#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):
''Hopefully the final rewrite of ticket 99 to address Jonathan’s comments.
Only issue where there is still a difference of opinion is the positioning
of the section in the document.
''Jonathan Gregory proposed that we should tidy the CF document by
promoting 6.1.1 on "Geographic regions" to 6.3 (i.e. remove it from 6.1),
and adding yours as 6.4. Then 6.1 and 6.2 will describe mechanisms in CF,
and 6.3 and 6.4 applications of these mechanisms.''
''My interpretation is that this section is an application of the
‘Alternative co-ordinates’ CF mechanism (Section 6.2) in the same way as
‘Geographic Regions’ are an application of the ‘Labels’ CF mechanism
(Section 6.1). Example 6.3. (Model level numbers) is also an application
of ‘Alternative co-ordinates’. Consequently, I would make Example 6.3
Section 6.1.1 and the following ‘Taxon names and identifiers’ text Section
6.1.2.''''
'''6.1.2. 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 organisms_in_taxon, and the taxa are
identified by auxiliary coordinate variables.
The taxon auxiliary coordinate variables are string-valued. The plain-
language name of the taxon must be contained in a variable with
standard_name of biological_taxon_name. A Life Science Identifier may be
contained in a variable with standard_name of 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.
The biological_taxon_name co-ordinate included for human readability is
mandatory. The biological_taxon_lsid co-ordinate included for software
agent readability is optional, but strongly recommended. If both are
present the biological_taxon_name must match the name resolved from the
biological_taxon_lsid exactly. If LSIDs are available for some taxa in a
dataset then the biological_taxon_lsid co-ordinate should be included and
missing data given for those taxa that do not 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_organisms_in_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:21>
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