NTR hazardous substances data in biota terms for EMODnet chemistry 5 [11 terms]

[roswri]

Terms requested:

• Concentration of beta-endosulfan {CAS 33213-65-9} per unit wet weight of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: muscle tissue]}
• Concentration of beta-endosulfan {CAS 33213-65-9} per unit wet weight of biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Sex: female Subcomponent: muscle tissue]}
• Concentration of perfluorooctanyl sulphonic acid {CAS 1763-23-1} per unit wet weight of biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Sex: female Subcomponent: muscle tissue]}
• Concentration of perfluorooctanyl sulphonic acid {CAS 1763-23-1} per unit wet weight of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: muscle tissue]}
• Concentration of beta-hexachlorocyclohexane {beta-HCH CAS 319-85-7} per unit wet weight of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: muscle tissue]}
• Concentration of 1,2,5,6,9,10-hexabromocyclododecane {HBCD CAS 3194-55-6} per unit wet weight of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: muscle tissue]}
• Concentration of 1,2,5,6,9,10-hexabromocyclododecane {HBCD CAS 3194-55-6} per unit wet weight of biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Sex: female Subcomponent: muscle tissue]}
• Concentration of 1-hydroxy phenanthrene CAS 2433-56-9 per unit wet weight of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: bile]}
• Concentration of 1-hydroxy phenanthrene CAS 2433-56-9 per unit wet weight of biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Sex: female Subcomponent: bile]}
• Concentration of 1-hydroxy pyrene CAS 5315-79-7 per unit wet weight of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: bile]}
• Concentration of 1-hydroxy pyrene CAS 5315-79-7 per unit wet weight of biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Sex: female Subcomponent: bile]}

1-hydroxy phenanthrene will be 1-phenanthrol https://github.com/nvs-vocabs/S27/issues/18 as per CHEBII substance name

S25s to be created: https://github.com/nvs-vocabs/S25/issues/31

[roy-lowry]

@gwemon Don't know if it's an issue but I noticed perfluorooctanyl sulphonic acid rather than perfluorooctanyl sulfonic acid. Looking at S27 I see we use the US convention (sulf) in many cases with 'sulph' in the alternative label, but there are 26 occurrences of 'sulph' in the preferred label. @roswri Unless Gwen says otherwise I wouldn't let this observation block your generating these P01 terms.

[gwemon]

Thanks a lot @roy-lowry well spotted. Yes, you're right that we need to make sure we are consistent. We decided a while ago to align with IUPAC (https://www.nature.com/articles/nchem.301) and have the 'sulf' spelling in the preferred label (and the 'sulph' spellings in the alternative label field). I must have missed those 26! @roswri could you correct them when you get a chance please?

[roswri]

New terms created:

• Concentration of 1-hydroxypyrene {CAS 5315-79-7} per unit volume of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: bile]} (http://vocab.nerc.ac.uk/collection/P01/current/CHBI4049)
• Concentration of 1-hydroxypyrene {CAS 5315-79-7} per unit volume of biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Sex: female Subcomponent: bile]} (http://vocab.nerc.ac.uk/collection/P01/current/PFBI4049)
• Concentration of 1-phenanthrol {1-hydroxyphenanthrene CAS 2433-56-9} per unit volume of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: bile]}(http://vocab.nerc.ac.uk/collection/P01/current/CHBI4457)
• Concentration of 1-phenanthrol {1-hydroxyphenanthrene CAS 2433-56-9} per unit volume of biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Sex: female Subcomponent: bile]}(http://vocab.nerc.ac.uk/collection/P01/current/PFBI4457)
• Concentration of 1,2,5,6,9,10-hexabromocyclododecane {HBCD CAS 3194-55-6} per unit wet weight of biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Sex: female Subcomponent: muscle tissue]}(http://vocab.nerc.ac.uk/collection/P01/current/PFMU2517)
• Concentration of perfluorooctanyl sulphonic acid {CAS 1763-23-1} per unit wet weight of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: muscle tissue]}(http://vocab.nerc.ac.uk/collection/P01/current/CHMU3715)
• Concentration of perfluorooctanyl sulphonic acid {CAS 1763-23-1} per unit wet weight of biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Sex: female Subcomponent: muscle tissue]}(http://vocab.nerc.ac.uk/collection/P01/current/PFMU3715)
• Concentration of 1,2,5,6,9,10-hexabromocyclododecane {HBCD CAS 3194-55-6} per unit wet weight of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: muscle tissue]}(http://vocab.nerc.ac.uk/collection/P01/current/CHMU2517)
• Concentration of beta-endosulfan {CAS 33213-65-9} per unit wet weight of biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Sex: female Subcomponent: muscle tissue]}(http://vocab.nerc.ac.uk/collection/P01/current/PFMU3282)
• Concentration of beta-endosulfan {CAS 33213-65-9} per unit wet weight of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: muscle tissue]}(http://vocab.nerc.ac.uk/collection/P01/current/CHMU3282)
• Concentration of beta-hexachlorocyclohexane {beta-HCH CAS 319-85-7} per unit wet weight of biota {Clupea harengus (ITIS: 161722: WoRMS 126417) [Sex: female Subcomponent: muscle tissue]}(http://vocab.nerc.ac.uk/collection/P01/current/CHMU2349)

[roswri]

@gwemon, slight problem with updating the 'sulph's to 'sulf's... I think we have a set of duplicates: CS003522 - alpha-endosulphan+beta-endosulphan+endosulphan sulphate CS004455 - alpha-endosulfan+beta-endosulfan+endosulfan sulfate

Both are 'accepted'. Neither have been used in chem_model or cs_model.
CS003522 is in vocmap, but it's just linked to S01:S016 - chemical entity

I think we might need to deprecate the original term (CS003522) because if we deprecated the more recently created term and then updated the original the preflabel wouldn't be unique which is one of the constraints in the table. Would you agree with this?

Thanks, Roseanna

[gwemon]

Hi @roswri yes I agree.

[roswri]

Updated all sulph spellings to sulf in preflabel and vice versa for altlabels.

CS003522 deprecated. Updated CS004455 to include a definition and added 'sulph' spellings and CAS numbers to the altlabel. also added vacmap mapping between S27:CS004455 and S01:S016.

@gwemon - I don't have permission to insert into codedep, can I be granted permission to insert into codedep, or should I just get you/Dani to run that statement for me?