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.moustahfid at 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. <rkl at bodc.ac.uk> 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-bounces at cgd.ucar.edu] On Behalf Of
> Jonathan Gregory [j.m.gregory at reading.ac.uk]
> Sent: 25 March 2013 09:00
> To: cf-metadata at 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
> _______________________________________________
> CF-metadata mailing list
> CF-metadata at cgd.ucar.edu
> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>
> This message (and any attachments) is for the recipient only. NERC is
> subject to the Freedom of Information Act 2000 and the contents of this
> email and any reply you make may be disclosed by NERC unless it is exempt
> from release under the Act. Any material supplied to NERC may be stored in
> an electronic records management system.
> _______________________________________________
> CF-metadata mailing list
> CF-metadata at cgd.ucar.edu
> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <
http://mailman.cgd.ucar.edu/pipermail/cf-metadata/attachments/20130325/ba15d913/attachment.html>
Received on Mon Mar 25 2013 - 12:33:21 GMT
