Taxon Names and Identifiers

[davidhassell]

Title: Taxon Names and Identifiers
Moderator: @davidhassell
Moderator Status Review [last updated: 2019-12-02]: Converted from accepted Trac ticket 99 to GitHub issue.
Requirement Summary:
Technical Proposal Summary: Add support for better handling of biological taxa data
Benefits:
Status Quo:
Detailed Proposal:

Complete proposal

The complete proposal is for a stand-alone new section (6.1.2), that is contained in pull request #219

This issue was resolved as accepted in the old Trac system about a year ago, at the time of the transition to GitHUb, but didn't get converted to a pull request. This issue addresses this.

The previous discussion and evolution of this issue may be read in full at https://cf-trac.llnl.gov/trac/ticket/99

The Trac ticket's original contributors are still happy with the proposal in it's pull request form, and therefore if there are no further comments (which would be welcome, of course! - but please read the history in Trac first), this issue can therefore be accepted after the usual three weeks.

Consequences for Standard Names

The following new Standard Names are required to describe the label variables and to support the bacterial data request that inspired the creation of this ticket.

Note that these names have not yet been included in the standard name table, but there does not affect the enhancement issue.

taxon_name: The human-readable label for the taxon such as Calanus finmarchicus. The label should be registered in either WoRMS or ITIS and spelled exactly as registered.

taxon_identifier: The machine-readable identifier for the taxon registration in either WoRMS (the AphiaID) or ITIS (the taxonomic serial number or TSN), including namespace. The namespace strings are 'aphia:' or 'tsn:'. For example, Calanus finmarchicus is encoded as either 'aphia:104464' or 'tsn:85272'. For the marine domain WoRMS has more complete coverage and so aphia Ids are preferred.

colony_forming_unit_number_concentration_of_taxon_in_sea_water: "Colony Forming Unit" means an estimate of the viable bacterial or fungal numbers determined by counting colonies grown from a sample. "Number concentration" means the number of particles or other specified objects per unit volume. "Taxon" means an organism named in the taxon_name and taxon_identifier variables.

number_concentration_of_taxon_in_sea_water: "Number concentration" means the number of particles or other specified objects per unit volume. "Taxon" means an organism named in the taxon_name and taxon_identifier variables.

[twhiteaker]

Interesting choice using LSIDs. My first reaction was, "CF should allow more flexibility when specifying the identifier and classification system, without forcing the user to use the LSID specification." There's also apparently some controversy over LSIDs, and I don't now how stable the specification is. But, the systems I typically use (WoRMS and ITIS) can be expressed with LSIDs, and I see merit in sticking with a particular convention for compatibility's sake. So at this point I'm not suggesting a change...I'm just curious to see how it works out in practice.

FYI, my perspective is biased by EML's recent adoption of a way of expressing taxon IDs, as I've been working with EML files lately.

[roy-lowry]

Hi Tim,

The Trac ticket this is based on has been running for over seven years. My primary motivation for proposing it was to establish taxon identifiers as a dimension so we didn't end up with a Standard Name for the abundance of every taxon in the ocean. A second objective was to establish the tagging of measurements based on either AphiaIDs or ITIS TSNs which seems totally in line with your thinking.

The LSID entered the equation during the ticket discussion 6 years ago as a method to bring these identifiers under a common umbrella and enable them to be encoded as URIs. There may well be better ways of doing this developed since. BTW thanks for bringing the LSID URL root up to date.

I really appreciate your making it clear that you are not requesting change in the proposal now - it's taken a long time and a lot of effort to get this far. I would really like to get the basic principle of taxa as auxiliary co-ordinates and the recommendation of the WorMS and ITIS taxonomic vocabularies written into the CF conventions with as little further delay as possible. Note that in the proposal the plain language taxon identifier (biological_taxon_name) is mandatory but the LSID (biological_taxon_lsid) is not. This was done to allow other taxon identifiers to be used as well as (or instead of) LSIDs by evolution rather than revolution in future tickets.

[davidhassell]

Thanks for these comments - it looks like we're still OK to accept this in a few days' time, if nothing further happens ...

[davidhassell]

OK - over three weeks has passed with no further comment, so we can accept this enhancement, merge the associated pull request (#219) and close this issue.

Many thanks to all those who took part, both in the original Trac ticket and here.