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Units: mutations per megabase

Vocabulary Users
#1

So of all the units of measurement we have, mutations per megabase is the only one not in any vocabulary I can find. Not sure how to go about coding this in Measurement.

#2

According to the documentation https://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary:ucum
“All UCUM Concepts are manually curated, and additions and changes can be made on request.”
So we can add this concept.
@Christian_Reich do we have any routine of new concepts adding like someone should approve or something?

#3

No. We just add. Something like concept_code “{mutations}/{megabase}”, concept_name “mutations per megabase”.

Of course, neither “mutation” nor “megabase” are not canonical units, not even physical ones. They are just enumerations. Like “Cells” or “Colony Forming Units”.

#4

here you go
http://athena.ohdsi.org/search-terms/terms/32608

#5

@Dymshyts @Christian_Reich
Can you please help find this units? Or what do you think of us adding some new concepts?

Thanks!

#6

Can you use conversion factor?

#7

@Dymshyts
In theory, everything may be converted to familiar units, but who is doing this in fact?
Unit domain has a comprehensive list of possible combinations covering ~99% of things people ordinary use. Why don’t we simply add everything someone has used if it’s not mistaken, but still uncommon practice?

Another thing is the above-mentioned list of units/tests from @zhuk.
It’s a common practice for these tests and sometimes the only possible/non-convertible option.
Let’s not confuse users asking to measure the bone density in water column centimeters or protein mass in daltons :slight_smile:

#8
  • Attogram per cell: We have 8704 pg/{cell} “picogram per cell”. Needs to be created as ag/{cell}.
  • ‘pmol/mg’: We have 44777643 pmol/kg “picomole per kilogram”. Needs to be created.
  • ‘kilodalton’: That is a very small amount of weight. Where do you need that?
  • ‘mL/min/mmHg’: Would need to be craeted as mL/min/mm[Hg]. You really have that?
  • ‘Liters/sec’: Would need to be created as L/h.
  • ‘g/cm2’: We have 9513 g/m2 “gram per square meter”. Would have to be created as g/cm2.
  • ‘g/mmol’: Are you sure this is not g/mmole?

We will roll this out, @Vojtech_Huser and @aostropolets are working on it. But we will still need the Source Concepts.

#9

So, the recent Vocabulary update contains some new UCUM concepts:

concept_id concept_name concept_code
32695 attogram per cell ag/{cell}
32696 picomole per milligram pmol/mg
32697 dalton Da
32698 kilodalton kDa
32699 milliliter per minute per millimeter mercury column mL/min/mm[Hg]
32700 liter per second L/s
32701 gram per square centimeter g/cm2
32702 gram per millimole g/mmol
32703 dyne-second per centimeter to the fifth power dyn.sec/cm5
32704 millimeter mercury column-minute per liter mm[Hg].min/L
32705 wood unit [wood’U]
32706 ten thousand per microliter 10*4/uL
32707 nanogram of fibrinogen equivalent unit per milliliter ng{FEU}/mL
2 Likes
#10

Hello!
We need to create a new concept for
‘L/min/m2’ with concept_name Liter per minute per square meter
The unit for Cardiac Index measurement, used by critical care specialists.
what do you think about it?

#11

@Vlad_Korsik:

If you have data about cardiac index you need the unit. We will create all necessary units. Will put it in the backlog.

#12

Hello! We need new concept for ‘teragenome copies/ml’. Could you please add it?

#13

@nzvyagina What tests or target_concept_ids are associated with this unit?

Cannot find any relevant explanation on ‘teragenome’ or why not just use 8799 copies per milliliter.

#14

@Alexdavv
25836-8 - HIV 1 RNA [#/volume] (viral load) in Unspecified specimen by NAA with probe detection
38349-7 - Herpes virus 6 DNA [#/volume] (viral load) in Unspecified specimen by NAA with probe detection
23869-1 - Hepatitis B virus DNA [Mass/volume] (viral load) in Serum by Probe
29495-9 - Herpes virus 6 DNA [Presence] in Unspecified specimen by NAA with probe detection

#15

You will be really ok with 8799 copies per milliliter.

#16

@nzvyagina
Sorry, my fault. Didn’t recognize tera as 10^12 prefix.

Need to add 10*12.{copies}/mL.
Or general 10*12/mL will be better, @Christian_Reich?

#17

Hi all, @Alexdavv why it’s need to create new concept instead of use conversion_factor with standard UCUM concept 10*12/L ?

#18

I suppose the idea of conversion is not to convert sporadic test/unit combinations when we simply haven’t created the proper unit for the figures in source. It’s about having all the units for source data and then convert the figures in ETL in automated way.

#19

The former, since we already have 10*3.{copies}/mL. Let’s stay consistent. And while you are at it also add 10*6.{copies}/mL.

#20

@Vlad_Korsik @nzvyagina Here you go:

concept_id concept_name concept_code
32708 trillion copies per milliliter 10*12.{copies}/mL
32709 million copies per milliliter 10*6.{copies}/mL
32710 liter per minute per square meter L/min/m2

Let’s send all further UNIT requests to this thread.

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