Re: [CF-metadata] proposed standard names for Enterococcus and?Clostridium perfringens

[Hassan Moustahfid - NOAA Federal]

Hi folks. I don't know if you received what I sent early about IOOS
Biological Data services termnilogy and Darwin Core standards.
If you want to create your own vocab  go ahead. we will keep talking to our
self. I think there is now an opportunity to figure out how to talk between
CF and Darwin Core.
FYI- Darwin Core is the standard used by Biodiversity community, GBIF
http://www.gbif.org/ and by IOOS Biological group.
Thanks
Hassan

*Hassan Moustahfid, PhD.
Biology/Ecosystem Observing Lead
*NOAA/ U.S. Integrated Ocean Observing System (IOOS) Program Office
Operations Division
1100 Wayne Avenue – Suite 1225
Silver Spring, MD  20910
Tel: 301-427-2447
Email: hassan.moustah...@noaa.gov
http://www.ioos.noaa.gov/

*Imagination is more important than knowledge.
knowledge is limited. Imagination encircles the world.

-Albert Einstein*





On Mon, Mar 25, 2013 at 2:38 PM, John Graybeal
wrote:

> +1 Nan, great summary
>
> CF should prepare for the day when it needs to interoperate with multiple
> authorities, e.g., 2 different species vocabularies.  It will not be
> possible for one vocabulary to serve all the scientific needs.  We are on
> the right track here, let's see if we can solve the whole issue by ensuring
> that the species name reference either be a unique identifier, or be
> convertible, using automated means, to a unique identifier.
>
> John
>
>
>
> On Mar 25, 2013, at 11:18, Nan Galbraith  wrote:
>
> > Hi all -
> >
> > Species taxonomies are not like chemical vocabularies, in that terms for
> > organisms change over time. There are some big projects involved in
> > maintaining these taxonomies, and we probably don't want to commit
> > to launching a parallel effort.
> >
> > The ubio project has a decent description of the problem, at
> > http://www.ubio.org/index.php?pagename=background_intro
> >
> > So, it seems to me that if we're going to expand CF to accommodate
> > biological  data,  we should follow Roy's advice, and have a 'generic'
> > standard name that means 'organism count' and add at least one required
> > attribute pointing to a taxonomic name server (with a version date). The
> > 'current' species name could be included in the long_name attribute.
> >
> > Although it's a valid point that existing search tools don't know about
> > extra attributes, the effort of keeping up with the changes in terms
> could
> > render CF useless for this kind of data otherwise.
> >
> > Regards - Nan
> >
> >
> > On 3/25/13 5:00 AM, Jonathan Gregory wrote:
> >> Dear all
> >>
> >> I agree with Philip that cfu should be spelled out. I was also going to
> make
> >> the same point about Roy's proposal being different from our treatment
> of
> >> chemical species, which are encoded in the standard name; this system
> seems to
> >> be working. One reason for keeping this approach was the "green dog"
> problem.
> >> That particular phrase is actually Roy's, if I remember correctly. That
> is, we
> >> wish to prevent nonsensical constructions, by approving each name which
> makes
> >> (chemical) sense individually.
> >>
> >> However Roy argues that there is an order of magnitude more biological
> species
> >> to deal with than chemical. I don't think that keeping the same approach
> >> (encoding in the standard name) would break the system, but it would
> make the
> >> standard name table very large. Perhaps more importantly, if there were
> so
> >> many species, I expect that data-writers would simply assume that each
> of the
> >> possible combinations of pattern and species did already exist in the
> standard
> >> name table, without bothering to check or have them approved. That
> would defeat
> >> the object of the system of individual approval.
> >>
> >> We don't have to follow the chemical approach. For named geographical
> >> regions and surface area types (vegetation types etc.) we use
> string-valued
> >> coordinate variables, rather like Roy proposes here. To follow that
> approach
> >> we would need a new table, subsidiary to the standard name table,
> containing
> >> a list of controlled names of biological species. We would use the same
> >> approval process to add names to this list as we do for the standard
> name
> >> table. (This is what we do for geographical regions and area types.) We
> would
> >> then have a standard_name such as
> >>   number_concentration_of_biological_species_in_sea_water
> >> whose definition would note that a data variable with this
> standard_name must
> >> have a string-valued auxiliary coordinate variable of biological_species
> >> containing a valid name from the biological species table. If there is
> just
> >> one species, the auxiliary coordinate variable wouldn't need a
> dimension,
> >> but this construction would also allow a single data variable to
> contain data
> >> for several species, by having a dimension of size greater than one.
> >>
> >> Cheers
> >>
> >> Jonathan
> >> ___
> >> CF-metadata mailing list
> >> CF

Re: [CF-metadata] proposed standard names for Enterococcus and?Clostridium perfringens

[Jim Biard]

Hi.

This sounds like a good plan.  I think there should be an attribute with a 
specific name to carry the taxonomic details.  It probably will occur in the 
long name as well, but I don't like the idea of making the long name the 
"official" repository for that information.  It's not my arena, so I can't say 
with authority, but couldn't we come up with a new attribute that was named and 
described generically enough that it could handle species taxonomy info as well 
as chemical species info or whatever else may come up along these lines.

Grace and peace,

Jim

Jim Biard
Research Scholar
Cooperative Institute for Climate and Satellites
Remote Sensing and Applications Division
National Climatic Data Center
151 Patton Ave, Asheville, NC 28801-5001

jim.bi...@noaa.gov
828-271-4900

On Mar 25, 2013, at 2:18 PM, Nan Galbraith  wrote:

> Hi all -
> 
> Species taxonomies are not like chemical vocabularies, in that terms for
> organisms change over time. There are some big projects involved in
> maintaining these taxonomies, and we probably don't want to commit
> to launching a parallel effort.
> 
> The ubio project has a decent description of the problem, at
> http://www.ubio.org/index.php?pagename=background_intro
> 
> So, it seems to me that if we're going to expand CF to accommodate
> biological  data,  we should follow Roy's advice, and have a 'generic'
> standard name that means 'organism count' and add at least one required
> attribute pointing to a taxonomic name server (with a version date). The
> 'current' species name could be included in the long_name attribute.
> 
> Although it's a valid point that existing search tools don't know about
> extra attributes, the effort of keeping up with the changes in terms could
> render CF useless for this kind of data otherwise.
> 
> Regards - Nan
> 
> 
> On 3/25/13 5:00 AM, Jonathan Gregory wrote:
>> Dear all
>> 
>> I agree with Philip that cfu should be spelled out. I was also going to make
>> the same point about Roy's proposal being different from our treatment of
>> chemical species, which are encoded in the standard name; this system seems 
>> to
>> be working. One reason for keeping this approach was the "green dog" problem.
>> That particular phrase is actually Roy's, if I remember correctly. That is, 
>> we
>> wish to prevent nonsensical constructions, by approving each name which makes
>> (chemical) sense individually.
>> 
>> However Roy argues that there is an order of magnitude more biological 
>> species
>> to deal with than chemical. I don't think that keeping the same approach
>> (encoding in the standard name) would break the system, but it would make the
>> standard name table very large. Perhaps more importantly, if there were so
>> many species, I expect that data-writers would simply assume that each of the
>> possible combinations of pattern and species did already exist in the 
>> standard
>> name table, without bothering to check or have them approved. That would 
>> defeat
>> the object of the system of individual approval.
>> 
>> We don't have to follow the chemical approach. For named geographical
>> regions and surface area types (vegetation types etc.) we use string-valued
>> coordinate variables, rather like Roy proposes here. To follow that approach
>> we would need a new table, subsidiary to the standard name table, containing
>> a list of controlled names of biological species. We would use the same
>> approval process to add names to this list as we do for the standard name
>> table. (This is what we do for geographical regions and area types.) We would
>> then have a standard_name such as
>>   number_concentration_of_biological_species_in_sea_water
>> whose definition would note that a data variable with this standard_name must
>> have a string-valued auxiliary coordinate variable of biological_species
>> containing a valid name from the biological species table. If there is just
>> one species, the auxiliary coordinate variable wouldn't need a dimension,
>> but this construction would also allow a single data variable to contain data
>> for several species, by having a dimension of size greater than one.
>> 
>> Cheers
>> 
>> Jonathan
>> ___
>> CF-metadata mailing list
>> CF-metadata@cgd.ucar.edu
>> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>> 
> 
> 
> -- 
> ***
> * Nan GalbraithInformation Systems Specialist *
> * Upper Ocean Processes GroupMail Stop 29 *
> * Woods Hole Oceanographic Institution*
> * Woods Hole, MA 02543 (508) 289-2444 *
> ***
> 
> 
> ___
> CF-metadata mailing list
> CF-metadata@cgd.ucar.edu
> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata

___
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CF-metadata@cgd.ucar.edu
http://mai

Re: [CF-metadata] proposed standard names for Enterococcus and?Clostridium perfringens

[John Graybeal]

+1 Nan, great summary

CF should prepare for the day when it needs to interoperate with multiple 
authorities, e.g., 2 different species vocabularies.  It will not be possible 
for one vocabulary to serve all the scientific needs.  We are on the right 
track here, let's see if we can solve the whole issue by ensuring that the 
species name reference either be a unique identifier, or be convertible, using 
automated means, to a unique identifier.

John



On Mar 25, 2013, at 11:18, Nan Galbraith  wrote:

> Hi all -
> 
> Species taxonomies are not like chemical vocabularies, in that terms for
> organisms change over time. There are some big projects involved in
> maintaining these taxonomies, and we probably don't want to commit
> to launching a parallel effort.
> 
> The ubio project has a decent description of the problem, at
> http://www.ubio.org/index.php?pagename=background_intro
> 
> So, it seems to me that if we're going to expand CF to accommodate
> biological  data,  we should follow Roy's advice, and have a 'generic'
> standard name that means 'organism count' and add at least one required
> attribute pointing to a taxonomic name server (with a version date). The
> 'current' species name could be included in the long_name attribute.
> 
> Although it's a valid point that existing search tools don't know about
> extra attributes, the effort of keeping up with the changes in terms could
> render CF useless for this kind of data otherwise.
> 
> Regards - Nan
> 
> 
> On 3/25/13 5:00 AM, Jonathan Gregory wrote:
>> Dear all
>> 
>> I agree with Philip that cfu should be spelled out. I was also going to make
>> the same point about Roy's proposal being different from our treatment of
>> chemical species, which are encoded in the standard name; this system seems 
>> to
>> be working. One reason for keeping this approach was the "green dog" problem.
>> That particular phrase is actually Roy's, if I remember correctly. That is, 
>> we
>> wish to prevent nonsensical constructions, by approving each name which makes
>> (chemical) sense individually.
>> 
>> However Roy argues that there is an order of magnitude more biological 
>> species
>> to deal with than chemical. I don't think that keeping the same approach
>> (encoding in the standard name) would break the system, but it would make the
>> standard name table very large. Perhaps more importantly, if there were so
>> many species, I expect that data-writers would simply assume that each of the
>> possible combinations of pattern and species did already exist in the 
>> standard
>> name table, without bothering to check or have them approved. That would 
>> defeat
>> the object of the system of individual approval.
>> 
>> We don't have to follow the chemical approach. For named geographical
>> regions and surface area types (vegetation types etc.) we use string-valued
>> coordinate variables, rather like Roy proposes here. To follow that approach
>> we would need a new table, subsidiary to the standard name table, containing
>> a list of controlled names of biological species. We would use the same
>> approval process to add names to this list as we do for the standard name
>> table. (This is what we do for geographical regions and area types.) We would
>> then have a standard_name such as
>>   number_concentration_of_biological_species_in_sea_water
>> whose definition would note that a data variable with this standard_name must
>> have a string-valued auxiliary coordinate variable of biological_species
>> containing a valid name from the biological species table. If there is just
>> one species, the auxiliary coordinate variable wouldn't need a dimension,
>> but this construction would also allow a single data variable to contain data
>> for several species, by having a dimension of size greater than one.
>> 
>> Cheers
>> 
>> Jonathan
>> ___
>> CF-metadata mailing list
>> CF-metadata@cgd.ucar.edu
>> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>> 
> 
> 
> -- 
> ***
> * Nan GalbraithInformation Systems Specialist *
> * Upper Ocean Processes GroupMail Stop 29 *
> * Woods Hole Oceanographic Institution*
> * Woods Hole, MA 02543 (508) 289-2444 *
> ***
> 
> 
> ___
> CF-metadata mailing list
> CF-metadata@cgd.ucar.edu
> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
> 


---
John Graybeal
Marine Metadata Interoperability Project: http://marinemetadata.org
grayb...@marinemetadata.org




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Re: [CF-metadata] proposed standard names for Enterococcus and?Clostridium perfringens

[Hassan Moustahfid - NOAA Federal]

I will encourage you to check bio terms in Darwin Core
http://rs.tdwg.org/dwc/terms/index.htm.
and http://www.ioos.noaa.gov/dmac/biology/welcome.html.
Hassan
*Hassan Moustahfid, PhD.
Biology/Ecosystem Observing Lead
*NOAA/ U.S. Integrated Ocean Observing System (IOOS) Program Office
Operations Division
1100 Wayne Avenue – Suite 1225
Silver Spring, MD  20910
Tel: 301-427-2447
Email: hassan.moustah...@noaa.gov
http://www.ioos.noaa.gov/

*Imagination is more important than knowledge.
knowledge is limited. Imagination encircles the world.

-Albert Einstein*





On Mon, Mar 25, 2013 at 1:04 PM, Lowry, Roy K.  wrote:

> Thanks Jonathan,
>
> I was indeed responsible for introducing 'green dogs' to discussions in
> CF, but since then my experience has expanded further into biological data
> and, in particular, into the world of contaminants in biota through EMODNET
> and our work in BODC with the Sea Mammal Research Unit.  This has shown
> what you say about invalid combination possibilities for taxa being much
> less of an issue to be exactly right.  It has also shown me that protection
> against 'green dogs' can in some circumstances become an unaffordable
> luxury.
>
> There are couple of points in your message where I would do things
> slightly differently.
>
> First, I would prefer 'number_concentration_of_taxon_in_sea_water' to
> 'number_concentration_of_biological_species_in_sea_water', because not all
> biological data are identified to the species level.  Often the counts are
> at the level of genus, class or even phylum.
>
> Secondly, I think that CF setting up a controlled vocabulary for taxa is
> an unnecessary duplication that will cause us a lot of unnecessary work and
> take us out of our domain expertise comfort zone.  In the marine domain,
> there is an almost universally accepted taxonomic controlled vocabulary
> with lashings of accompanying metadata that is extremely well governed by
> internationally recognised experts in the field with high quality technical
> governance in the form of tools, including a web service API.  This is the
> World Register of Marine Species (WoRMS). I fully appreciate that CF covers
> more than the marine domain, but there is an alternative governance in the
> form of the International Taxonomic Information System (ITIS) , which is
> aimed more at terrestrial life than marine. If we say that names used in CF
> should be registered in at least one of these then we should be OK.
>
> As you will see in a message that has just been released, I'm proposing
> taking this forward through a Trac ticket.
>
> Cheers, Roy.
>
>
>
> 
> From: CF-metadata [cf-metadata-boun...@cgd.ucar.edu] On Behalf Of
> Jonathan Gregory [j.m.greg...@reading.ac.uk]
> Sent: 25 March 2013 09:00
> To: cf-metadata@cgd.ucar.edu
> Subject: Re: [CF-metadata] proposed standard names for Enterococcus
> and?Clostridium perfringens
>
> Dear all
>
> I agree with Philip that cfu should be spelled out. I was also going to
> make
> the same point about Roy's proposal being different from our treatment of
> chemical species, which are encoded in the standard name; this system
> seems to
> be working. One reason for keeping this approach was the "green dog"
> problem.
> That particular phrase is actually Roy's, if I remember correctly. That
> is, we
> wish to prevent nonsensical constructions, by approving each name which
> makes
> (chemical) sense individually.
>
> However Roy argues that there is an order of magnitude more biological
> species
> to deal with than chemical. I don't think that keeping the same approach
> (encoding in the standard name) would break the system, but it would make
> the
> standard name table very large. Perhaps more importantly, if there were so
> many species, I expect that data-writers would simply assume that each of
> the
> possible combinations of pattern and species did already exist in the
> standard
> name table, without bothering to check or have them approved. That would
> defeat
> the object of the system of individual approval.
>
> We don't have to follow the chemical approach. For named geographical
> regions and surface area types (vegetation types etc.) we use string-valued
> coordinate variables, rather like Roy proposes here. To follow that
> approach
> we would need a new table, subsidiary to the standard name table,
> containing
> a list of controlled names of biological species. We would use the same
> approval process to add names to this list as we do for the standard name
> table. (This is what we do for geographical regions and area types.) We
> would
> then have a standard_name such a

Re: [CF-metadata] proposed standard names for Enterococcus and?Clostridium perfringens

[Nan Galbraith]

Hi all -

Species taxonomies are not like chemical vocabularies, in that terms for
organisms change over time. There are some big projects involved in
maintaining these taxonomies, and we probably don't want to commit
to launching a parallel effort.

The ubio project has a decent description of the problem, at
http://www.ubio.org/index.php?pagename=background_intro

So, it seems to me that if we're going to expand CF to accommodate
biological  data,  we should follow Roy's advice, and have a 'generic'
standard name that means 'organism count' and add at least one required
attribute pointing to a taxonomic name server (with a version date). The
'current' species name could be included in the long_name attribute.

Although it's a valid point that existing search tools don't know about
extra attributes, the effort of keeping up with the changes in terms could
render CF useless for this kind of data otherwise.

Regards - Nan


On 3/25/13 5:00 AM, Jonathan Gregory wrote:

Dear all

I agree with Philip that cfu should be spelled out. I was also going to make
the same point about Roy's proposal being different from our treatment of
chemical species, which are encoded in the standard name; this system seems to
be working. One reason for keeping this approach was the "green dog" problem.
That particular phrase is actually Roy's, if I remember correctly. That is, we
wish to prevent nonsensical constructions, by approving each name which makes
(chemical) sense individually.

However Roy argues that there is an order of magnitude more biological species
to deal with than chemical. I don't think that keeping the same approach
(encoding in the standard name) would break the system, but it would make the
standard name table very large. Perhaps more importantly, if there were so
many species, I expect that data-writers would simply assume that each of the
possible combinations of pattern and species did already exist in the standard
name table, without bothering to check or have them approved. That would defeat
the object of the system of individual approval.

We don't have to follow the chemical approach. For named geographical
regions and surface area types (vegetation types etc.) we use string-valued
coordinate variables, rather like Roy proposes here. To follow that approach
we would need a new table, subsidiary to the standard name table, containing
a list of controlled names of biological species. We would use the same
approval process to add names to this list as we do for the standard name
table. (This is what we do for geographical regions and area types.) We would
then have a standard_name such as
   number_concentration_of_biological_species_in_sea_water
whose definition would note that a data variable with this standard_name must
have a string-valued auxiliary coordinate variable of biological_species
containing a valid name from the biological species table. If there is just
one species, the auxiliary coordinate variable wouldn't need a dimension,
but this construction would also allow a single data variable to contain data
for several species, by having a dimension of size greater than one.

Cheers

Jonathan
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--
***
* Nan GalbraithInformation Systems Specialist *
* Upper Ocean Processes GroupMail Stop 29 *
* Woods Hole Oceanographic Institution*
* Woods Hole, MA 02543 (508) 289-2444 *
***


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Re: [CF-metadata] proposed standard names for Enterococcus and?Clostridium perfringens

[Jonathan Gregory]

Dear Roy

I think it would be fine and preferable to use someone else's controlled
vocabulary so long as it has an appropriate format and content and/or we
can define rules for using it in CF.

Best wishes

Jonathan
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Re: [CF-metadata] proposed standard names for Enterococcus and?Clostridium perfringens

[Lowry, Roy K.]

Thanks Jonathan,

I was indeed responsible for introducing 'green dogs' to discussions in CF, but 
since then my experience has expanded further into biological data and, in 
particular, into the world of contaminants in biota through EMODNET and our 
work in BODC with the Sea Mammal Research Unit.  This has shown what you say 
about invalid combination possibilities for taxa being much less of an issue to 
be exactly right.  It has also shown me that protection against 'green dogs' 
can in some circumstances become an unaffordable luxury.

There are couple of points in your message where I would do things slightly 
differently.

First, I would prefer 'number_concentration_of_taxon_in_sea_water' to 
'number_concentration_of_biological_species_in_sea_water', because not all 
biological data are identified to the species level.  Often the counts are at 
the level of genus, class or even phylum.

Secondly, I think that CF setting up a controlled vocabulary for taxa is an 
unnecessary duplication that will cause us a lot of unnecessary work and take 
us out of our domain expertise comfort zone.  In the marine domain, there is an 
almost universally accepted taxonomic controlled vocabulary with lashings of 
accompanying metadata that is extremely well governed by internationally 
recognised experts in the field with high quality technical governance in the 
form of tools, including a web service API.  This is the World Register of 
Marine Species (WoRMS). I fully appreciate that CF covers more than the marine 
domain, but there is an alternative governance in the form of the International 
Taxonomic Information System (ITIS) , which is aimed more at terrestrial life 
than marine. If we say that names used in CF should be registered in at least 
one of these then we should be OK.

As you will see in a message that has just been released, I'm proposing taking 
this forward through a Trac ticket.

Cheers, Roy.




From: CF-metadata [cf-metadata-boun...@cgd.ucar.edu] On Behalf Of Jonathan 
Gregory [j.m.greg...@reading.ac.uk]
Sent: 25 March 2013 09:00
To: cf-metadata@cgd.ucar.edu
Subject: Re: [CF-metadata] proposed standard names for Enterococcus 
and?Clostridium perfringens

Dear all

I agree with Philip that cfu should be spelled out. I was also going to make
the same point about Roy's proposal being different from our treatment of
chemical species, which are encoded in the standard name; this system seems to
be working. One reason for keeping this approach was the "green dog" problem.
That particular phrase is actually Roy's, if I remember correctly. That is, we
wish to prevent nonsensical constructions, by approving each name which makes
(chemical) sense individually.

However Roy argues that there is an order of magnitude more biological species
to deal with than chemical. I don't think that keeping the same approach
(encoding in the standard name) would break the system, but it would make the
standard name table very large. Perhaps more importantly, if there were so
many species, I expect that data-writers would simply assume that each of the
possible combinations of pattern and species did already exist in the standard
name table, without bothering to check or have them approved. That would defeat
the object of the system of individual approval.

We don't have to follow the chemical approach. For named geographical
regions and surface area types (vegetation types etc.) we use string-valued
coordinate variables, rather like Roy proposes here. To follow that approach
we would need a new table, subsidiary to the standard name table, containing
a list of controlled names of biological species. We would use the same
approval process to add names to this list as we do for the standard name
table. (This is what we do for geographical regions and area types.) We would
then have a standard_name such as
  number_concentration_of_biological_species_in_sea_water
whose definition would note that a data variable with this standard_name must
have a string-valued auxiliary coordinate variable of biological_species
containing a valid name from the biological species table. If there is just
one species, the auxiliary coordinate variable wouldn't need a dimension,
but this construction would also allow a single data variable to contain data
for several species, by having a dimension of size greater than one.

Cheers

Jonathan
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Re: [CF-metadata] proposed standard names for Enterococcus and?Clostridium perfringens

[Jonathan Gregory]

Dear all

I agree with Philip that cfu should be spelled out. I was also going to make
the same point about Roy's proposal being different from our treatment of
chemical species, which are encoded in the standard name; this system seems to
be working. One reason for keeping this approach was the "green dog" problem.
That particular phrase is actually Roy's, if I remember correctly. That is, we
wish to prevent nonsensical constructions, by approving each name which makes
(chemical) sense individually.

However Roy argues that there is an order of magnitude more biological species
to deal with than chemical. I don't think that keeping the same approach
(encoding in the standard name) would break the system, but it would make the
standard name table very large. Perhaps more importantly, if there were so
many species, I expect that data-writers would simply assume that each of the
possible combinations of pattern and species did already exist in the standard
name table, without bothering to check or have them approved. That would defeat
the object of the system of individual approval.

We don't have to follow the chemical approach. For named geographical
regions and surface area types (vegetation types etc.) we use string-valued
coordinate variables, rather like Roy proposes here. To follow that approach
we would need a new table, subsidiary to the standard name table, containing
a list of controlled names of biological species. We would use the same
approval process to add names to this list as we do for the standard name
table. (This is what we do for geographical regions and area types.) We would
then have a standard_name such as
  number_concentration_of_biological_species_in_sea_water
whose definition would note that a data variable with this standard_name must
have a string-valued auxiliary coordinate variable of biological_species
containing a valid name from the biological species table. If there is just
one species, the auxiliary coordinate variable wouldn't need a dimension,
but this construction would also allow a single data variable to contain data
for several species, by having a dimension of size greater than one.

Cheers

Jonathan
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Re: [CF-metadata] proposed standard names for Enterococcus and Clostridium perfringens

[Steve Emmerson]

On 03/22/2013 03:57 AM, Lowry, Roy K. wrote:
> An additional point is that I would prefer not to have the semantics of
> what was measured encoded into the units of measure.

I couldn't agree more. The NIST also agrees. See sections 7.4 and 7.5 of
.

--Steve
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Re: [CF-metadata] proposed standard names for Enterococcus and Clostridium perfringens

[Lowry, Roy K.]

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
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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Re: [CF-metadata] proposed standard names for Enterococcus and Clostridium perfringens

[Steve Emmerson]

On 03/21/2013 02:12 PM, John Maurer wrote:
> 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.

Yup. If the dimension of the physical quantity is number per volume,
then the SI unit would be "m-3". (The problem with the atmospheric
surface density quantities is that they need to be convertable with
areic amount of substance; consequently, "moles" and "molecules" creep in).

--Steve
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[CF-metadata] proposed standard names for Enterococcus and Clostridium perfringens

[John Maurer]

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 . 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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