New notebook for matching taxonomic names to authoritative sources

[MathewBiddle]

• [ ] What is language(s) for used in the example?
  • Python (I think)
• [ ] Is it focused on a particular module/software or an IOOS data service?
  • No (maybe it could be built into a package?)
• [ ] Can you provide a minimum example of the expected code and results in a notebook?
  • See this gist

Please provide a detailed description of the suggested example below:

• A requirement for OBIS is that all scientific names match to the World Register of Marine Species (WoRMS) and a scientificNameID is included. A scientificNameID looks like this urn:lsid:marinespecies.org:taxname:275730 with the last digits after the colon being the WoRMS aphia ID. In some cases, data providers need to go out to WoRMS to grab this information (or verify its correctness).In other cases a user might want to capture an lsid from another service, like ITIS. In the example linked above, it takes a data file and matches a column of taxanomic names to data sources using the Global Names Resolver. http://resolver.globalnames.org/api

[adyork]

It's python. The point of this notebook was to compare match results from various sources. WoRMS results and the LSID are included in the example.

I added an explanation at the end to clarify that results vary depending upon data source whether they supply the global LSID or local identifier. Also pointed out in my example what column the WoRMS LSID was and mentioned the DarwinCore scientificNameID. Gave an example of how you would turn the ITIS results into an LSID.

[adyork]

Oh, also maybe relevant to bullet point 2 about relevance to an IOOS data service. Within the notebook I show both how to pull the data table with species names from a csv file, but also BCO-DMO's ERDDAP instance.

The example could be re-worked to pull from any other ERDDAP instance with a dataset containing taxonomic names in a data column.

[adyork]

Feel free to grab and rework!