Standard names: Phytoplankton Functional Type

[cderval]

Proposer's name Corinne Derval Date Nov 13 2020

- Term mass_concentration_of_cryptophytes_expressed_as_chlorophyll_in_sea_water - 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". The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. 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. Cryptophytes are flaggellated unicellular organisms attributable to nanophytoplanktonic component, very rich in fatty acids and therefore a high quality food source for herbivorous zooplankton. - Units mg m-3

- Term mass_concentration_of_greenalgae_expressed_as_chlorophyll_in_sea_water - 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". The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. 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. Green Alge are small green unicellular flagellates caractherized by the presence of Chlorophyll b. - Units mg m-3

- Term mass_concentration_of_haptophytes_expressed_as_chlorophyll_in_sea_water - 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". The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. 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. Haptophytes are mainly unicellular marine algae which play an important role in the DMSP production and in calcifying. - Units mg m-3

- Term mass_concentration_of_prokaryotes_expressed_as_chlorophyll_in_sea_water - 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". The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. 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. Prokaryotes group refers to those phytoplankters characterized by a prokaryotic cell and represents the main component of picophytoplankton. - Units mg m-3

- Term mass_concentration_of_dinoflagellates_expressed_as_chlorophyll_in_sea_water - 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". The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. 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. Dinoflagellates (dinophytes) are mostly unicellular, rarely colonial, biflagellated algae with cell walls firm, or reinforced with polygonal plates. They produce some of the most potent toxins known. - Units mg m-3

- Term mass_concentration_of_prochlorococcus_expressed_as_chlorophyll_in_sea_water - 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". The phrase "expressed_as" is used in the construction A_expressed_as_B, where B is a chemical constituent of A. It means that the quantity indicated by the standard name is calculated solely with respect to the B contained in A, neglecting all other chemical constituents of A. 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. Prochlorococcus are marine Prokaryotes with an extremely small cell, containing divinyl chlorophyll a and b as their primary photosynthetic pigments and adapted to the high-light, oligotrophic, warm waters of the tropical and subtropical regions of the world’s oceans. - Units mg m-3

It would be usefull to add these standard names to describe the various phytoplankton functional types

[roy-lowry]

My first question is whether this is a case that could be handled using the convention for biological entities described in Section 6.1.2 in the CF Conventions document (1.8) under the single new Standard Name mass_concentration_of_biological_taxon_expressed_as_chlorophyll_in_sea_water?

This is possible to do even though only two (possibly three - not sure about green algae) of the biological entities are taxa (dinoflagellates and prochlorococcus) rather than functional groups (the links to the standard taxon references would have to be left null for these).

[roy-lowry]

This ticket has me concerned. CF is heading down a road of using one convention for taxa (a single multi-dimensional storage array with taxa as a co-ordinate under a single Standard Name) and another for functional/morphological groups (a separate array for each group each with its own Standard Name).

This proposal includes a mixture of taxa (Prochlorococcus is a Genus and dinoflagellates is the common name for a Class). My previous comment suggested solving the problem by adopting a single convention which would mean treating functional/trophic/morphological groups as 'honorary taxa'. I'm really torn on whether this is good practice. I have just made enquiries about what restrictions Darwin Core (a primary biological standard) places on population of its scientificName field for taxa. However, I would really appreciate input, especially from anybody handling biological data.

[gwemon]

Would it be possible to simply have a CF standard name defined as e.g. mass_concentration_of_biological_taxon_expressed_as_chlorophyll_in_sea_water

where "taxon" is a biological entity defined in https://www.bodc.ac.uk/resources/vocabularies/vocabulary_search/S25/ (at least for freshwater and marine organisms) and handled as you suggested @roy-lowry. S25 has the capability of handling any biological entity name (not just Linnean taxonomomy) It can then be used to connect with authoritative registries of biological organism names or identifiers.

[gwemon]

Ah okay just saw the other thread; it looks like we may have a solution.

[roy-lowry]

@gwemon Hi Gwen. There's quite a lot going on in parallel discussions triggered by the discovery that I'd made a mistake setting up the Standard Names for Trac ticket 99.

Currently, the CF Conventions document states that the co-ordinate entity should be a taxon defined as 'named level within a biological classification'. What I'm asking here is whether the Conventions document should be modified to use the broader concept of 'biological entity'. It's important to note that this is asking the question again - the idea has been discussed and rejected (not by me) previously.

Should the previous decision be reversed then S25 provides a potential identifier resource providing it can be encoded into a resolvable (returns a document not an error when typed into a browser) LSID.

[roy-lowry]

I am trying to sort out what constitutes a taxon. This is essential if we are going to handle taxa differently in CF to other biological entities like trophic groups as decided during a previous discussion on Cyanobacteria Standard Names.

Darwin Core (the primary biological data standard) defines a taxon as 'A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit.' This doesn't help me a lot because I'm not a taxonomist and can't get inside a taxonomist's head to see what they consider a 'homogenous unit'. However, the more I dig, the more I come to the conclusion that this homogenous unit has to form a part of a network of hierarchically related homogenous units, which is an exact match with the current definition of taxon in the CF document.

At the start of this thread I was questioning whether the Cyanobacteria decision was correct. Having researched Darwin Core over the past couple of days I am now convinced that I was wrong to do this and that trophic/morphological/functional groups should NOT be considered taxa so CF maintains semantic compatibility with Darwin Core. I may have missed something and so would love to hear from anybody who has encoded data for these groups into Darwin Core.

With these rules in place the $64,000 question with a Standard Name request like this thread is whether or not the proposed biological entities are taxa. The CF community is not strong on biological specialists so I would suggest using resources like ITIS and WoRMS put together by biological specialists as tools to guide our decision making in CF. Anybody any comments on this?

[MathewBiddle]

@albenson-usgs might have some experience.

[roy-lowry]

Thanks. I've been communicating with her on this subject in a parallel thread cf-convention/cf-conventions#309

[roy-lowry]

Apologies for the delay but I have now researched all of the 'Functional Types' proposed here. Four are definitely taxa - I've now identified Cryptophyta and Haptophyta are Phyla in addition to Prochlorococcus being a Genus and dinoflagellates the common name for a Class. Consequently, these should not be given Standard Names and should be managed as taxa.

I also have serious concerns about the term 'greenalgae' defined as 'small green unicellular flagellates characterised by the presence of Chlorophyll b'. To me, the term 'green algae' covers the majority of phytoplankton plus the green macroalgae (seaweeds). I can't find any online reference where the term is restricted to flagellates.

The only term in this proposal that is not a taxon is prokaryote which is a grouping of two taxa (Bacteria and Archaea). I feel a better definition of prokaryote is 'A cellular organism that lacks an envelope-enclosed nucleus'. The definition given (phytoplankters characterized by a prokaryotic cell and represents the main component of picophytoplankton) makes me think what @cderval really means is the photosynthetic subset of prokaryotes that I would describe as 'prokaryotic_picophytoplankton'.

This leads me to a possible way forward for this proposal which would be to replace the current taxonomical terms with terms that are truly functional/morphological groups such as 'prokaryotic_picophytoplankton' and 'green_flagellates'? @cderval What do you think?

[cderval]

Dear @roy-lowry @gwemon ,

Apologies for the very long delay without an answer from me. And thank you very much for your discussions.

We have taken into account your remarks and recommendations to initiate discussions with the CMEMS producers of PFT. In order to make sure that we have understood your recommendations: the following SN proposed: mass_concentration_of_cryptophytes_expressed_as_chlorophyll_in_sea_water.. mass_concentration_of_haptophytes_expressed_as_chlorophyll_in_sea_water mass_concentration_of_prochlorococcus_expressed_as_chlorophyll_in_sea_water mass_concentration_of_dinoflagellates_expressed_as_chlorophyll_in_sea_water following the name rule : mass_concentration_of_biological_taxon_expressed_as_chlorophyll_in_sea_water would be accepted?

Regarding the greenalgae, prokaryote we will discuss with our producers and come back to you with propositions that follow your recommendations.

A remark concerning the link provided by @gwemo seems to be inactiv : https://www.bodc.ac.uk/resources/vocabularies/vocabulary_search/S25/ ? Thanks again

[roy-lowry]

Many thanks,

It's been a while so I'll give this thought after the holiday weekend and get back to you. There has been a major change to our vocabulary website that may explain the broken URL. I'll leave that to @gwemon to check out.

Cheers, Roy.

[roy-lowry]

Dear Corinne,

I'm afraid the simple answer is 'No'. As I have tried to explain previously the problem is that you have the names of taxa in your proposed standard names. CF has a specific mechanism for dealing with taxa, which is to store the data in an array with an additional dimension for taxon, giving the array a generic standard name such as 'mass_concentration_of_biological_taxon_expressed_as_chlorophyll_in_sea_water'. That is an actual standard name, not a standard name template.

It is permissible to include functional or morphological groups in standard names. I strongly suspect that the data you are handling are model data and that you want standard names to describe model compartments, which my instincts tell me are functional groups. As I tried to explain earlier in this thread if this is the case then we have a way forward, which I suggested but got no response. This is to replace the taxon names in your proposals by functional group names. For example, 'haptophytes' could be replaced by 'calcifying_phytoplankton', 'dimethylsulfide_producing_phytoplankton' or even 'dimethylsulfide_producing_calcifying_phytoplankton' depending upon the functional properties of your model component.

Whilst I can help with this it needs somebody with knowledge of your data - I guess the people you describe as your producers - for the descriptions to be accurate. Consequently, to take things forward I need to to respond and suggest functional group names for your proposed names.

Cheers, Roy.

[gwemon]

Many thanks,

It's been a while so I'll give this thought after the holiday weekend and get back to you. There has been a major change to our vocabulary website that may explain the broken URL. I'll leave that to @gwemon to check out.

Cheers, Roy.

@roy-lowry @cderval Thank you for highlighting the issue. It looks like a series of redirect links has not been implemented. We are going to fix these. In the mean time, please use https://vocab.nerc.ac.uk/search_nvs/S25/

[cderval]

@roy-lowry @gwemon Thank you very much for your clarifications, it seems that we have misunderstood what you have detailed. Our data comes from satellite data of ocean colour. We will communicate your suggestions and rules to our producers and will come back to you with more information.

Thank you again for your availability and your reply, Kind Regards, Corinne

[feggleton]

I have added these to the cfeditor to try and progress these terms.

[efisher008]

Hello @cderval @gwemon @roy-lowry,

I am revisiting this issue as it is a long-standing open proposal which has not reached a conclusion. It looks as though they were added to the CF editor last year, and I have found the current entries:

mass_concentration_of_cryptophytes_expressed_as_chlorophyll_in_sea_water https://cfeditor.ceda.ac.uk/proposal/4968/edit

mass_concentration_of_greenalgae_expressed_as_chlorophyll_in_sea_water https://cfeditor.ceda.ac.uk/proposal/4969/edit

mass_concentration_of_haptophytes_expressed_as_chlorophyll_in_sea_water https://cfeditor.ceda.ac.uk/proposal/4970/edit

mass_concentration_of_prokaryotes_expressed_as_chlorophyll_in_sea_water https://cfeditor.ceda.ac.uk/proposal/4971/edit

mass_concentration_of_dinoflagellates_expressed_as_chlorophyll_in_sea_water https://cfeditor.ceda.ac.uk/proposal/4972/edit

mass_concentration_of_prochlorococcus_expressed_as_chlorophyll_in_sea_water https://cfeditor.ceda.ac.uk/proposal/4973/edit

Would you still like to pursue the proposal? If so, perhaps we could revive the discussion and hopefully move these towards acceptance.

Best wishes, Ellie

[roy-lowry]

Hi Ellie,

Those Standard Names as entered into the editor are unacceptable to me because they include taxon names as labels of convenience for functional groups. I suggested a way forward whereby the taxon names could be replaced by names that explicitly describe the functional group - e.g. replacing haptophytes by 'calcifying_phytoplankton', 'dimethylsulfide_producing_phytoplankton' or even 'dimethylsulfide_producing_calcifying_phytoplankton' depending upon the properties assigned in the model to the functional group. This replacement obviously needs an understanding of the model and Corinne was going to ask the modellers and come back with more information. This was in April 2021 but I've heard nothing since.

[efisher008]

Hi Roy @roy-lowry,

I understand that you are not satisfied with the current status of the names, but I am hoping through continuing the discussion now we should be able to come to a decision which works for all involved. If you are able to contact Corinne @cderval directly, it may help to fill in some of this missing information/understand regarding the model and therefore to move the proposal along?

If there is anything you think I might be able to support with on this, please let me know.

Best wishes, Ellie

[roy-lowry]

@efisher008 Implementing my suggested workaround isn't a big job. All I need are the model compartment specifications to enable me to knock together initial straw man labels that shouldn't need a lot of additional work. However, communication is the issue. I retired 8 years ago and although I have emeritus status I only access former work e-mail once a week at best. I don't have contact with Corinne outside GitHub and its been a long time so she could well have changed jobs.

I suggest you suggest a reasonable time for her to respond to the recent activity on this ticket and if nothing happens then the proposals should be considered as withdrawn.

[efisher008]

Hi Roy @roy-lowry,

I see, thank you for explaining the situation. Let's give the proposal a month for further comments, and if there is no more interaction with the issue, this can then be withdrawn.

Best wishes, Ellie

[abiardeau]

Hello @efisher008 and @roy-lowry , I work with Corinne and I can take over on this issue. We are still interested in the Phytoplankton Functional Types. I understand that we have to use a generic standard_name and that we can't integrate the taxon name in the standard_name is that right ?

We have some similar questions about micronekton but I will open another issue on this topic.

Thanks, Aurore

[roy-lowry]

Hi Aurore,

To clarify, For TAXA - i.e. biological entities that are part of a taxonomy such as found in WoRMS or ITIS then you store your data in a 2D array (like a spreadsheet page) with the rows labelled using a standardised label for the taxon (that itself has a Standard Name) and the columns labelled using a generic Standard Name like ''mass_concentration_of_biological_taxon_expressed_as_chlorophyll_in_sea_water'.

However, in this case I think you have functional groups rather than taxa and these can be incorporated into specific Standard Names. The problem is that the labels you are using for the functional groups are labels that are also used for taxa. Were these to be used in Specific Standard Names the result would be confusion. The solution is to find acceptable labels for the functional groups. For example, replace your suggestion of 'mass_concentration_of_prokaryotes_expressed_as_chlorophyll_in_sea_water' with something like 'mass_concentration_of_prokaryotic_picophytoplankton_expressed_as_chlorophyll_in_sea_water'.

So, all we have to do is agree alternative labels for:

crypyophytes ( my suggestion fatty_acid_rich_nanophytoplankton) greenalgae (my suggestion 'chlorophyll_b_bearing_unicellular_flagellates' haptophytes (my suggestions 'calcifying_phytoplankton' or 'dimethylsulfide_producing_phytoplankton' or 'dimethylsulfide_producing_calcifying_phytoplankton') prokaryotes (my suggestion 'prokaryotic_picophytoplankton') dinoflagellates (my suggestion 'toxin_producing_phytoplankton') prochlorococcus (my suggestion would be 'divinyl_chlorophyll_a_and_b_bearing_phytoplankton')

My suggestion are very much draft based on the Standard Name definitions, but if we can agree a modified set then a set of specific Standard Names can easily be created.

Roy.

[roy-lowry]

If you want me to look at any new proposals please tag me as I no longer watch all new Standard Name proposals.

[efisher008]

Hi Roy @roy-lowry,

If you want me to look at any new proposals please tag me as I no longer watch all new Standard Name proposals.

Noted, thank you for the message.

Best, Ellie

[abiardeau]

Thanks a lot Roy for your detailed answer. I will discuss that with my colleagues and come back to you. Aurore