#99: Taxon Names and Identifiers
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Reporter: lowry | Owner: cf-conventions@…
Type: enhancement | Status: new
Priority: high | Milestone:
Component: cf-conventions | Version:
Resolution: | Keywords:
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Comment (by lowry):
Draft text for CF Conventions to complete this ticket
'''Taxon names and identifiers'''
A taxon is a named level within a biological classification, such as a
class, genus and species. Quantities dependent on taxa have generic
standard_names containing the phrase biological_taxon, and the taxa are
identified by auxiliary coordinate variables.
The taxon co-ordinate variables consist of a plain language name
(biological_taxon_name) plus one or more identifiers referring to internet
resources from sources agreed by discussion on the CF list. The currently
accepted identifiers and their Standard Names are:
• Life Science Identifier (LSID): biological_taxon_lsid. This is a
URN with the syntax
urn:lsid:<Authority>:<Namespace>:<ObjectID>[:<Version>]. This includes the
reference classification in the <Authority> element and these are
restricted by the LSID governance. It is strongly recommended in CF that
the authority chosen is World Register of Marine Species (WoRMS) for
oceanographic data and Integrated Taxonomic Information System (ITIS) for
freshwater and terrestrial data. WoRMS LSIDs are built from the AphiaID
such as urn:lsid:marinespecies.org:taxname:104464 for AphiaID 104464. This
may be converted to a URL by adding prefixes such as http://lsid.twg.org/.
ITIS LSIDs are built from the TSN, such as
urn:lsid:itis.gov:itis_tsn:180543.
It is an error if the biological_taxon_name does not agree with the name
resolved from the biological_taxon_lsid or other accepted identifier.
Missing data can be given for any taxon which doesn't have an identifier.
A skeleton example for taxonomic abundance time series is:
{{{
time=100; string80=80; taxon=2;
variables:
float time (time)
time:standard_name="time"
float abundance(time,taxon);
abundance:standard_name="number_concentration_of_biological_taxon_in_sea_water";
abundance:coordinates="taxon_lsid taxon_name";
char taxon_name(taxon,string80);
taxon_name:standard_name="biological_taxon_name";
char taxon_lsid(taxon,string80);
taxon_lsid:standard_name="biological_taxon_lsid";
data; time = ……100 values
abundance = ….200 values
taxon_name = "Calanus finmarchicus", "Calanus helgolandicus"
taxon_lsid = "urn:lsid:marinespecies.org:taxname:104464",
"urn:lsid:marinespecies.org:taxname:104466"
}}}
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Ticket URL: <https://cf-trac.llnl.gov/trac/ticket/99#comment:19>
CF Metadata <http://cf-convention.github.io/>
CF Metadata
