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.