Hello Hassan,
My understanding from my collaborators in EurOBIS and hence GBIF is that the WoRMS taxonomy is fully compatible with Darwin Core, the former being a standardised description within the latter, which is a metadata model. Consequently, I'm pretty sure I'm heading in the direction you want.
Cheers, Roy.
________________________________
From: CF-metadata [cf-metadata-bounces at cgd.ucar.edu] On Behalf Of Hassan Moustahfid - NOAA Federal [hassan.moustahfid at noaa.gov]
Sent: 25 March 2013 19:20
To: John Graybeal
Cc: cf-metadata at cgd.ucar.edu
Subject: Re: [CF-metadata] proposed standard names for Enterococcus and?Clostridium perfringens
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.moustahfid at noaa.gov<mailto: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
[
http://www.ioos.gov/images/ioos_blue2.png]
On Mon, Mar 25, 2013 at 2:38 PM, John Graybeal <graybeal at marinemetadata.org<mailto:graybeal at marinemetadata.org>> 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 <ngalbraith at whoi.edu<mailto:ngalbraith at whoi.edu>> 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 at cgd.ucar.edu<mailto:CF-metadata at cgd.ucar.edu>
>> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>>
>
>
> --
> *******************************************************
> * Nan Galbraith Information Systems Specialist *
> * Upper Ocean Processes Group Mail Stop 29 *
> * Woods Hole Oceanographic Institution *
> * Woods Hole, MA 02543 (508) 289-2444<tel:%28508%29%20289-2444> *
> *******************************************************
>
>
> _______________________________________________
> CF-metadata mailing list
> CF-metadata at cgd.ucar.edu<mailto:CF-metadata at cgd.ucar.edu>
> http://mailman.cgd.ucar.edu/mailman/listinfo/cf-metadata
>
---------------
John Graybeal
Marine Metadata Interoperability Project:
http://marinemetadata.org
graybeal at marinemetadata.org<mailto:graybeal at marinemetadata.org>
_______________________________________________
CF-metadata mailing list
CF-metadata at cgd.ucar.edu<mailto: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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <
http://mailman.cgd.ucar.edu/pipermail/cf-metadata/attachments/20130325/2060c6e3/attachment.html>
Received on Mon Mar 25 2013 - 14:42:20 GMT
