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A controlled vocabulary for units of measurement
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NTR: Request for Femtogram Particulate Organic Carbon per cell (BODCNVS-1651) #44

Closed timvdstap closed 1 year ago

timvdstap commented 1 year ago

Required

Term name (PrefLabel)

Femtogram Particulate Organic Carbon per cell

Short name (AltLabel)

fg POC/cell

Definition

One 10^18 part of the SI standard unit of mass of particulate organic carbon per cell.

Sources/references

Not really a reference source, but perhaps useful: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6606879/#B9

roy-lowry commented 1 year ago

In the same way that a unit of measure (P06) shouldn't contain semantics, a parameter description (P01) shouldn't contain a unit of measure like femtogram.

gwemon commented 1 year ago

@timvdstap For this parameter I would say that what is being measured or reported is the amount of organic carbon per cell and the unit of measure is femtogram. I am not clear why it is labelled as "POC" per cell though. Is this because what we have here is not a direct measurement but a derived ratio of 2 measured quantities: POC concentration and abundance of cells in a water sample? Do you have more info about the parameter?

timvdstap commented 1 year ago

Hi @gwemon my apologies for the late reply! I have relayed your question to the data provider, and I hope to get back to you soon with an answer. :) I think indeed the unit of measure would be femtogram (for which I believe currently no controlled vocab exists) (or perhaps femtogram per cell?) with parameter = amount of organic carbon (?) but hope to get more information regarding POC/cell.

timvdstap commented 1 year ago

Hi all, for the sake of discussion I wanted to share the data provider's POV:

[...] I would have said the unit is fgC/cell, not just fg. The important part is that this is not the cell abundance (cells per ml), nor is it a concentration as concentration by definition has a denominator of volume (e.g., L). It is derived, but not from the measured bulk POC and cell number. It is estimated from the calibrated magnitude of the light scatter signature as in Casey et al. 2013.

gwemon commented 1 year ago

Thank you @timvdstap. I had a look at similar codes we may already have in our P01 vocabualry and I found this one: TCCFEM01 I think this is equivalent to what we have here but per cell. i.e. the units for me would definitely need to be femtograms as we cannot have semantics like "cell" or "carbon" in a unit of measure. The methodology paper is not free access unfortunately so I could not check the kind of parameters that would need to be described.

timvdstap commented 1 year ago

Thank you for your reply @gwemon. I think the work around for me then would be to include POC per cell in the measurementType column of DwC, and femtogram as the measurementUnit. I think this would make it understandable for data users. I apologize - I thought the paper was open access. I've forwarded you the email from the data provider where he added the paper as attachment. Let me know if it's helpful / what's the best way to proceed here :)

gwemon commented 1 year ago

Thank you @timvdstap. Yes that would work. We will create an entry in P06 for Femtograms.

gwemon commented 1 year ago

New term FMTG added to P06 and linked to QUDT: http://qudt.org/vocab/unit/FemtoGM The concept has been queued for publication on the NVS.

timvdstap commented 1 year ago

Thank you @gwemon - and for 'particulate organic carbon per cell' -- would this fall under P01 / should I create a separate ticket for this?

gwemon commented 1 year ago

@timvdstap yes that would be a P01 but I can create the ticket. I never received the paper you mentioned sending by email. The Casey et al paper. Could you send it again please? Also could you let me know what is this POC per cell referring to? cells of what? where is this defined? In the occurrence record of the DwCA? or does it need to be included in the P01 code?

timvdstap commented 1 year ago

@gwemon I think it refers to cells of different microbial groups, which will be recorded in the occurrence table. I'm not sure if those microbial groups will have to be included in the P01 definition?

I have jsut sent the paper to your email again.

gwemon commented 1 year ago

@timvdstap that's perfect thank you. We could create a P01 of the form: "Mass of carbon per cell of biota {biological entity specified elsewhere}" to keep to the conventions we have for measurements associated with biological entities in OBIS. To help discovery we can add the tag "cellular carbon content" inside the P01 preferred label.

gwemon commented 1 year ago

New unit is live on the NVS: http://vocab.nerc.ac.uk/collection/P06/current/FMTG/