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.deneudt at vliz.be]
Sent: 22 March 2013 15:06
To: sdn2-tech at listes.seadatanet.org; 'John Maurer'; cf-metadata at 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-request at listes.seadatanet.org [mailto:sdn2-tech-request at listes.seadatanet.org] On Behalf Of Neil Holdsworth
Sent: 22 March 2013 11:42
To: sdn2-tech at listes.seadatanet.org; John Maurer; cf-metadata at 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-request at listes.seadatanet.org<mailto:sdn2-tech-request at listes.seadatanet.org> [mailto:sdn2-tech-request at listes.seadatanet.org] On Behalf Of Lowry, Roy K.
Sent: 22. marts 2013 10:58
To: John Maurer; cf-metadata at cgd.ucar.edu<mailto:cf-metadata at cgd.ucar.edu>
Cc: sdn2-tech at listes.seadatanet.org<mailto:sdn2-tech at 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-bounces at cgd.ucar.edu] On Behalf Of John Maurer
Sent: 21 March 2013 20:12
To: cf-metadata at cgd.ucar.edu<mailto:cf-metadata at 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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