Closed gwemon closed 11 months ago
danibodc
commented
12 months ago P06 for Nanomoles per milligram per minute is live: http://vocab.nerc.ac.uk/collection/P06/current/NPMM
S27 for acetylcholinesterase is live: https://vocab.nerc.ac.uk/collection/S27/current/CS004473/
gwemon
commented
12 months ago @jakjonbodc In a first instance, I am proposing to model these new P01 codes as follows: S06='Activity" S27='acetylcholinesterase' S02='per unit time per unit mass of protein in the' NEW S26='biota' then for the SIMM dataset, we will need one P01 for each of these 3 S25 biological entities: Limanda limanda muscle tissue BE006608 Platichthys flesus muscle tissue BE006616 Mytilus edulis gill BE010319
Please associate the first 2 with unit http://vocab.nerc.ac.uk/collection/P06/current/NPMM The latter with http://vocab.nerc.ac.uk/collection/P06/current/PMMM
For the P02 grouping I would like to avoid creating new groupings at this stage so I would place the first 2 under https://vocab.nerc.ac.uk/collection/P02/current/FATM/ and the last one under https://vocab.nerc.ac.uk/collection/P02/current/SATM/ since enzyme activity is part of normal fish and shellfish physiology.
Acetylcholinesterase activity measurement is used as a biomarker for exposure to contaminants so it could be that in the future we will need a specific P02 categories for these kinds of measurements. But for the time being I am happy with using FATM and SATM.
So all that is needed now is to create the S02 and then compile the 3 P01s.
jakjonbodc
commented
11 months ago Created new S02 term S063 - per unit time per unit mass of protein in the
jakjonbodc
commented
11 months ago Created new P01 terms:
ACBI0319 - Activity of acetylcholinesterase {AChE CAS 9000-81-1} per unit time per unit mass of protein in the biota {Mytilus edulis (ITIS: 79454: WoRMS 140480) [Subcomponent: gill]}
ACBI6608 - Activity of acetylcholinesterase {AChE CAS 9000-81-1} per unit time per unit mass of protein in the biota {Limanda limanda (ITIS: 172881: WoRMS 127139) [Subcomponent: muscle tissue]}
ACBI6616 - Activity of acetylcholinesterase {AChE CAS 9000-81-1} per unit time per unit mass of protein in the biota {Platichthys flesus (ITIS: 172894: WoRMS 127141) [Subcomponent: muscle tissue]}
New P01 code needed for the alignment of Sandre/Quadrige terms with NVS P01 as part of Ifremer-SIMM contract.
Requires new record in chemical substance vocab S27 for acetylcholinesterase (CAS 9000-81-1; not in ChEBI) and new units (Nanomoles per minute per milligram or Nanomoles per milligram per minute, the latter being the convention followed in P06 of placing he time dimension at the end - quick search seem to show the 2 conventions being used).