Hello Philip,
I think that the problem for taxa is at least an order of magnitude greater than for atmospheric chemical species - I am currently supporting around 8,000 taxon abundance concepts, which covers less than one per cent of life in the sea. The data Alessandra is responsible for are contaminants in biota, which covers a hundreds of chemical species in not just different taxa, but different bits of taxa (e.g. concentration of mercury in flounder liver).
A point recently made to me by Simon Cox is that whilst I've got tools that will comfortably handle collections with tens or even hundreds of thousands of concepts, others - particularly those on the far end of XML servings from our system - don't. Many tools simply break when accessing the parameter discovery vocabulary with its 30,000 entries.
I readily admit that had I been as exposed to biological and contaminant data back in 1989 I would have taken a different path from encoding taxa in parameter names. However, having taken that path I'm finding it very difficult to change due to the momentum of legacy data and, especially, legacy data models. Consequently, my 'U-turn' in opinion has to be extremely measured and controlled if I am to avoid breaking existing data systems and rendering huge quantities of data non-interoperable. In my opinion CF is currently at a stage where it can pull back from the brink for biological data and to say 'let's open the gates and see what happens' is a bit like an ostrich burying its head in the sand. A single cruise can generate a taxa list of several hundred. A project can generate a taxa list running into thousands.
Another reason why I'm angling towards separating out the taxa is that virtually all biological data has come as tabular spreadsheets with sample reference (a representation of x, y, z and t dimension) as one axis and the taxa as the other. Being deliberately provocative, I could ask whether the taxon possibly has a role as a co-ordinate variable?
I'll raise and quosh one other argument in support of propogating taxa into Standard Names, which is that significant quantities of biological data will never find their way into NetCDF because biologists would never accept a binary format. However, I would argue that XLS is as opaque as NetCDF and all that biologists would need to accept netCDF is a tool to import it into Excel.
Cheers, Roy.
________________________________________
From: CF-metadata [cf-metadata-bounces at cgd.ucar.edu] On Behalf Of Cameron-smith, Philip [cameronsmith1 at llnl.gov]
Sent: 22 March 2013 23:36
To: Alessandra Giorgetti; sdn2-tech at listes.seadatanet.org
Cc: cf-metadata at cgd.ucar.edu; Klaas Deneudt; 'John Maurer'
Subject: Re: [CF-metadata] [sdn2-tech] RE: proposed standard names for Enterococcus and Clostridium perfringens
Hi,
I would have no idea of what CFU was, so I suggest it be spelled out if it is used in a std_name.
We had a very similar discussion when atmospheric chemicals started to be included in CF std_names. In that case it was decided to include them one-by-one, and defer the discussion until the current system stopped working. In defense of that decision it has worked OK: once the pattern has been established, new std_names with different species get approved fairly quickly.
There were complications with doing it as you suggest. I think those objections could have been overcome, but it would have required work and changes to CF. I have a dream that this capability will become part of CF2.0 someday :-).
The two main problems that I recall were 'green dogs', ie names that would be allowed but nonsensical (eg mass of CO2 expressed as nitrogen, or surface area of O3), and the CF convention would need to be formally altered (and the discussion eventually ran out of steam).
I believe that 'green dogs' are 'red herrings', ie even if a 'green dog' is allowed, no user would ever actually use it. Hence this is not a problem. Changes to the CF convention seem to be going faster now, but they still take time and effort.
Good luck,
Philip
-----------------------------------------------------------------------
Dr Philip Cameron-Smith, pjc at llnl.gov, Lawrence Livermore National Lab.
-----------------------------------------------------------------------
> -----Original Message-----
> From: CF-metadata [mailto:cf-metadata-bounces at cgd.ucar.edu] On Behalf Of
> Alessandra Giorgetti
> Sent: Friday, March 22, 2013 8:42 AM
> To: sdn2-tech at listes.seadatanet.org
> Cc: cf-metadata at cgd.ucar.edu; Klaas Deneudt; 'John Maurer'
> Subject: Re: [CF-metadata] [sdn2-tech] RE: proposed standard names for
> Enterococcus and Clostridium perfringens
>
> 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: agiorgetti at 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.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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