search

nvs-vocabs / S27

BODC parameter semantic model chemical substances
0 stars 0 forks source link

NTR: 3 new S27 terms required that reference branched and linear forms #30

Closed danibodc closed 3 months ago

danibodc commented 4 months ago

Term name (PrefLabel) - REQUIRED

perfluorodecanesulfonic acid (branched + linear)

CAS Registry Number - REQUIRED

335-77-3

Definition - REQUIRED

An organofluorine. The sum of all branched and linear forms.

Sources/references - REQUIRED

https://chem.nlm.nih.gov/chemidplus/rn/335-77-3 A variant of existing term https://vocab.nerc.ac.uk/collection/S27/current/CS003707/

Mapping to external terminologies - OPTIONAL

https://chem.nlm.nih.gov/chemidplus/rn/335-77-3

Term name (PrefLabel) - REQUIRED

perfluorohexanesulfonic acid (branched + linear)

CAS Registry Number - REQUIRED

355-46-4

Definition - REQUIRED

An organofluorine. The sum of all branched and linear forms.

Sources/references - REQUIRED

https://chem.nlm.nih.gov/chemidplus/rn/355-46-4 A variant of existing term https://vocab.nerc.ac.uk/collection/S27/current/CS003711/

Mapping to external terminologies - OPTIONAL

https://chem.nlm.nih.gov/chemidplus/rn/355-46-4

Term name (PrefLabel) - REQUIRED

perfluorooctanyl sulfonic acid (sum of linear isomers)

CAS Registry Number - REQUIRED

1763-23-1

Definition - REQUIRED

An organofluorine. The sum of all isomers with linear forms.

Sources/references - REQUIRED

https://chem.nlm.nih.gov/chemidplus/rn/1763-23-1 A variant of existing term https://vocab.nerc.ac.uk/collection/S27/current/CS004546/

Mapping to external terminologies - OPTIONAL

https://chem.nlm.nih.gov/chemidplus/rn/1763-23-1

danibodc commented 4 months ago

Required as part of https://github.com/nvs-vocabs/P01/issues/252

gwemon commented 3 months ago

@danibodc We have already mapped our S27 term: http://vocab.nerc.ac.uk/collection/S27/current/CS003707/ to ICES http://vocab.ices.dk/services/rdf/collection/PARAM/PFDS with a sameAs relationship therefore taking the approach that if linear or branched is unspecified then the term would have a mixture of both forms. This sound reasonable to me. It would be good reaching out to EMODnet chemistry or ICES about this. Please liaise with @SLBlakeman.

Osanna123 commented 3 months ago

CAS numbers are usually including all isomer forms or are specific to a single isomer. If there are some isomers (or groups of such) without a specific CAS, we do not assign them the parent CAS. Thus, CAS 335-77-3 is same as ICES PARAM PFDS (branched + linear) https://vocab.ices.dk/?codeguid=328d7744-c6fd-4e62-9c12-e44c7eb60317 CAS 355-46-4 is same as PFHXS (branched + linear) https://vocab.ices.dk/?codeguid=21e111db-6e41-40c7-bab2-80397ad14052 But CAS 1763-23-1 is same as PFOS (branched + linear) https://vocab.ices.dk/?codeguid=2dfc3fd6-fb8d-41b7-bc50-527fa94ae582. A separate PARAM n-PFOS is created for linear forms only, and no (same as) CAS link https://vocab.ices.dk/?codeguid=d0e92d5e-6d18-4786-892d-c6f3111541a1

gwemon commented 3 months ago

Thank you @Osanna123. We could make the mapping relationship between the grouping of linear or branched forms and the CAS number to be Broader/Narrower? It would enable us to maintain that link without stating that they are the same because they are not?

Osanna123 commented 3 months ago

Hi @gwemon. Yes, it sounds like a good solution if you can use the broader/narrower relations in the cases for only linear or branched isomers

danibodc commented 3 months ago

Single new term created: CS004550 - perfluorooctanyl sulfonic acid (linear)