Standard names: Sea floor sediment measurements

[lhmarsden]

I work with some benthic biologists and chemists who I help to publish CF-NetCDF files. The CF standard names have seldom ventured to the bottom of the oceans, so here is a list of standard names that I think would be useful based on benthic data that I have seen and discussed. Thanks!

Proposer's names:

Luke Marsden ([lukem@unis.no](mailto:lukem@unis.no))

Contributor's names:

Arunima Sen ([arunimas@unis.no](mailto:arunimas@unis.no))

(1) Term: mass_concentration_of_chlorophyll_a_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Chlorophylls are the green pigments found in most plants, algae and cyanobacteria; their presence is essential for photosynthesis to take place. There are several different forms of chlorophyll that occur naturally. All contain a chlorin ring (chemical formula C20H16N4) which gives the green pigment and a side chain whose structure varies. The naturally occurring forms of chlorophyll contain between 35 and 55 carbon atoms. Chlorophyll-a is the most commonly occurring form of natural chlorophyll. The chemical formula of chlorophyll-a is C55H72O5N4Mg. Unit: [kg m-3]

(2) Term: mass_concentration_of_phaeopigments_in_sea_floor_sediment Description: Concentration of phaeopigment per unit volume of the water body, where the filtration size or collection method is unspecified (equivalent term in the NERC P01 Parameter Usage Vocabulary may be found at http://vocab.nerc.ac.uk/collection/P01/current/. "Mass concentration" means mass per unit volume and is used in the construction "mass_concentration_of_X_in_Y", where X is a material constituent of Y. A chemical species or biological group denoted by X may be described by a single term such as "nitrogen" or a phrase such as "nox_expressed_as_nitrogen". Phaeopigments are a group of non-photosynthetic pigments that are the degradation product of algal chlorophyll pigments. Phaeopigments contain phaeophytin, which fluoresces in response to excitation light, and phaeophorbide, which is colorless and does not fluoresce (source: https://academic.oup.com/plankt/article/24/11/1221/1505482). Phaeopigment concentration commonly increases during the development phase of marine phytoplankton blooms, and declines in the post bloom stage (source: https://www.sciencedirect.com/science/article/pii/0967063793901018). Unit: [kg m-3]

Note that I have copied the wording for existing standard name mass_concentration_of_phaeopigments_in_sea_water here. However, I would prefer the URLs were replaced with the DOIs, so we are using persistent identifiers that aren’t vulnerable to change in future. Can this also be done for the existing standard names?

Replace first URL with https://doi.org/10.1093/plankt/24.11.1221 Replace second URL with https://doi.org/10.1016/0967-0637(93)90101-8

(3) Term: mass_concentration_of_phosphorus_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Phosphorus means phosphorus in all chemical forms, commonly referred to as "total phosphorus". Unit: [kg m-3]

(4) Term: mass_concentration_of_zinc_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Zinc means zinc in all chemical forms, commonly referred to as "total zinc". Unit: [kg m-3]

(5) Term: mass_concentration_of_copper_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Copper means copper in all chemical forms, commonly referred to as "total copper". Unit: [kg m-3]

(6) Term: mass_concentration_of_total_nitrogen_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Total nitrogen means nitrogen in all chemical forms. Unit: [kg m-3]

(7) Term: mass_concentration_of_total_organic_carbon_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Organic carbon describes a family of chemical species and is the term used in standard names for all species belonging to the family that are represented within a given model. The list of individual species that are included in a quantity having a group chemical standard name can vary between models. Where possible, the data variable should be accompanied by a complete description of the species represented, for example, by using a comment attribute. Unit: [kg m-3]

(8) Term: mass_concentration_of_lead_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Lead means lead in all chemical forms, commonly referred to as "total lead". Unit: [kg m-3]

(9) Term: mass_concentration_of_cadmium_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Cadmium means cadmium in all chemical forms, commonly referred to as "total cadmium". Unit: [kg m-3]

(10) Term: mass_concentration_of_silver_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Silver means silver in all chemical forms, commonly referred to as "total silver". Unit: [kg m-3]

(11) Term: mass_concentration_of_arsenic_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Arsenic means arsenic in all chemical forms, commonly referred to as "total arsenic". Unit: [kg m-3]

(12) Term: mass_concentration_of_nickel_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Nickel means nickel in all chemical forms, commonly referred to as "total nickel". Unit: [kg m-3]

(13) Term: mass_concentration_of_cobalt_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Cobalt means cobalt in all chemical forms, commonly referred to as "total cobalt". Unit: [kg m-3]

(14) Term: mass_concentration_of_iron_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Iron means iron in all chemical forms, commonly referred to as "total iron". Unit: [kg m-3]

(15) Term: mass_concentration_of_aluminium_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Aluminium means aluminium in all chemical forms, commonly referred to as "total aluminium". Unit: [kg m-3]

Or the american-english spelling? Though I think the consensus is to use the queens on this one in science.

(16) Term: mass_concentration_of_mercury_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Mercury means mercury in all chemical forms, commonly referred to as "total copper". Unit: [kg m-3]

(17) Term: mass_concentration_of_manganese_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Manganese means manganese in all chemical forms, commonly referred to as "total manganese". Unit: [kg m-3]

(18) Term: mass_concentration_of_vanadium_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Vanadium means vanadium in all chemical forms, commonly referred to as "total vanadium". Unit: [kg m-3]

(19) Term: mass_concentration_of_chromium_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Chromium means chromium in all chemical forms, commonly referred to as "total chromium". Unit: [kg m-3]

(20) Term: mass_concentration_of_lithium_in_sea_floor_sediment Description: 'Mass concentration' means mass per unit volume and is used in the construction mass_concentration_of_X_in_Y, where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as 'nitrogen' or a phrase such as 'nox_expressed_as_nitrogen'. Lithium means Lithium in all chemical forms, commonly referred to as "total lithium". Unit: [kg m-3]

(21) Term: volume_fraction_of_oxygen_in_sea_floor_sediment_pore_water "Volume fraction" is used in the construction "volume_fraction_of_X_in_Y", where X is a material constituent of Y. It is evaluated as the volume of X divided by the volume of Y (including X). It may be expressed as a fraction, a percentage, or any other dimensionless representation of a fraction. Unit: [1]

(22) Term: mole_concentration_of_dissolved_inorganic_carbon_in_sea_floor_sediment_pore_water "Mole concentration" means number of moles per unit volume, also called "molarity", and is used in the construction "mole_concentration_of_X_in_Y", where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as "nitrogen" or a phrase such as "nox_expressed_as_nitrogen". "Dissolved inorganic carbon" describes a family of chemical species in solution, including carbon dioxide, carbonic acid and the carbonate and bicarbonate anions. "Dissolved inorganic carbon" is the term used in standard names for all species belonging to the family that are represented within a given model. The list of individual species that are included in a quantity having a group chemical standard name can vary between models. Where possible, the data variable should be accompanied by a complete description of the species represented, for example, by using a comment attribute. Unit: [mol m-3]

(23) Term: mole_concentration_of_dissolved_organic_carbon_in_sea_floor_sediment_pore_water "Mole concentration" means number of moles per unit volume, also called "molarity", and is used in the construction "mole_concentration_of_X_in_Y", where X is a material constituent of Y. A chemical or biological species denoted by X may be described by a single term such as "nitrogen' or a phrase such as "nox_expressed_as_nitrogen". "Organic carbon" describes a family of chemical species and is the term used in standard names for all species belonging to the family that are represented within a given model. The list of individual species that are included in a quantity having a group chemical standard name can vary between models. Where possible, the data variable should be accompanied by a complete description of the species represented, for example, by using a comment attribute. Unit: [mol m-3]

[roy-lowry]

These all look fine to me for acceptance and follow well established patterns for sea water chemistry. I'll leave any decisions on replacing URIs with DOIs to others other than to say I would consider permanent identifiers to be better practice.

[lhmarsden]

Glad to hear this @roy-lowry, thanks for your time.

[JonathanGregory]

Thanks for these proposals, Luke @lhmarsden, and thanks for checking, @roy-lowry. They look fine to me as well, except for the _total_ for carbon and nitrogen. Usually we don't include that word, because its meaning is context-specific, depending on domain knowledge rather than being self-explanatory. Instead, in other such cases, we would just omit it, because the default meaning is the comprehensive one. Qualifications are needed if you don't mean everything. Can we do that in these cases? Thanks, Jonathan

[lhmarsden]

It is fine for me. I have tried to follow the standards for the existing standard names, so if I have made a mistake in doing this I am happy for it to be fixed.

[roy-lowry]

@JonathanGregory Well spotted. I missed that and totally agree with your point.

[JonathanGregory]

Thanks a lot, Luke and Roy. Making that change, we would have mass_concentration_of_nitrogen_in_sea_floor_sediment and mass_concentration_of_organic_carbon_in_sea_floor_sediment.

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This issue has had no activity in the last 30 days. This is a reminder to please comment on standard name requests to assist with agreement and acceptance. Standard name moderators are also reminded to review @feggleton @japamment

[lhmarsden]

I am happy with the suggested standard names

[github-actions[bot]]

This issue has had no activity in the last 30 days. This is a reminder to please comment on standard name requests to assist with agreement and acceptance. Standard name moderators are also reminded to review @feggleton @japamment

[efisher008]

Hello @lhmarsden,

I have added the above names to the CF editor, and I can see that there has already been discussion on them in this issue. While adding the terms I noticed a couple of discrepancies in the definitions. These are not major, but I wanted to make you aware of them.

In (15) mass_concentration_of_aluminium_in_sea_floor_sediment, I have looked into previous standard names containing a spelling of aluminium, which there don't appear to be any of. I believe that generally the convention is to use US-English spellings in new standard names, but if there is an accepted practice in the academic community for the British-English spelling of "aluminium", this would be worth considering. Do @japamment, @feggleton or @JonathanGregory have thoughts on this?

In (16) mass_concentration_of_mercury_in_sea_floor_sediment, mercury has the following definition: "Mercury means mercury in all chemical forms, commonly referred to as "total copper"." I believe this is just a copying error so have changed the final word to "mercury".

In (20) mass_concentration_of_lithium_in_sea_floor_sediment, lithium is capitalised again in the middle of its definition: "Lithium means Lithium in all chemical forms, commonly referred to as "total lithium"." I have decapitalised this so that it conforms to the same format as other definitions of metals you have made in the proposed terms.

I would also add that I agree with @roy-lowry regarding the use of permanent identifiers (DOIs) in the definitions (raised on term (2) mass_concentration_of_phaeopigments_in_sea_floor_sediment). This would ensure that the articles are accessible in the long-term despite possible future changes to the page links themselves. If @japamment or @feggleton would like to weigh in on this it would be appreciated, but my opinion is to use the DOIs @lhmarsden has provided.

Best regards, Ellie

[lhmarsden]

Thanks @efisher008 I agree with everything you have written.

[JonathanGregory]

Dear all

I'm not familiar with chemical literature, so I don't know what US scientific authors write for element 13! I've just found several web sources that say the IUPAC name is aluminium, with aluminum as an acceptable variant.

Cheers

Jonathan

[efisher008]

Dear all,

Having also found through search results that aluminium is the generally-accepted international version of the name, and for the fact that it is also consistent with the spelling of other elements with the same -ium ending (e.g. lithium, calcium, beryllium), especially as these appear in the CF standard names tables, I am inclined to go with the British-English spelling for term (15), meaning the name would appear as originally written: mass_concentration_of_aluminium_in_sea_floor_sediment. These names should now be ready for approval - unless there are any further comments within the next 7 days, they will be marked accepted and appear in the next update to the standard names table. Thanks again for the discussion on this.

Best regards, Ellie

[efisher008]

Hello @lhmarsden,

The time period mentioned above has now passed and so these names have been accepted. Thanks again for the proposal!

Best regards, Ellie

[efisher008]

This issue has been closed as the above names were published in version 84 of the standard names table (visible here).