indexing.

peterdesmet commented 2 years ago

:+1: I write the full LSIDs:

https://github.com/inbo/esas2obis/blob/2647552601e5ad322a182ab50d511ee2f4882dd5/sql/dwc_occurrence.sql#L35

Closing this issue since current implementation is ok. Improvements (e.g. verbatimIdentification) can be suggested via new issue.