Re: [CF-metadata] [sdn2-tech] RE: proposed standard names for Enterococcus and Clostridium perfringens
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-boun...@cgd.ucar.edu] On Behalf Of Cameron-smith, Philip [cameronsmi...@llnl.gov] Sent: 22 March 2013 23:36 To: Alessandra Giorgetti; sdn2-t...@listes.seadatanet.org Cc: cf-metadata@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, p...@llnl.gov, Lawrence Livermore National Lab. --- -Original Message- From: CF-metadata [mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of Alessandra Giorgetti Sent: Friday, March 22, 2013 8:42 AM To: sdn2-t...@listes.seadatanet.org Cc: cf-metadata@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
Re: [CF-metadata] [sdn2-tech] RE: proposed standard names for Enterococcus and Clostridium perfringens
Hi John, Which is exactly how it is in CF for 2-m air temperature or irradiance of a specified wavelength. Trac ticket 96 is aimed at providing your magical connection and could be used for taxon names. Ever get the feeling that some of the CF discussions (e.g. ISO8601) are a case of identifying the lesser of two evils by people with different opinions on what constitutes evil? Cheers, Roy. From: CF-metadata [cf-metadata-boun...@cgd.ucar.edu] On Behalf Of John Graybeal [grayb...@marinemetadata.org] Sent: 22 March 2013 23:52 To: Cameron-smith, Philip Cc: sdn2-t...@listes.seadatanet.org; Alessandra Giorgetti; cf-metadata@cgd.ucar.edu; Klaas Deneudt; 'John Maurer' Subject: Re: [CF-metadata] [sdn2-tech] RE: proposed standard names for Enterococcus and Clostridium perfringens I think the other obvious concern is that you could no longer use the standard name as the be-all and end-all of searching for comparable data. If the entity of interest, say the species, is in an auxiliary term, the search has to magically connect the standard name with the auxiliary term, which requires more custom search capabilities than are currently widespread. On Mar 22, 2013, at 16:36, Cameron-smith, Philip cameronsmi...@llnl.gov wrote: 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, p...@llnl.gov, Lawrence Livermore National Lab. --- -Original Message- From: CF-metadata [mailto:cf-metadata-boun...@cgd.ucar.edu] On Behalf Of Alessandra Giorgetti Sent: Friday, March 22, 2013 8:42 AM To: sdn2-t...@listes.seadatanet.org Cc: cf-metadata@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: agiorge...@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.dene...@vliz.be] Sent: 22 March 2013 15:06 To: sdn2-t...@listes.seadatanet.org; 'John Maurer'; cf-metadata@cgd.ucar.edu Subject: RE: [sdn2-tech] RE: [CF-metadata] proposed standard names for Enterococcus
