Remap P01 codes related to hydrocarbon mixtures to correct P02 code about emodnetchemvocabs HOT 16 OPEN

P01 codes linked to CS003044 IMS PAH mixture I in biota remapped to P02=BCAH

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There is currently no appropriate P02 codes for hydrocarbons in biota other than BCAH for PAHs concentrations in biota. This means that P02=BCOC for concentration of other contaminants in biota is currently the only possible P02 mapping for P01 codes relating to non-aliphatic hydrocarbons in biota.

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In order to have an accurate discovery mechanism for EMODnet chemistry using P36>P02>P01/S27 we will need to review the P02 coverage for hydrocarbon substances. We currently have the following categories:
BCAH Concentration of polycyclic aromatic hydrocarbons (PAHs) in biota
SCAH Concentration of polycyclic aromatic hydrocarbons (PAHs) in sediment samples
PCAH Concentration of polycyclic aromatic hydrocarbons (PAHs) in suspended particulate material
GP050 Concentration of polycyclic aromatic hydrocarbons (PAHs) in the atmosphere
PCHW Concentration of polycyclic aromatic hydrocarbons (PAHs) in the water column
SALK Concentration of aliphatic hydrocarbons in sediment samples
OHAT Concentration of other hydrocarbons in the atmosphere
OHWC Concentration of other hydrocarbons in the water column

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To avoid inconsistency between mapping of TPH in sediment/biota/water bodies these have all been mapped to P02 codes corresponding to concentrations of PAHs. However this might need to be reviewed if/when new P02 groups are created.

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This article https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717746/ seems to be a good reference regarding hydrocarbons classification.
@mmolinajack
If I understand rightly substances like CS002685 (total petroleum hydrocarbons) and CS002816 (unresolved complex mixture) are a mixture of aliphatic and aromatic hydrocarbons hence, in addition to the P02 codes for PAHs in the various matrices we need codes for "Other hydrocarbons" in the various matrices that encompass TPH and UCM.
So my proposal would be to:
We already have:
http://vocab.nerc.ac.uk/collection/P02/current/OHWC/ for water bodies
so unless we need a specific code for "aliphatic hydrocarbons in sediments" I am proposing to broaden that terms to cover all "Other hydrocarbons in sediments" i.e. non-PAHs hydrocarbons. The definition is slightly different from "Other hydrocarbons in water bodies" because, in water bodies, we have separate codes for alkenes, alkynes, and alkanes, so these need to be excluded from the "Other hydrocarbons" category too.
If this is acceptable, then we can propose to the P02 governance group to create a new P02 code for "Other hydrocarbons in biota" to link to non-PAH hydrocarbons P01 variables including those related to UCM and TPH.

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I would suggest to keep the same "structure" for P02 in the different matrixes. I would not exclude that there are (or may arrive) "aliphatic hydrocarbons in sediments". For the same substance, I would leave the possibility to create P02 in (at least) water, biota and sediment. Not have the same substance linked to a broader P02 (Other hydrocarbons...) for one matrix and to a narrower P02 in another matrix. I agree with the "other..." in case of mixtures.

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@mlipizer yes I think I understand.
To clarify, my proposal was to have:
BCAH Concentration of polycyclic aromatic hydrocarbons (PAHs) in biota
SCAH Concentration of polycyclic aromatic hydrocarbons (PAHs) in sediment samples
PCAH Concentration of polycyclic aromatic hydrocarbons (PAHs) in suspended particulate material
GP050 Concentration of polycyclic aromatic hydrocarbons (PAHs) in the atmosphere
PCHW Concentration of polycyclic aromatic hydrocarbons (PAHs) in the water column
SALK Concentration of aliphatic hydrocarbons in sediment samples > broaden this term to become "Concentration of other hydrocarbons in sediment samples"
OHAT Concentration of other hydrocarbons in the atmosphere
OHWC Concentration of other hydrocarbons in the water column
NEW_CODE Concentration of other hydrocarbons in biota
NEW_CODE Concentration of other hydrocarbons in suspended particulate material

"other hydrocarbons" definition would specify that this category covers total and non-PAHs hydrocarbons in sediments, biota, SPM, water bodies and atmosphere however in water bodies and atmosphere it also excludes alkanes, alkenes, alkynes (because these groups already exists as separate P02. For water bodies these are http://vocab.nerc.ac.uk/collection/P02/current/DALK/
http://vocab.nerc.ac.uk/collection/P02/current/AQYN/
).

In order to try and keep the same definitions across the matrices we have a couple of choices. What would be your preference: to explicitly exclude alkanes, alkenes and alkynes from the biota, sediments and spm definitions or to ask P02 governance group if it could be possible to deprecate alkanes/alkenes/alkynes in water bodies and atmosphere P02 groups and replace them with the broader OHWC and OHAT term?

What could help decide would be knowing if there are any chemical substances from the alkane, alkene and alkyne groups that are measured individually as contaminants?

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I agree with the very last sentence. It's safer

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Having corrected a number of inconsistent mappings between sediments and water bodies, I have now generated a list of all our substances mapped to P02 groups related to alkanes/enes/ynes. Please see S27_P02_AlkX.csv
@mlipizer could you advise: are any of these substances of interest to EMODnet chemistry? Do any qualify as contaminants?

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Dear Gwen, I am checking. But why are the substances repeated twice?
Thanks

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@mlipizer thanks for pointing this out! Duplicated lines removed and new file version uploaded.

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@mlipizer Thank you. So do you agree that we can exclude the following P02 groupings from the mapping to P36 hydrocarbons (http://vocab.nerc.ac.uk/collection/P36/current/HCARBS/)?
AALK Concentration of alkanes in the atmosphere
AEYN Concentration of alkenes and alkynes in the atmosphere
AQYN Concentration of alkenes and alkynes in the water column
DALK Concentration of alkanes in the water column

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@mlipizer I see that the JRC report is mainly concerned with Polycyclic Aromatic Hydrocarbons. Would it be worth proposing to deprecate the existing "Hydrocarbons" term present in P36 and replace it with a new term, specifically setup for PAHs? I would obviously adjust all the mappings to reflect the change.
This would allow us to clearly map PAHs in P36 to PAHs groups in P02 for water bodies, sediments and biota, and leave the other hydrocarbon out of the EMODnet chemistry current mappings? If, in a next phase of EMODnet chemistry, there is a need to consider other types of hydrocarbons then we can create a new category (distinct from PAH) in P36.

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Dear Gwen, within the new EMODnet phase we should update the P36 list with "Other contaminants" (those removed from Hydrocarbons for example) and verify the need to have a P36 term "PAH". This should be agreed within EMD chem group.
Just a reminder for us. Thanks!

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