Saturday, January 27, 2018

Biomedical Concepts, LOINC and CDISC

Very recently, my colleagues from A3 Informatics published a very interesting article on "Understanding Biomedical Concepts", explaing how a "metadata repository" (MDR) with biomedical concepts (BCs) can help developing from the CRF

Unfortunately, most protocols are unprecise in what exactly should be measured. Even our "CDISC Therapeutic Area Guides" (TAUGs) suffer from the same problem. Here is an extract of the "TAUG-Diabetes" which can be downloaded from the CDISC website:

It listens a number of relevant tests, but does not describe them in detail at all. So it leaves it open to the sponsors, CRF developers or in the worse case, to the site to decide what test exactly will be performed. This means that when the FDA wants to compare the results from ten diabetes studies, it might find twenty different ways of measuring e.g. triglycerides, or even worse, find values that originate from different tests but received the same values for LBTESTCD, LBCAT, LBMETHOD in the SDTM. So for FDA reviewers, it looks as the triglycerides measurement from study A is identical to that of study D, although this is not the case at all. The reason is that the combination of LBTESTCD, LBCAT, LBSPEC and LBMETHOD does NOT uniquely describe a laboratory test.

So, I started annotating the TAUG-Diabetes, or at least tried starting. Here are some first results, from page 20: "Lipid Panel":
  • Amylase/Serum: LOINC 1798-8: Amylase [Enzymatic activity/volume] in Serum or Plasma
  • Triglycerides, Serum,Plasma: LOINC 2571-8: Triglyceride [Mass/volume] in Serum or Plasma
  • Total Cholesterol, Serum, Plasma: LOINC 2093-3: Cholesterol [Mass/volume] in Serum or Plasma
and so on. I did not try to annotate everything, that is something that the TAUG development team, with a much better use case knowledge, should have done (they didn').
When it is about lab tests, using LOINC coding is most appropriate. Therefore, it is very surprising that the word "LOINC" does even not appear in the TAUG-Diabetes.
Also remark that such an annotation exercise does not always lead to a single test  (at the contrary). For example for "glucose in serum, plasma", leads to 645 (!) different tests!.
On page 21 of the TAUG-Diabetes, table "Kidney function", a test "blood urea nitrogen" is listed, for which one can find 11 different tests in LOINC:

which will mostly obtain the same combination of "identifying variables values" in SDTM, suggesting the results come from exactly the same test although this may not be true.

Coming back to the Biomedical Concepts (BC). The more I think about it, the more I get convinced that LOINC codes are just implementations of BCs.
The typical example that is given when explaining BCs is "diastolic blood pressure" as a "vital sign". Please see the A3 Informatics article for a picture.

The BC of "systolic blood pressure" consists of the test itself (CDISC coded SYSBP or NCI coded C25298 - the hyperlinks will lead you to the RESTful web services that you can use in your own applications), a body position (sitting, standing, suppine), and a unit (almost always millimeter mercury column), and the result is expressed as an integer or a floating point number.

Is this the complete picture? No, it isn't. "Systolic blood pressure" is one of the tests in a "blood pressure panel", which is part of the "vital signs test panel". In CDISC, the latter is an SDTM domain (VS), but for the middle part ("blood pressure panel") there is no CDISC term as far as I know.

When using LOINC, each of these can be assigned a LOINC code, with the remark that LOINC codes are "pre-coordinated". So you will find a LOINC code for each of the combination of parts of the BC that make sense. SDTM-CT is mostly "post-coordinated", meaning that you take the parts and then assemble them using LBTESTCD (which is not the test code, but essentially the code for the analyte or compound that is measured), LBSPEC (specimen, e.g. "blood", "serum", "urine", ...), LBMETHOD (e.g. "dip stick") etc., and combine these in a record AFTER (therefore "post") you did the test. This post-coordination requires extensive validation in order to find out whether the combination makes sense, whereas you know in advance that the combination makes sense when you use a pre-coordinated code. For example, it does not make sense in SDTM to combine test code "height" with position "sitting", and you will need to write software to check this. In LOINC, you just won't find a code for "body height, sitting".

The more I think about it, the more I get convinced that LOINC codes are "implementations" of BCs. For example, if you take the BC "systolic blood pressure", and select "sitting" for the position, and that you want a number as an outcome ("quantitative measurement), this will lead you to LOINC code

8459-0 (Systolic blood pressure--sitting, quantitative).
BUT, you can also easily find out that this test is a member of the test "blood pressure panel" with LOINC code 35094-2:

but is also is a member of  the panel "Orthostatic blood pressure panel" (LOINC code 34553-8):

which additionally contains 3 "types" of heart rate.

and all of these are "vital signs measurements" (LOINC code 29274-8). Other such "panels" are "Vital signs, weight & height panel" (LOINC Code 34565-2) and "Vital signs, weight, height, head circumference, oxygen saturation & BMI panel" (LOINC Code 85353-1), each of these forming a tree structure. For example for
"Vital signs, weight & height panel" (LOINC Code 34565-2): 

where it is interesting to see that this tree structure also contains "Body position with respect to gravity" (LOINC code 8361-8) with possible values "standing", "sitting" and "lying":

And here we see that even LOINC is not perfect or complete: it does not differentiate between "supine" (lying horizontally with the face and torso facing up) and "prone" (face and torso down), although we do find a (pre-coordinated) term for "systolic blood pressure, supine" (8461-6): I did however not find a LOINC code for "systolic blood pressure, prone", which may be related to the fact that it seems that it does not make a difference for the value itself. When I then looked back to the picture of the A3 Informatics arcticle, I found that it lists "supine", but it doesn't list "prone". However, in the CDISC "VS Codetable", the combination "systolic blood pressure" with "prone" is listed as a valid combination. Something to discuss when we develop and coordinate BCs...

Now, is our BC picture for "systolic blood pressure" perfect? Not at all!
It does not account for tests like "maximum systolic blood pressure in a time period of 24 hours" or "mean systolic blood pressure in 10 hours". These kind of tests cannot be handled by CDISC controlled terminology at all! That such tests are important was recently discussed during the development of the "TAUG-Ebola" where "maximum body temperature within 24 hours" is a very important indicator. But CDISC-SDTM and CDISC-CT could not find a way to represent this test in SDTM! The same applies for ebola to "highest pulse in 24 hours".
So for our systolic blood pressure BC, we still have add information about things that have to do with timing. And this is again where LOINC helps us enormously, as one of the "dimensions" of the LOINC system is the "time aspect". For an "ordinary" systolic blood pressure, the value for the "time aspect" is "Pt" ("point in time). But we also find many other systolic blood pressure tests where this value is not "Pt" (or otherwise said: "now"):

and a number more ...
Similarly, we find different tests with different values for the "time aspect" for "body temperature", "pulse", but also for "glucose in urine", where a very important one "Glucose [Mass/volume] in 24 hour Urine" (LOINC Code 21305-8) is again not well covered by CDISC-CT and SDTM (SDTM suggests to do something with adding "end of collection" to "start of collection" (see further on).

Ready? Looks like ... But how do we state "high systolic blood pressure"? This may be of interest e.g. when the patient was asked "did you already have a high blood pressure five years ago?" and there is no possibility to find out the exact numbers. Also for this, LOINC has codes, for example for the question "Do you have hight blood pressure?", the LOINC code is 64496-3

We made some statements about relations between LOINC codes. How can you find out about these? You can of course start browsing through the "LOINC details" pages and follow links, but a better way is probably to use to write an application using the UMLS RESTful web services of the National Library of Medicine, and filter the results on LOINC as the coding system: the UMLS tries to describe relations between ALL possible coding systems in the medical world (including CDISC-CT). One of the students at the university is currently developing an interactive graphical user interface to build such "networks". This GUI will e.g. allow to filter on LOINC and SNOMED-CT, so that you can also include the SNOMED-CT terms and relationships.

If we look at the different "6 dimensions" of LOINC, the more I get convinced that for the case of vital signs and laboratory tests, these six dimensions form the "ingredients" of the BCs for these domains. For other domains, other coding systems may be suitable. For examples for domains about microorganism, the NCBI coding and taxonomy is probably very suitable. I haven't looked into this however yet. For many other domains, SNOMED-CT is probably very suitable.
And then saying that SNOMED-CT is not used at all in SDTM or CDISC anyway, except for a few parameters in the "trial summary" domain. 

How does this fit with SDTM? It does not well.
For laboratory tests, we already know for a longer time that the "identifying variables" (LBTESTCD/LBTEST, LBSPEC, LBMETHOD, ...) do not uniquely identify lab tests. For "24h urine", the SDTM-IG states that that "the start date/time of the collection goes into LBDTC and the end date/time of collection goes into LBENDTC", which at first glance seems OK. However, when the data is coming from an EHR or from the hospital information (HIS) system, the exact "start of collection" and "end of collection" times will often not be known, and the sponsor will probably (need to) derive LBENDTC by simply adding 24 hours to the collection date/time? You can already guess where this leads to when it is known that it was "24 urine" but only the start collection (or only end collection) date was know with no time. This is what we call "imputation".
In vital signs it is even worse, as has been shown by the "Ebola" case "maximum temperature in 24 hours", which cannot be modeled in VS at all.

So essentially, when the LOINC code is known (from the lab itself or as it was predefined) then there is no reason at all to populate --TESTCD, --SPEC, --METHOD (and --POS in the case of VS), as it is all in the code yet. Even worse, "deriving" these variables may and will lead to confusion. Therefore, in the case the data e.g. come from EHRs, we should use alternative SDTM domains that are suited for EHR or other systems where a precoordinated code is available. For LB, I have made a proposal for such a domain already 3 years ago, which allows to be used both by the pre-coordinated case as well as for the post-coordinated use case. It is a proposal that needs to be adapted for the more general case, also allowing more flexibility in SDTM. For example, if an exact code for a test (whatever the domain is), one essentially only needs to provide three or four values, the code, the code system, the value and the unit. Sometimes additional variables will needed to be added, but whether it is really needed essentially depends on the code system. For example when a LOINC code is used, there is no need at all to provide a categorized "specimen" or "method". But these may be necessary when an NCBI code is used for the microorganism that is tested. What kind of information needs to be added additionally to the code itself is something we need to investigate for each domain (with "we" I essentially mean the SDTM teams).

This will also be a very nice exercise in order to try developing BCs for more complicated cases like for the microbiology domains MS and MB (using NCBI or SNOMED-CT coding) or MI (microcospic findings). In my opinion, CDISC should free resources by stopping developing of some "reinvention of the wheel" codelists and assign these to the development of BCs.

Friday, January 5, 2018

CDISC-CT 2017-12-22: PK Units

A few days ago, I reported about "more madness" in the newest CDISC controlled terminology (version 2017-12-22), especially regarding the addition of more CDISC lab test codes whereas LOINC coding is made mandatory by the FDA anyway. When I see this, I sometimes I ask myself who is the "better standardization organization", the FDA or us, CDISC?

Even the survey that CDISC did on LOINC (under the lead of the former CSO who blocked every progress) was shaped in such a way that it was mostly about the difficulties of LOINC adaption, rather than on any of the advantages and opportunities of the use of LOINC.

But today I want to discuss another part of the new controlled terminology. If you inspect the "changes" file, you will notice that 235 "PK units of measure" have been added, bringing the number of CDISC "PK Units" to a total of 528.
This is crazy! I will explain you why.

Units for PK (pharmacokinetics) usually consist of a relative high number of parts. An example is "g/mL/(mg/kg/day)" (gram per milliliter per (milligram per kilogram per day)). CDISC publishes these "units" as a list, and not as a system (as UCUM does). Taking into account that any of these parts can vary enormously in magnitude (for e.g. the first part from nanogram to kilogram), you can already imagine the number of possible combinations which need to be added to the "list" to come to complete coverage. So, in principle, this list may and will grow to almost infinity. UCUM however is a "system" where any possible combination can be tested on its validity, e.g. using the NLM RESTful web services and website as well as our RESTful web services. UCUM also has the additional advantage that conversions can completely be automated, e.g. also using RESTful web services.

So, what I did was to add the UCUM notation for each of the newly published CDISC "unit". If you want a copy of the file, please just send me an e-mail. We will also soon add these UCUM notations to our web service to find the UCUM notation of any CDISC "unit".

Why does CDISC continue "lists" of units that "must" grow into infinity and can never be complete? Why doesn't it allow UCUM notation, which is used by 99% of the medical world, whereas CDISC "units" is used by less than 1% of the world? "Not invented here"?

A few arguments I have heard or found in the past:

  • "UCUM expressions, in order to support computability, represent familiar units in unfamiliar ways, with curly brackets and other symbols" (CDISC CT team - see image above).
    When I inspect the UCUM notation I assigned to the new "PK units" however, I see nothing "unfamiliar" and even if that would be the case, the advantages (like automation of unit conversions) far outweigh any disadvantages. Furthermore, we must take into account that implementors must also learn the CDISC "units" in addition to their own notation, so this argument is nonsense. Why should people be forced to learn a notation that is not used in the healthcare world anyway? UCUM however is extremely popular in the healthcare world.
  • "The CDISC notation is very similar and strongly overlaps with UCUM notation. So there is no problem". I checked for this case (PK units) and found that for only about 80 of the 235 "PK units", so about one third, the CDISC "unit" and UCUM notation are identical.
  • "UCUM allows some alternative representations, like l or L for liter. For aggregators and others who want to have a single expression, this is not ideal". This is really nonsense! Any computer system can easily be teached that "1L" = "1l". It can even be automated, using a RESTful web service. For example, try for yourself:
UCUM also allows to automate unit conversions easily, as it is a "system" and any UCUM notation can be reduced to a set of base units. For example, try to find out how many "millimeter mercury" corresponds to 25 "pounds per square inch". Can you find the conversion factor from what has been published by the CDISC-CT team?
Using UCUM, this is "piece of cake", as both can easily be reduced to the base units ("g.s-2.m-1" in this case). Using UCUM, the anwer can easily be found using one of the RESTful web services available (and "YES", you can also use these from within your SAS programs). Try it yourself:[psi]/to/mm[Hg]

One of the things I did is the following: I tried to find out for how many of the 235 "PK units" can be converted into one another, using the UCUM notation and using our RESTful web services. Using CDISC notation, this number is zero, as CDISC-CT does not provide any information at all about what the "units" mean and how they relate to other units.

So I wrote a "quick-and-dirty" Java program,  using the aforementioned "UCUM RESTful web services", and found that of the 54,990 possible combinations (235x234), there is a conversion factor for 1158 of them, meaning that the two units represent the same property. For a good number of them, we found that the conversion factor is a power of 10, meaning that they just differ in the order of magnitude (just like "cm" and "m"). For example:

However, when using the CDISC-CT term, there is no way at all to find out what that conversion factor is (remark that in CDISC-CT, the notation "day" is used instead of the internationally recognized notation "d"), or that two "units" refer to the same property.

We also found a number of related terms for which the conversion factor is exactly 1.0. For example:

or: two ways of writing the same unit, which is forbidden by the SDTM-IG.
"Wait a minute" you will say, "these pair members correspond to different properties!".
And yes, you are right, but to what properties?

For example, for the first entry in the above list (here in CDISC notation): "day*g/mL/g" and "mg/mL/(mg/day)" have a conversion factor of 1 (difficult to find out when using CDISC notation) but do indeed correspond to different properties, the first being something like "day times gram (of what?) per milliter (of what?) per gram (of what?). Using CDISC notation, you will never find out about the "what?". Using UCUM, you can easily do so using "annotations".
For example (fictitious - I am not a specialist in pharmacokinetics): "d.g{analyteXYZ}/mL{blood}/g{drug}", explaining very well what the unit is about, without endangering applying conversions - the annotations in curly brackets can be taken into account automatically. These "annotations" is exactly what the CDISC-CT team does not like at all: "... represent familiar units in unfamiliar ways, with curly brackets and other symbols. This is off-putting to some users." (sic). That the annotations enormously help, was even recognized by LOINC, where such annotations have been standardized. E.g.:

showing that LOINC standardized on annotations like "RBCs" (red blood count), "titer", "creat" (creatinine) and many others. Of the over 80,000 LOINC codes, there are over 7,600 having such an annotation in the "preferred UCUM unit", which is almost 10%.

So, rather than extending an ever growing list of "units" over and over again, the CDISC-CT team should better, in close cooperation with LOINC (the Regenstrief Institute), concentrate on standardizing such annotations for use in clinical research.
As LOINC coding for lab tests in SDTM is required by the FDA anyway, use of UCUM notation should be allowed immediately, the CDISC-CT team should stop generating lists of units, and should work on "UCUM annotations" for use in clinical research instead.
This should bring the usability of SDTM to a much higher level than it has today.