Suggested new P02 codes (BODCNVS-1717) about emodnetchemvocabs HOT 17 OPEN

2- Broaden MDBO by adding inorganic selenium to Trace metalloid concentrations in biota and remap selenium P01 codes to MDBO instead of BCMT (Metal concentrations in biota) - will make it consistent with what we have done for codes in water bodies and sediments

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3- correct mappings of antimony, arsenic, boron to metalloids instead of metals

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4. OK, if that is an option, it needs to be discussed with Marina and Eugenia first.

And possibly with Dick and the whole Technical Steering Committee too because it might affect other processes in the pipeline.

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thanks for raising @gwemon - i will take this up with the team at ICES

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@gwemon @MeganAnneFrench Thanks for adding us to the thread. Our Pargroup list (https://vocab.ices.dk/?codetypeguid=9e697af5-d9f9-4ae4-8c14-f1ed3bfab434) is targeting the assessment outputs, where grouping contaminants by chemical structure is not always the focus, so we have a bit of mix of concepts, where contaminants might be characterized by either their chemical class (i.e. nitroaromatics, PAHs) or their target use (i.e.herbicides, pharmaceuticals). Presently, if a contaminant can belong to more than one Pargroup, we map to the one requested by the data submitter (or our content governance bodies). However, I don't think there's a big issue for organobromines and organochlorines.

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The spreadsheet contains multiple requests/suggestions:
1- to create a number of new P02 categories for contaminants that are currently held under BCOC, WCOC, SCOC (Concentration of other organic contaminants in biota/water/sediments) for:
organobromines
organofluorines
organochlorines
chlorinated paraffins
phenols/chlorophenols
dioxins
organo esters

@MeganAnneFrench in a first instance we are proposing to only create a new series of P02 for "dioxins"; I think tha the other categories are too fine-grain and present risk of too many overlaps with some chemical substances coming under more than one category. We can review this decision at a later stage.

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4- to add a new P02 for Organometallic and organometalloid species concentration parameters in suspended particulate material (instead of your suggested very specific "Concentration of methylmercury in suspended particulate material" for methyl mercury @MeganAnneFrench
is that okay?)

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1. In terms of the number of P01s and data held in EMODnet, it is actually the creation of organobromines and organochlorines (general) that is most urgent (496 and and 149 P01s in Dick's list from last year, respectively, and 10128 and 24187 data counts in the 2021 contaminant collections, respectively). These chemical groupings are the same as those used by ICES and we have been asked to try to align with ICES where possible, and they group together many substances included in Priority Substances Directive 2013. This was discussed and agreed in the EMODnet Chemistry meeting in March. I will ask Marina to comment but she is on annual leave for the next week.

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4. The problem with the mapping of methlymercury is that the P02s "Organometallic and organometalloid species concentration parameters in water bodies" and "Organometallic and organometalloid species concentration parameters in sediments" (and thus by logic "Organometallic and organometalloid species concentration parameters in suspended particulate material") are mapped to the P36 ANTIFL, and methlymercury should not really be mapped as an antifoulant as it is formed naturally by microbes in the marine environment. I show this issue in the attached file.
   Methylmercury.xlsx

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1. In terms of the number of P01s and data held in EMODnet, it is actually the creation of organobromines and organochlorines (general) that is most urgent (496 and and 149 P01s in Dick's list from last year, respectively, and 10128 and 24187 data counts in the 2021 contaminant collections, respectively). These chemical groupings are the same as those used by ICES and we have been asked to try to align with ICES where possible, and they group together many substances included in Priority Substances Directive 2013. This was discussed and agreed in the EMODnet Chemistry meeting in March. I will ask Marina to comment but she is on annual leave for the next week.

@MeganAnneFrench I think that if we want to align with ICES then we need ICES to be involved too. I was under the impression that ICES was still considering how best to categorise contaminants and the categorisation they currently have one just one of many possible and still being reviewed. But I might have misunderstood. @neil-ices-dk could you relay this to Hans or/and Anna's please? I don't seem to have their github contact.

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4. The problem with the mapping of methlymercury is that the P02s "Organometallic and organometalloid species concentration parameters in water bodies" and "Organometallic and organometalloid species concentration parameters in sediments" (and thus by logic "Organometallic and organometalloid species concentration parameters in suspended particulate material") are mapped to the P36 ANTIFL, and methlymercury should not really be mapped as an antifoulant as it is formed naturally by microbes in the marine environment. I show this issue in the attached file.
   Methylmercury.xlsx

@MeganAnneFrench The problem here is that P36 (a EMODnet chemistry grouping vocabulary) is mapped to P02 (a non-EMODnet chemistry grouping vocabulary) instead of being linked directly to the chemical substances. Maybe this is the decision we need to make. Would we be best curating mappings between P36 and S27 instead of between P36 and P02 and trying to change P02 in order to fit EMODnet chemistry's requirements?

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4. OK, if that is an option, it needs to be discussed with Marina and Eugenia first.

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1. In terms of the number of P01s and data held in EMODnet, it is actually the creation of organobromines and organochlorines (general) that is most urgent (496 and and 149 P01s in Dick's list from last year, respectively, and 10128 and 24187 data counts in the 2021 contaminant collections, respectively). These chemical groupings are the same as those used by ICES and we have been asked to try to align with ICES where possible, and they group together many substances included in Priority Substances Directive 2013. This was discussed and agreed in the EMODnet Chemistry meeting in March. I will ask Marina to comment but she is on annual leave for the next week.

@MeganAnneFrench I think that if we want to align with ICES then we need ICES to be involved too. I was under the impression that ICES was still considering how best to categorise contaminants and the categorisation they currently have one just one of many possible and still being reviewed. But I might have misunderstood. @neil-ices-dk could you relay this to Hans or/and Anna's please? I don't seem to have their github contact.

Adding @HansMJ and @Osanna123 to the thread. Hans and Anna what do you think of Megan's suggestion? Thanks @neil-ices-dk for forwarding.

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Thanks @Osanna123 and sorry for the delay in acknowledging. I have been away from my desk a lot recently. Picking this up again. From your comment I understand that the 2 categories organobromines and organochlorines are well defined and stable grouping categories in ICES and they would be worth creating as separate P02 entities for better alignment between ICES and SDN/EMODnet/NVS. However Organochlorine are also pesticides and from looking at our grouping many currently fall under our P02 groups for "Pesticides in biota/water/sediments". So @MeganAnneFrench if we were to create a set of organochlorine P02 codes for biota/water/sediment then would you suggest deprecating the P02 for "pesticides"? Presumably there must also be some "non-organochlorine pesticides" so would we have to also create a new group for these?

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@MeganAnneFrench have you been able to discuss the S27 route suggested in #34 (comment) ?

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First, I want to apologise for the long response below and say that I understand that the grouping of contaminants can be challenging and frustrating. As mentioned by Anna, as we are dealing with the management of contaminant data that are often used for environmental assessments, it is necessary to group contaminants by their chemical class, main use, or a mixture of both. For instance, organophosphorus substances include pesticides and flame retardants; therefore, ICES’s PARGROUPs include organophosphorus pesticides and organophosphorus flame retardants.
To answer Gwen’s question, I would NOT suggest deprecating the P02 for "pesticides" because it is possible that EMODnet might adopt more refined subgroups at the P02 level within the P36 of pesticides and biocides to better align with ICES in the future (this is only me imagining this possibility, and it has only been mentioned in passing, not discussed). Also, from EMODnet’s perspective, as the existing pesticide P02s are already mapped to the P36 for pesticides and biocides, having these changed to new P02s for organochlorines would mean that these P02s would be mapped to the P36 for pesticides and NULL that may become a new P36 in the future (see the last remark). I understand that ICES currently have 10 PARGROUPs that substances used mainly as pesticides can be grouped into: cyclodienes, dichloro-diphenyl-trichloroethane (DDTs), hexachlorocyclohexanes, triazine pesticides, toxaphene congeners, organophosphorus pesticides, pesticides (general), fungicides, herbicides, and insecticides. Here, cyclodienes, dichloro-diphenyl-trichloroethane (DDTs), hexachlorocyclohexanes, triazine pesticides, and toxaphene congeners all contain chlorine and are established subgroups of organochlorine pesticides used in pollution studies and assessments. On the contrary, many fungicides, for example, do not contain chlorine and have many applications (e.g. in agriculture/crops, pharmaceuticals, wood preservatives, and paint).
Organochlorines represent a very wide group and ICES’s PARGROUPs also include: organochlorines (general), chlorobiphenyls (a subgroup of which is polychlorobiphenyls, PCBs, i.e. already has specific P02s and a P36), chlorinated paraffins, and dioxins. These are all organochlorines (although dioxins can be organochlorines or organobromines) that are mainly used in industry (which is also a very wide term). The ‘general’ group of organochlorines can be used for chloroalkenes, chloroalkanes, chlorobenzenes, and styrenes etc. As mentioned previously, the work I did last year with Dick’s list of P01s focused on aligning with ICES for terms currently grouped into the P02s of ‘other organic substances’; excluding chlorobiphenyls as we already have P02s for PCBs, ICES’s relevant PARGROUPs are: organochlorines (general), organobromines, dioxins, chlorinated paraffins, organofluorines, and organic esters. I believe I used organochlorines instead of organochlorines (general) because I recall Gwen saying that she does not much like the term ‘general’; however, it (or another word) can be included. In summary, the new set of organochlorine P02 codes for biota/water/sediment would be used for organochlorine substances that are mainly used in industry, not as pesticides. Perhaps this information can be provided in the definition of the P02.
Finally, as mentioned above, polychlorobiphenyls (PCBs) already have specific P02s and a P36. After Gwen left the steering group meeting in March, this was discussed briefly when informing everyone about the proposed creation of new P02s to manage and make non-pesticide organochlorine substances and organobromines substances findable. After saying that although these could potentially have a new P36 of ‘organohalogens’ but we had decided to just deal with the P02 level for now, I was asked if PCBs were above the class of ‘organohalogens’…and I said ‘no, they are below’. Dick and Alessandra tentatively suggested changing the P36 for PCBs into ‘organohalogens’, but it was decided to take no action at this time and to resolve things first at the P02 level. Therefore, there is a possibility that this could happen in the future, whereby the P02s of PCBs, organochlorines, organobromines, organofluorines, and dioxins etc. would all be mapped to that P36 to refer to organohalogen substances that are mainly used in industry and not as pesticides. Although mapping directly between S27 and P36 codes is a possibility (I did mention this to Marina and Eugenia and asked them to read the feed on ticket 34, but no real discussion was had), the P36 codes were designed to be as broad as possible (even though this is not always the case) and I’ve understood that the creation of new P36s is not really desired; instead, we really need to have a way to manage and find main contaminant subgroups, and currently, the only way is via the P02 codes. Gwen, perhaps you want to speak to Marina about this as it is really out of my remit.

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