Dear all,
I want to underline that also in the chemical lot, for contaminants in
biota as an example, we have a similar issue like the biological one.
We would like to keep Standard Name from the species name separated.
So, I agree with Neil when saying
'Anyway, I would agree that the species entity needs to be separated
from the ‘standard name’. I think discussions in SDN tech about the
draft biological format for ODV would also highlight this as a ‘must have’.'
We look forward in the discussion.
With kind regards,
Alessandra and Matteo
----------------------------------------------
Alessandra Giorgetti
Istituto Nazionale di Oceanografia e di Geofisica Sperimentale-OGS
Sezione di Oceanografia - OCE
National Oceanographic Data Center/IOC - NODC
Borgo Grotta Gigante 42/c, 34010 Sgonico, Trieste (ITALY)
Phone: +39 040 2140391
Mobile: +39 320 4644653
Fax: +39 040 2140266
E-mail: agiorge...@ogs.trieste.it
The NODC site with free data access http://nodc.ogs.trieste.it/
Il 22/03/2013 16:15, Lowry, Roy K. ha scritto:
Hi Klaas,
What I was trying to say in my e-mail to CF was that I strongly suggest that CF
decouples the Standard Name from the species name. However, should they choose
not to then the cfu semantics should be removed from the units of measure into
the Standard Name. The example you quote is what I would suggest should -
unfortunately in my current view - CF choose to include species names in
Standard Names.
Apologies if I didn't make this clear.
Cheers, Roy.
________________________________
From: Klaas Deneudt [klaas.dene...@vliz.be]
Sent: 22 March 2013 15:06
To: sdn2-t...@listes.seadatanet.org; 'John Maurer'; cf-metadata@cgd.ucar.edu
Subject: RE: [sdn2-tech] RE: [CF-metadata] proposed standard names for
Enterococcus and Clostridium perfringens
Hi, since my knowledge on standard name conventions is limited I am not well
placed to give input on the raised
request for a new item in the list.
However I share the concern to include the biological entity in the Standard
Name.
Am I wrong If I say that the suggested "cfu_number_concentration_of enterococcus
_in_sea_water" seems to do just that?
best regards,
Klaas.
From: sdn2-tech-requ...@listes.seadatanet.org
[mailto:sdn2-tech-requ...@listes.seadatanet.org] On Behalf Of Neil Holdsworth
Sent: 22 March 2013 11:42
To: sdn2-t...@listes.seadatanet.org; John Maurer; cf-metadata@cgd.ucar.edu
Subject: RE: [sdn2-tech] RE: [CF-metadata] proposed standard names for
Enterococcus and Clostridium perfringens
Hi Roy,
First off, i thought ICES tried to persuade you way before SDN that this was
perhaps not the right approach ;)
Anyway, I would agree that the species entity needs to be separated from the
‘standard name’. I think discussions in SDN tech about the draft biological
format for ODV would also highlight this as a ‘must have’.
We did however struggle to understand entirely what you mean by having a
separate metadata element related to species. What does the metadata element
hang-off? If this was to be an attribute of the standard name, then I don’t
really understand how this decouples the relationship. But if you mean that you
would have a variable ‘Gadus morhua’ that had an attribute ‘aphiaID = xxx’ then
that would be logical.
Look forward to hearing what the intention is.
Best, Neil
From:
sdn2-tech-requ...@listes.seadatanet.org<mailto:sdn2-tech-requ...@listes.seadatanet.org>
[mailto:sdn2-tech-requ...@listes.seadatanet.org] On Behalf Of Lowry, Roy K.
Sent: 22. marts 2013 10:58
To: John Maurer; cf-metadata@cgd.ucar.edu<mailto:cf-metadata@cgd.ucar.edu>
Cc: sdn2-t...@listes.seadatanet.org<mailto:sdn2-t...@listes.seadatanet.org>
Subject: [sdn2-tech] RE: [CF-metadata] proposed standard names for Enterococcus
and Clostridium perfringens
Dear All,
I see Pandora's Box opening before us. I have been down the road of setting up
my equivalent to Standard Names (the BODC Parameter Usage Vocabulary) with
concepts that include specification of the biological entity, which is why I
have a vocabulary with getting on for 30,000 concepts. So I have things like
'Abundance of species X','Carbon biomass of species X', 'Nitrogen biomass of
species X', 'Average specimen length of species X' and so on.
In recent discussions within SeaDataNet and the EU ODIP project I have been
persuaded that this approach is unsustainable and that what we should be aiming
for in these projects is an approach where the Standard Name equivalent is
something like 'Abundance of biological entity' and then have a separate
metadata element (i.e. variable attribute) for the biological entity that
should be related an established taxonomic standard such as WoRMS
(http://www.marinespecies.org/). So, which path should CF follow?
An additional point is that I would prefer not to have the semantics of what
was measured encoded into the units of measure. The way I've approached CFU is
through concepts phrased like ' Abundance (colony-forming units) of Vibrio
cholerae (WoRMS 395085) per unit volume of the water body' where colony-forming
units is a qualifying semantic on abundance (the term I prefer to
number_concentration, but I appreciate the precedent in existing Standard
Names). So, IF we choose the path of naming the beasties in the standard name
my preferred syntax would be:
cfu_number_concentration_of enterococcus _in_sea_water with canonical units of
m-3 as John suggested.
I have copied this response to the SeaDataNet Technical Task Team so they are
aware that this issue is being discussed in CF.
Cheers, Roy.
Please note that I now work part-time from Tuesday to Thursday. E-mail
response on other days is possible but not guaranteed!
From: CF-metadata [mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of John
Maurer
Sent: 21 March 2013 20:12
To: cf-metadata@cgd.ucar.edu<mailto:cf-metadata@cgd.ucar.edu>
Subject: [CF-metadata] proposed standard names for Enterococcus and Clostridium
perfringens
Aloha CF group,
I would like to propose the following standard names related to water quality
measurements of the bacteria Enterococcus and Clostridium perfringens:
number_concentration_of_enterococcus_in_sea_water
number_concentration_of_clostridium_perfringens_in_sea_water
These are normally measured with units of CFU/100 mL, where CFU stands for Colony-Forming
Units<http://en.wikipedia.org/wiki/Colony-forming_unit>. I believe the canonical units in
UDUNITS parlance would translate to "m-3", which is what I find in the standard name
table for other number_concentration_* quantities.
For descriptions of each, I would propose:
number_concentration_of_enterococcus_in_sea_water:
"Number concentration" means the number of particles or other specified objects
per unit volume. In this context, it represents the number of colony-forming units (CFU)
of bacteria belonging to the genus Enterococcus. This indicator bacteria has been
correlated with the presence of human pathogens (disease-causing organisms) and therefore
with human illnesses such as gastroenteritis, diarrhea, and various infections in
epidemiological studies. As such, it is commonly measured in beach water quality
monitoring programs.
number_concentration_of_clostridium_perfringens_in_sea_water:
"Number concentration" means the number of particles or other specified objects
per unit volume. In this context, it represents the number of colony-forming units (CFU)
of bacteria belonging to the species Clostridium perfringens. Because this bacteria is a
normal component of the human intestinal tract, its presence in samples of sea water can
be used as a tracer of sewage contamination. As such, it is commonly measured in beach
water quality monitoring programs.
Thanks,
John Maurer
Pacific Islands Ocean Observing System (PacIOOS)
University of Hawaii at Manoa
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