Wikidata:Property proposal/reference value

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reference value[edit]

Originally proposed at Wikidata:Property proposal/Natural science

Done: reference value (P5446) (Talk and documentation)

Description	value or range of values for a medical test, used to evaluate whether the results of the test are normal or not
Represents	reference range (Q1626599)
Data type	Item
Domain	biomedical measurand type (Q42014143)
Allowed values	"reference range as qualifier", "one-sided cutoff value as qualifier", "equivocal interval as qualifier" (dummy items, not yet created)
Example	red blood cell count (Q48632255) → 〈reference range as qualifier〉 applies to part (P518) man (Q8441) 〈lower limit〉 4.3 x10^12/L 〈upper limit〉 5.9 x10^12/L FEV1/FVC ratio (Q1988796) → 〈one-sided cutoff value as qualifier〉〈lower limit〉 70% 〈c-ANCA concentration (in serum)〉 → 〈equivocal interval as qualifier〉〈lower limit〉 2.0 IU/mL 〈upper limit〉 3.0 IU/mL
Source	w:en:Reference ranges for blood tests, w:en:Clinical urine tests, etc.

lower limit[edit]

Originally proposed at Wikidata:Property proposal/Natural science

Done: lower limit (P5447) (Talk and documentation)

Description	lower limit of a range or an interval; (qualifier) used with a dummy value which specifies the type of the range or interval
Data type	Quantity
Allowed values	any
Allowed units	any
Example	see above examples of the main property
Source	w:en:Reference ranges for blood tests, w:en:Clinical urine tests, etc.

upper limit[edit]

Originally proposed at Wikidata:Property proposal/Natural science

Done: upper limit (P5448) (Talk and documentation)

Description	upper limit of a range or an interval; (qualifier) used with a dummy value which specifies the type of the range or interval
Data type	Quantity
Allowed values	any
Allowed units	any
Example	see above examples of the main property
Source	w:en:Reference ranges for blood tests, w:en:Clinical urine tests, etc.

Motivation

A lot of medical tests (medical test (Q2671652)) are conducted on a daily basis, by physicians or other members of medical staff. Many of the tests have reference range (Q1626599), which is used to interpret the results of the test, but to my knowledge, no other open database provides structured data of reference values. This property will be useful to make a diagnosis support system.

Some reference values differ with genders, age, countries, or other factors. If the upper limit of the reference value and lower limit of it are separately stored, it is very inconvenient to use and to maintain. So I propose we adopt "dummy items and qualifiers" solution for this property, like the way used in union of (P2737). Okkn (talk) 12:14, 27 February 2018 (UTC)[reply]

Notified participants of WikiProject Medicine

Discussion

Comment@Okkn: Please provide an example of an item data type on the first property.Thanks David (talk) 15:12, 27 February 2018 (UTC)[reply]
- @ديفيد عادل وهبة خليل 2: Thank you for your comment. The subject of the first property is an instance of reference range (Q1626599), such as items of blood tests, blood pressure, respiratory function test, and so on. And the data type of the value of the first property is item, and allowed values are dummy items named something like "reference range as qualifier", "one-sided cutoff value as qualifier", and "equivocal interval as qualifier", but I haven't created them. --Okkn (talk) 17:12, 27 February 2018 (UTC)[reply]
- @ديفيد عادل وهبة خليل 2: Let me know if you have still any questions or need clarifications on these properties. Many thanks, --Okkn (talk) 05:58, 10 March 2018 (UTC)[reply]

Not done Lack of support. Micru (talk) 08:53, 11 April 2018 (UTC)[reply]

Although the discussion is stagnant, no one oppose this proposal. @Was a bee: If it's not too much trouble, could you please give me some comments? --Okkn (talk) 11:22, 11 April 2018 (UTC)[reply]

Comment @Okkn: This is interesting property. If such data exist in Wikidata, that's nice. But at the same time, I feel one difficulty. "Normal range" can vary depend on source by source. Although almost same range are shared by all sources, exact threshold would be blur. I have read that in medicine, sometimes outside of 2 standard deviation (2σ) is treated as abnormal. But average and distribution varies depend on samples (age, sex, race, etc). And pessimicstic docters/researchers would take narrower normal range, and optimistic take broader. How can we think about this kind of blurriness?--Was a bee (talk) 20:14, 12 April 2018 (UTC)[reply]
- @Was a bee: Thank you for commenting. That's a good point. I think we can have multiple different values for this property, and all of them should be sourced (difference sources sometimes say different range), and can be separated by using applies to part (P518) (age, sex, race, etc...) or statement supported by (P3680) (guideline, society, doctor, etc). We can also specify the determination method (P459) if it is available. --Okkn (talk) 03:38, 13 April 2018 (UTC)[reply]
  - @Okkn: OK. But it is difficult for me to imagine actual usage. So I made example with Template:Statement+. Which has 2 values, one for adult and one for child (values and references are randomly pick-uped. It doesn't have meaning). Is this usage right? Or if wrong, please fix that. --Was a bee (talk) 02:22, 14 April 2018 (UTC)[reply]

reference value

red blood cell count

edit

lower limit

3.0 x10^12/L

upper limit

7.0 x10^12/L

applies to part

adult man

1 reference

Viral infections in laboratory persnnel

add reference

red blood cell count

edit

lower limit

1.0 x10^12/L

upper limit

10.0 x10^12/L

applies to part

child

1 reference

Therapeutic approaches to primary and secondary brain tumours

add reference

add value

@Was a bee: I'm planning to use dummy values like list of values as qualifiers (Q23766486), which is used in union of (P2737) statements. Here are some examples:

In case of red blood cell count,

reference value

reference range as qualifier (dummy value)

edit

lower limit

4.35 x10^12/L

upper limit

5.55 x10^12/L

applies to part

statement supported by

Japanese Committee for Clinical Laboratory Standards

1 reference

JCCLS Common Reference Intervals (JCCLS共用基準範囲)

http://www.jccls.org/techreport/public_comment_201406.pdf

add reference

reference range as qualifier (dummy value)

edit

lower limit

3.86 x10^12/L

upper limit

4.92 x10^12/L

applies to part

statement supported by

Japanese Committee for Clinical Laboratory Standards

1 reference

JCCLS Common Reference Intervals (JCCLS共用基準範囲)

http://www.jccls.org/techreport/public_comment_201406.pdf

add reference

add value

In case of serum p-ANCA (Q7116884) concentration (item not yet created),

reference value

one-sided cutoff value as qualifier (dummy value)

edit

upper limit

3.5 IU/mL

2 references

http://www.southend.nhs.uk/pathology-handbook/test-directory/test-directory-m-index/mpo-pr3-antibodies/

http://uwb01.bml.co.jp/kensa/search/detail/3803903

add reference

equivocal interval as qualifier (dummy value)

edit

lower limit

3.5 IU/mL

upper limit

5.0 IU/mL

2 references

http://www.southend.nhs.uk/pathology-handbook/test-directory/test-directory-m-index/mpo-pr3-antibodies/

http://uwb01.bml.co.jp/kensa/search/detail/3803903

add reference

add value

--Okkn (talk) 13:45, 14 April 2018 (UTC)[reply]

@Okkn: Oh, I got it. That's clear and logical way to save data.

I have one remaining question. It is about names of "lower limit" and "upper limit". I've searched some max-min kind properties and I have found followings.

Compared with these property's name, "lower limit" and "upper limit" is very broader name (in other words, it seems that these properties looks usable at everywhere). So I think that it is better to...

1. Change description of "lower limit" and "upper limit" into "less restrictive" text. For example, change to "You can use this property everywhere".
2. Or change property name to more restrictive name. For example, change to "upper limit (reference value)" and "lower limit (reference value)"

What do you think? --Was a bee (talk) 06:54, 15 April 2018 (UTC)[reply]

@Was a bee: You are right. I changed the descriptions of the qualifiers to less restrictive texts. In the future if someone create a property that adopts the dummy value solution to store the range of values, these general qualifiers will be useful. Also, if the subjective item is about an interval, such as closed interval from −1 to 1 (Q21813730), I think these properties can be used as usual properties. --Okkn (talk) 10:51, 15 April 2018 (UTC)[reply]

@Okkn: OK. Then finally let me make sure. If properties are created, do you import certain amount of data? Because this is interesting but complex data. So if you don't import, I think no one won't import. Formerly, you imported very complex thousand of data, after properties which you proposed were created (Wikidata:Property proposal/recognition sequence). So I assume the same in this case. Am I right? --Was a bee (talk) 19:45, 16 April 2018 (UTC)[reply]

@Was a bee: Of course! I will use this property effectively. At first, I will import all of the JCCLS Common Reference Intervals (PDF) to show how to use this property. --Okkn (talk) 00:46, 17 April 2018 (UTC)[reply]

Thank you. Then all my questions have been solved. So I put here icon

Support. --Was a bee (talk) 20:15, 17 April 2018 (UTC)[reply]

@Was a bee: I appreciate your kind advice and support! --Okkn (talk) 05:51, 18 April 2018 (UTC)[reply]

@Okkn: I'm a bit torn about the use of dummy items for values - I think we should generally try to avoid that as much as we can. Did you know that quantities in Wikidata can have lower and upper bounds? This can be inserted in the UI by typing quantities such as "1,034.56±3.6". Don't you think that it would be more suitable? − Pintoch (talk) 07:57, 28 April 2018 (UTC)[reply]

@Pintoch: I know it, but I gave up on the idea of using the lower and upper bounds of quantity data type for two reasons. First, not all reference values have an ideal value and some are not normally distributed, so we can't express them as "true value ± tolerance" or "mean ± 2SD". Second, some medical tests have only one-sided cutoff value, so we can't use the native data type. The advantages of using dummy items include that we can store all types of reference values in one way. Does my answer make sense? --Okkn (talk) 09:51, 28 April 2018 (UTC)[reply]

Yes it makes sense, especially given the fact that it is not possible to give only one upper bound for instance (so your examples where there is only one bound could not be modeled in this way). Given that I am not entirely sure about this, and considering that only few people have commented here so far, I will hold off from creating this right now, just in case someone comes up with a better solution soon. − Pintoch (talk) 12:06, 28 April 2018 (UTC)[reply]

When I look at the values I think the miss a specification about the authority that defined the reference values. I think it would be great if we get clear about how the authority should be specificed before we create this property. ChristianKl ❪✉❫ 17:32, 6 May 2018 (UTC)[reply]
- References or statement supported by (P3680) are not enough to specify the authority? --Okkn (talk) 23:25, 9 May 2018 (UTC)[reply]

Notified participants of WikiProject Medicine Are there more opinions about how this property should work? ChristianKl ❪✉❫ 17:32, 6 May 2018 (UTC)[reply]

In considering the domain of these tests, should it not be made explicit the species the ranges apply to? The same test may be useful for humans, mice, or even C. elegans, but the expected range of results will generally differ.LeadSongDog (talk) 14:27, 7 May 2018 (UTC)[reply]
- I think the domain of items about medical concepts (diseases, medical findings, medical attributes) defaluts to human. If necessary, we should have different instances of biomedical measurand type (Q42014143) for each taxon, like the relations of genes (ex. HES1 (Q18027301) vs Hes1 (Q18251176)). --Okkn (talk) 23:25, 9 May 2018 (UTC)[reply]
@ChristianKl: It has passed two months since you pinged WikiProjecct Medicine, but there is no better ideas or opinions. I am convinced that this property is necessary for modeling medical attributes and medical findings, which are linked using evaluation of (P5134) and has evaluation (P5133). Could you please support this proposal or create it? Regards, --Okkn (talk) 22:04, 7 July 2018 (UTC)[reply]
Done all three.

@Okkn, Was a bee: who are interested in this
--- Jura 20:26, 8 July 2018 (UTC)[reply]

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