Stream: terminology
Topic: UCUM Code variants/MegaBase
Patrick Werner (Jul 19 2019 at 12:24):
In the clinical genomic domain we have the concept of a tumor mutational burden which is expressed as variants/Megabase (mutations per 1000000 base pairs)
I tried to express this in UCUM but run into an issue with the prefix. I tried to use {variants}/M{Base} but this leads to a syntax error in the LHC ucum validator: https://ucum.nlm.nih.gov/ucum-lhc/demo.html
Patrick Werner (Jul 19 2019 at 12:25):
i could write {variants}/1000000{Base} but i like the prefix better. Are prefixes only allowed before actual ucum units?
Paul Lynch (Jul 19 2019 at 15:22):
I think so. See the grammar in 2.2.10 of http://unitsofmeasure.org/ucum.html.
Paul Lynch (Jul 19 2019 at 15:40):
'M' by itself is also not valid as a unit, and "annotations have no semantic value" (2.4.12). (Personally, I wish they did have semantic value, but they don't.)
Christof Gessner (Jul 19 2019 at 16:40):
Do you like {variants}/10^6{Base} or {variants}/(10^6.{Base}) ?
Funny: the validator also would accept {variants}/(1E6.{Base}) - which I think is not valid UCUM ;-) The rules say "Only a pure string of decimal digits (‘0’–‘9’) is interpreted as a number. If after one or more digits there is any non-digit character found that is valid for unit atoms, all the characters (including the digits) will be interpreted as a simple unit symbol."
Paul Lynch (Jul 19 2019 at 17:17):
Funny: the validator also would accept {variants}/(1E6.{Base}) - which I think is not valid UCUM ;-)
@Christof Gessner That sounds like a bug. Would you care to open an issue on the ucum-lhc package?
Patrick Werner (Sep 13 2019 at 17:18):
i lost track about this topic. Thanks for all the input @Paul Lynch @Christof Gessner {variants}/10^6{Base} looks good to me. Will bring it to the CG WG
Last updated: Apr 12 2022 at 19:14 UTC
