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: [email protected] 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. <[email protected]> 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 [[email protected]] On Behalf Of > Jonathan Gregory [[email protected]] > Sent: 25 March 2013 09:00 > To: [email protected] > 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 > [email protected] > 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 > [email protected] > http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata >
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