Une ontologie de spécification de laboratoire
Jean-François Ethier
Paul Fabry
An ontology of laboratory test specifications
Adrien Barton
The inverse relationship of directs.
directed by
The relationship between a directive information entity and the process it directs.
directs
has minimal value
has maximal value
x
1
'accession-id #150' in 'accession-id #150 whole blood 3 ml'
A centrally registered identifier that denotes a particular specimen on which a laboratory test is intended to be executed or has already been executed.
TODO
identification d'échantillon d'examen de laboratoire
laboratory test specimen ID
'whole blood' in 'accession-id #150 whole blood 3 ml'
An information content entity about the type of the specimen to be used for some laboratory tests.
Une donnée qui est supposée être une proposition vraie à propos du type de l'échantillon pour lequel des tests ont été prescrits.
laboratory test specimen type specification
spécification de type d'échantillon
A data item intended to be a truthful statement about the sampling method used to extract a sample from an entity.
Une donnée supposée être une proposition vraie à propos de la méthode d'échantillonnage utilisée pour extraire un échantillon particulier d'une entité.
sampling method specification
spécification de méthode échantillonnage
An information content entity that encompasses all relevant information pertaining to a given laboratory test prescription.
TODO
information de compte-rendu de test de laboratoire
prescribed laboratory test complete reporting information
A health care prescription specifying the realization of one or several laboratory test(s).
laboratory test prescription
prescription de test de laboratoire
An information content entity which reports on some aspect of a particular laboratory test.
Une entité de contenu informationnel qui documente un ou plusieurs aspects d'un certain test de laboratoire.
information de résultat pour un test de laboratoire (WIP)
laboratory test reporting information
'serum sodium 140 mmol/L, 2018/08/14'
(à revoir) Une partie d'un document d'analyse de laboratoire qui spécifie le résultat d'un test spécifique qui a été soit prescrit par une prescription de test de laboratoire, soit réalisé comme conséquence d'une prescription de test de laboratoire.
A laboratory test reporting item that includes the result of the laboratory test.
laboratory test result item
Example 1:
'CBC:
- WBC 12.1 10^9/L
- RBC 5.2 10^12/L
[...]'
in a report on tests directed by a complete blood count prescription.
Example 2:
'serum sodium in progress'
A laboratory test reporting information which reports on the test(s) directed by one laboratory test directive item.
Une partie d'un document d'analyse de laboratoire qui spécifie des résultats des tests.
A laboratory test reporting group does not necessarily provide the reporting information concerning a laboratory test directive item in a prescription - the directive item can also be specified e.g. in a research protocol.
A laboratory test reporting group can, but doesn't have to, include a laboratory test reporting item, as in 'CBC in progress' (which is not a laboratory test reporting item, because it reports on several tests, not just one).
groupement de résultats pour un test de laboratoire
laboratory test reporting group
A value specification that is the the lower bound or the upper bound of a range.
bound
valeur limite
1
1
1
'serum sodium in progress, 2018/07/25'
'serum sodium 140 mmol/L, 2018/08/14'
'blood group O, 2018/07/12 12:34 pm'
A laboratory test reporting information that is part of a laboratory test reporting group, that is about a laboratory test, and that mentions which characteristic of a specimen this test was supposed to assess, and a time at which this information was valid.
laboratory test reporting item
'in progress' in 'FSC, in progress, 2018/07/25'
'resulted' in 'blood group O, resulted, 2018/07/12 12:34 pm'
'validated' in 'serum sodium 140 mmol/L, validated, 2018/07/28'
A laboratory test reporting information that specifies the status of a laboratory test or a group of laboratory tests.
laboratory test status specification
'serum sodium concentration' in 'serum sodium concentration 140 mmol/L, validated, 2018/07/28'
An information content entity that specifies a particular characteristic of a specimen or a class of characteristics of specimens.
specimen characteristic specification
A document reporting on a laboratory test.
laboratory test report document
1
All tests (white blood cells, red blood cells, etc.) realized when executing a prescription of CBC for John Smith on 2018/07/28.
A health care process assay that is the mereological sum of laboratory test(s) that are directed by a single prescription directive item.
directed laboratory test group
'complete blood count'
'serum sodium'
An action specification that directs one or several laboratory tests and such that none of its proper parts directs some but not all of those laboratory tests.
A laboratory test directive item can direct several tests - consider e.g. 'CBC' (complete blood count), which directs more than 20 tests (red blood cells, white blood cells, hemoglobin, etc.)
Many laboratory test directive items are parts of a prescription, but not all - consider e.g. an instruction directing a laboratory test as part of a research study.
laboratory test directive item
'2018/08/22' in 'CBC on 2018/08/22'
An information content entity that specifies at what time a laboratory test should start.
Not all laboratory test prescription items specify a start time. It is sometimes implicit when it is to be done.
laboratory test start time specification
A measurement assay that has as input a specimen derived from an organism and that aims as having as output a data item that is about an entity related to the specimen.
Not all laboratory tests are directed by a prescription, e.g. a laboratory test executed as part of a research project, or an additional test realized by a laboratory technician in case a first prescribed laboratory test led to an abnormal result.
A laboratory test is directed by some instruction that is part of a plan specification with the objective to assess some entity related to a specimen (e.g. one of its quality) specified by a specimen characteristic specification. However, a laboratory test can be interrupted without leading to a completed laboratory test.
laboratory test
A completed laboratory test that has as specified output a laboratory finding.
A completed laboratory test that involved a problem of calibration can lead to some result, but this result does not support an inference about a quality of the patient, and therefore is not a laboratory finding.
validated laboratory test
A representation of an entity related to a specimen that is the output of a laboratory test.
A laboratory result is not necessarily a laboratory finding, as it cannot always support an inference to an assertion about some quality of the patient. For example, the serum sodium result of a miscalibrated machine is not a laboratory finding. Also, a laboratory result by automatic detection "70.10^3 /microliter" for platelets might be falsely low due to platelets clumping.
However, a laboratory finding is always a laboratory result.
laboratory result
'2018/07/25, 12:34 pm' in a laboratory test reporting information 'serum sodium in progress, 2018/07/25, 12:34 pm'
A laboratory test reporting information that specifies a time at which a laboratory test reporting item was valid.
This time specification does not refer to the time when a given lab document was generated, but rather the moment at which information from the laboratory test process was created as it unfolded.
laboratory test reporting item time specification
'to follow rhumatoid arthritis' on a prescription for a test of sedimentation rate
'to exclude pulmonary embolism' on a guideline document about d-dimer
A health care objective specification that specifies why a laboratory test should be performed.
laboratory test objective specification
A laboratory test objective specification that is a part of a laboratory test prescription.
prescription of laboratory test objective specification
1
'accession-id #150 whole blood 3 ml'
An information content entity that denotes a particular specimen on which a laboratory test is intended to be executed or has already been executed.
Une entité de contenu informationnel qui est à propos d'une entité biologique particulière ou d'une classe d'entité biologique sur laquelle quelqu'un a l'intention de prendre une mesure ou sur laquelle une mesure a déjà été prise.
laboratory test specimen specification
A generically dependent continuant that specifies a lower bound and an upper bound.
It can also specify whether each bound is included or not in the interval.
range
1
1
A range of values asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population.
Definition adapted from OGMS' definition for "normal value". "Normal value" and "normal range" should be coordinated.
laboratory test result normal range
A bound that is the lower bound of a range.
lower bound
A bound that is the upper bound of a range.
upper bound
A lower bound value of a laboratory test result normal range.
laboratory test result normal range lower bound
An upper bound value of a laboratory test result normal range.
laboratory test result normal range upper bound
'CBC, INR q2h start 2h post-op for 24h'
composed by the items 'CBC' and 'INR' and a starting condition statement '2h post-op', a continuing condition statement 'for 24h' and a testing condition statement 'q2h'
'CBC' that is composed by a single laboratory test directive item.
An action specification that has as parts one or several laboratory test directive items, as well as possibly some statements specifying a starting condition, a stopping condiiton and a testing condition.
laboratory test directive item group
A laboratory test result normal range that is reported in a laboratory test reporting item.
reported laboratory test result normal range
'140 g/L' as a result of hemgolobin concentration
A laboratory result that has a scalar value specification.
scalar laboratory result
'[20,80] APL units' as a result of anticardiolipin antibody
A laboratory result that is given as a range.
range laboratory result
'negative' as a result of HIV test
A laboratory result that is given as a textual entity.
textual laboratory result
[0, 100000] ppm of Hg
[-10 V,+30 V[
A range of values asserted as possible valid values by the testing lab or the kit manufacturer.
It is about all laboratory results from all laboratory tests of a given kind.
laboratory test definition range
result range
1
1
1
1
A range value specification that specifies a lower and an upper bound and wether each bound is included or excluded.
fully specified range value specification
- " [ " in "]1,3["
- "] " "]1,3["
- "strictly" in "lower or equal to 6 and strictly greater than 0"
- "or equal" in "lower or equal to 6 and strictly greater than 0"
An information content entity that specifies whether a cutoff value should be included or excluded in a range.
range inclusion specification
A range inclusion specification written with interval notation. There are only two individuals.
interval-notation range inclusion specification
A range inclusion specification for the lower bound of a range.
lower bound inclusion specification
A lower bound inclusion specification specifying the lower bound is included.
included lower bound inclusion specification
A lower bound inclusion specification specifying the lower bound is excluded.
excluded lower bound inclusion specification
A range inclusion specification for the upper bound of a range.
upper bound inclusion specification
An upper bound inclusion specification specifying the upper bound is included.
included upper bound inclusion specification
An upper bound inclusion specification specifying the upper bound is excluded.
excluded upper bound inclusion specification
'[0,10[ ml/m2' is the derived normalized result of laboratory result: '<10 ml/m2'.
A range laboratory result that is represented in a normalized way and that is the result of the transformation of an original laboratory result.
derived normalized range laboratory result
1
closed range laboratory result
1
1
1
1
scalar range
1
1
derived normalized closed range laboratory result
derived normalized scalar laboratory result
derived normalized textual laboratory result
A data item that was generated on the basis of a calculation.
The definition is based on OBI's definition of 'predicted data item'. However, a data item that is generated on the basis of a calculation doesn't have to be the result of a prediction; it can be the result of an estimation.
for example: the estimated glomerular filtration rate (eGFR)
calculated data item
1
1
1
1
1
' < 120 mmol'
'[15, 20['
'3.5 to 10.5 billion/L'
A value specification that has as part at least a lower bound or an upper bound.
range value specification
1
1
closed range value specification
1
6%
0.08
154 ppm
A value specification that specifies a ratio value, without any unit or with a dimensionless unit.
ratio value specification
'eGFR: 65 ml/min/1.73 m2'
A calculated data item that is produced by a calculation process that has as input a laboratory result.
laboratory result-based calculated data item
'6%' as a result for HbA1C measurement
'0.055' as a result for HbA1C measurement
'50%' as a result for hematocrit measurement on a complete blood count
A laboratory result that is given as a ratio.
ratio laboratory result
range calculated data item
ratio calculated data item
scalar calculated data item
laboratory result-based scalar calculated data item
laboratory result-based ratio calculated data item
laboratory result-based range calculated data item
derived normalized laboratory result-based range calculated data item
laboratory test specification
'12345' to refer to a serum creatinin test
laboratory test identifier
'serum creatinin test'
laboratory test name
1
laboratory test reporting item identifier
Can "a quality" be a mereological sum of qualities?
For example, if a finding is "A+", which represents (at least) two qualities of the specimen, does it represent one quality that would be the mereological sume of those qualities?
Note that a laboratory finding does not necessarily represent only a quality of a specimen. It can also represent e.g. a temporal duration (e.g. duration of coagulation).
Therefore, we suggest changing the definition to "A representation of an entity related to a specimen that is the output of a laboratory test and that can support an inference to an assertion about some specifically dependent continuant of the patient."
The output is not always about a quality of the specimen (it can be e.g. about a temporal duration when assessing the coagulation speed of a blood specimen).
A completed laboratory result might have as output several laboratory results such as a first nonvalidated result directly from the machine 'serum sodium 140 mmol/L' followed by a second validated result 'serum sodium 140 mmol/L'.
1
1
1
1
1
1
Note that a laboratory finding does not necessarily represent only a quality of a specimen. It can also represent e.g. a temporal duration (e.g. duration of coagulation).
Therefore, we suggest changing the definition to "A value for an entity reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population."
We suggest renaming this entity "lab report normal value", as "normal values" can appear in a variety of contexts.
It seems that "normal value" should be classified under "value specification".
To be changed using value specifications.