Changes for page Lab result file - SIKB0101 v14

Last modified by Robin Huisman on 2025/02/27 09:44

From version < 36.1 >

edited by Robin Huisman
on 2024/07/31 23:10

To version < 36.3 >

edited by Robin Huisman
on 2024/07/31 23:42

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--Lab result file - SIKB version 14
++Lab result file - SIKB0101 v14

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@@ -1,13 +1,14 @@
  = Exporting lab results to TerraIndex for a customer =
--The file that is used for the examples: [[Example file>>attach:LabResults.xml]]
++Returning the labresults to the client, that requested the analysis on samples.
--{{toc/}}
++(% class="box infomessage" %)
++(((
++More information about SIKB0101 can be found here: [[https:~~/~~/www.sikb.nl/datastandaarden/sikb0101-bodembeheer>>url:https://www.sikb.nl/datastandaarden/sikb0101-bodembeheer]]
++)))
--{{warning}}
--SIKB Version 9 is obsolete, and replaced with version 13 or version 14. Latest version can be found here: [[https:~~/~~/www.sikb.nl/datastandaarden/sikb0101-bodembeheer>>url:https://www.sikb.nl/datastandaarden/sikb0101-bodembeheer]]
--{{/warning}}
++
  == What is a Lab result file? ==
  A lab result file is an XML file contains all the lab results. The results are mapped tot their analyses samples. A lab result will be matched to the corresponding analyses sample based on the: “Labassignment Guid/SIKB-ID, projectCode, AnalysisSample Guid/SIKB-ID”
@@ -17,56 +17,48 @@
  **XSD**: Ask or SIKB Members can download from: [[https:~~/~~/www.sikb.nl/datastandaarden/richtlijnen/sikb0101>>url:https://www.sikb.nl/datastandaarden/richtlijnen/sikb0101]]
--**Controle XSLT**:
++**Controle XSLT**: [[attach:Labresult_Controle.xsl||rel=" noopener noreferrer" target="_blank"]]
  **Domaintable files**: [[immetingen lookup v14.8.0.xml>>url:https://wiki.terraindex.com/bin/download/Implementation%20documentation/Setting%20up%20Lab%20communication%20by%20REST%20services%20with%20TerraIndex/Lab%20assignment%20file/WebHome/immetingen%20lookup%20v14.8.0.xml?rev=1.2]]   [[imsikb0101 lookup v14.8.0.xml>>url:https://wiki.terraindex.com/bin/download/Implementation%20documentation/Setting%20up%20Lab%20communication%20by%20REST%20services%20with%20TerraIndex/Lab%20assignment%20file/WebHome/imsikb0101%20lookup%20v14.8.0.xml?rev=1.1]]
  extracted from: **[[https:~~/~~/codes.sikb.nl>>url:https://codes.sikb.nl/]] **
++{{toc/}}
++
++== Model Structure ==
++
  [[image:IMSIKB0101 - Labresults.png]]
--== File structure ==
++=== Metadata ===
  (% class="table-hover" %)
  |(% colspan="1" rowspan="1" %)**Attribute name**|(% colspan="1" rowspan="1" %)**Description**|(% colspan="1" rowspan="1" %)**Unit**
--|(% colspan="1" rowspan="1" %)**Versie**|(% colspan="1" rowspan="1" %)The SIKB version of the lab assignment. This must be: **9.0.0**|(% colspan="1" rowspan="1" %)string
--|(% colspan="1" rowspan="1" %)**Applicatiecode**|(% colspan="1" rowspan="1" %)This is the application code of your LIMS system that you will get from TerraIndex. Be careful this is not the same code as your laboratory number|(% colspan="1" rowspan="1" %)Integer
--|(% colspan="1" rowspan="1" %)**Datum**|(% colspan="1" rowspan="1" %)The date on which the lab result file was made|(% colspan="1" rowspan="1" %)(((
++|(% colspan="1" rowspan="1" %)**version**|(% colspan="1" rowspan="1" %)The SIKB version of the lab results file. This must be: **14.8.0 or 14.9.0**|(% colspan="1" rowspan="1" %)string
++|(% colspan="1" rowspan="1" %)**application**|(% colspan="1" rowspan="1" %)This is the application code of your LIMS system that you will get from TerraIndex. Be careful this is not the same code as your laboratory number. Your applicationcode can be requested of found here: [[https:~~/~~/codes.sikb.nl/tablet/domain-table-details/50be26c9-5e66-46c9-9373-9d402762876f>>https://codes.sikb.nl/tablet/domain-table-details/50be26c9-5e66-46c9-9373-9d402762876f]] |(% colspan="1" rowspan="1" %)Integer
++|(% colspan="1" rowspan="1" %)**reportDate**|(% colspan="1" rowspan="1" %)The date on which the lab result file was made|(% colspan="1" rowspan="1" %)(((
  date
  yyyy-mm-dd
  )))
--|(% colspan="1" rowspan="1" %)**Klantcode**|(% colspan="1" rowspan="1" %)This should be the customer code in the “//klantcode//” in the lab assignment|(% colspan="1" rowspan="1" %)string
--|(% colspan="1" rowspan="1" %)**Laboratorium**|(% colspan="1" rowspan="1" %)The number you get from TerraIndex. This needs to be the same as the laboratorium number in the lab delivery file|(% colspan="1" rowspan="1" %)integer
--|(% colspan="1" rowspan="1" %)**Taal**|(% colspan="1" rowspan="1" %)(((
--The language of the lab results this depends on the XSD used.
++|(% colspan="1" rowspan="1" %)**supplier**|(% colspan="1" rowspan="1" %)The number you get from TerraIndex. This needs to be the same as the laboratorium number in the lab delivery file. Your supplier code can be requested of found here: [[https:~~/~~/codes.sikb.nl/tablet/domain-table-details/dc2ad4df-f958-4146-aee8-31f8c2f1c74b>>https://codes.sikb.nl/tablet/domain-table-details/dc2ad4df-f958-4146-aee8-31f8c2f1c74b]]|(% colspan="1" rowspan="1" %)string
++|(% colspan="1" rowspan="1" %)**dataflow**|(% colspan="1" rowspan="1" %)Should be '1' in this case, what stands voor 'AnalysisResults'. Other option can be found here: [[https:~~/~~/codes.sikb.nl/tablet/domain-table-details/79365ded-f56a-4f10-ba45-16bac69752d9>>https://codes.sikb.nl/tablet/domain-table-details/79365ded-f56a-4f10-ba45-16bac69752d9]]|(% colspan="1" rowspan="1" %)integer
--dut = dutch
++===
++Labassignment ===
--eng = English
--)))|(% colspan="1" rowspan="1" %)string
--|(% colspan="1" rowspan="1" %)**Projectgegevens**|(% colspan="1" rowspan="1" %)This section contains all the result information|(% colspan="1" rowspan="1" %)-
++The labassignment is the same as in the labassignment file: [[Lab assignment file - SIKB0101 v14>>https://wiki.terraindex.com/bin/view/Implementation%20documentation/Setting%20up%20Lab%20communication%20by%20REST%20services%20with%20TerraIndex/Lab%20assignment%20file/#]]
--= Questions from Luca to Robin =
++With 3 differences:
--1. Do I need to add any other classes to the filestructure description apart from the ones below (those related to the IMMetingen::Result Class) ?
--1. uit de mail van Robin : "Je kunt de Labassignment pagina als basis gebruiken, en de extra klasses vanuit de Voorbeeld bestand LabResult aan toevoegen."
--11. De link naar een "LabResult" voorbeeld bestand wijst naar een directory. Daar staat wel een directory met naam "Example XML 14.8.01". maar die folder bevat niet 1 maar 4 verschillende "labresult_*" XMLs. Welke moet ik hebben? allemaal? en hoe moet ik afleiden welke klasses "extra" zijn? welke tool zou je aanbevelen om xml te lezen. ik heb er nog nooit mee gewerkt.
--1. Do i need to add screenshots of the xml classes as in the labassignment and labdelivery pages? if so, what software did you use?
--1. In Validation: ValidationScore. What are STOWA Protocols? is it Stichting Toegepast Onderzoek Waterbeheer?
--1. What to do with the domain tables refered to in the descriptions? Does it make sense to reference them? Should i translate the names of the domain tables or is that static? are they translated already? who manages these? is it SIKB stuff?
--1. in the section MeasureUncertainty > link to pdf file in description is invalid. What should it be?
--1. SIKB 14 Parameter result combinations> first sentence makes no sense to me. Please review so i can translate.
--1. What should i do with the sections from "Structure projectgegevens" to "What to exchange to store the right results?"? Is this a result of a copy paste and can they be discarded? If not, what classes do they refer to and where can i find the descriptions to be translated?
++* Status on the labassignment itself
++* Status on the labassignment.sample link
++* The labassignment Report number can be send in: LabAssignmentCertificate
--(% class="wikigeneratedid" %)
--~==== Added by luca: all Classes related to "IMMetingen::Results"
--==== MeasureResult ====
++=== Status ===
--
  |**Attribute Name**|**Description**
  |(((
  **numericValue** Measure
@@ -80,78 +80,55 @@
  Domain table: Value Processing Method
  )))
--|(((
--**qualityIndicatorType** GenericName
--)))|(((
--Quality Indicator/Judgement -> Detection limit, etc.
--Domain table: Quality Judgement
--)))
++=== LabAssignmentCertificate ===
--==== Accuracy ====
--
--
--|**Attribute Name**|**Description**|**Unit**
++|**Attribute Name**|**Description**
  |(((
--**recovery** Float
--)))|(((
--The part (percentage) of material that is recovered in an analysis.
--)))|Percentage [%]
++**numericValue** Measure
++)))|Numeric Value - the numerical value of the observation. When no unit for the measurement is known, the unit 'Dimensionless' should be used.
  |(((
--**spread** Float
--)))|Spread = the error measured (in %) in multiple repeated measurements of the same sample/situation (and by the same laboratory technician/measuring device).|Percentage [%]
--|(((
--**measurementUncertainty** Float
--)))|Measurement uncertainty = the total error in the analysis (in %), considering sample collection, variation in measuring equipment/lab technician, and repeated measurements. It practically represents the value indicating the uncertainty of the measurement result.|Percentage [%]
--|(((
--**zScore** Float
--)))|This is an optional value that indicates how the measurement value scores in relation to other techniques or laboratories. This could be from interlaboratory comparisons or comparisons between different measuring equipment.|
--|(((
--**drift** Float
--)))|This is the degree of sensor drift over time (in %/year). Sensors will age over time and experience more or less drift depending on the conditions. This drift can be quantified and depends partly on age. This is especially true for online sensors.|Percentage [%]
++**valueProcessingMethod** GenericName
++)))|(((
++Value Processing Method - a mathematical/statistical operation that is applied while the method of value determination/analysis standard remains unchanged.
--====   ====
++The operation can be applied to a series of measurement values with the same parameter (quantity/component or typing or taxon or object) or to a series of measurement values with the same analysis method that are summed up to a sum parameter.
--==== Validation ====
++Domain table: Value Processing Method
++)))
--This DataClass contains optional attributes and indicates which validation steps the measureResult (measurement value) has undergone.
++==== AnalyticResult (inherited from MeasureResult ====
  |**Attribute Name**|**Description**
  |(((
--**automatedControl** GenericName
++**numericValue** Measure
  )))|(((
--The first-line control is often an automated check of whether the measurement value is correct. It uses a domain table: ValidationSteps.
++Numeric Value - the numerical value of the observation. When no unit for the measurement is known, the unit 'Dimensionless' should be used.
--Various steps can be distinguished. For example, a check on hard/soft limits, ion balance, bandwidth, and dissolved not exceeding total analysis (chemistry) are part of the first-line control. The control can be approved or disapproved (see quality judgment). Different possible values are described in the domain table ValidationSteps. Example: pH of 78 and water temperature of 123 degrees Celsius are hard limits (not possible); pH=10.0 is a soft limit because the value is extremely high (but not impossible).
--
--Domain table: ValidationSteps
++Domaintable for Units: [[Eenheid>>https://codes.sikb.nl/tablet/domain-table-details/04f4f467-021b-4218-baa8-9742ed977c61]]
  )))
  |(((
--**expertControl** GenericName
++**valueProcessingMethod** GenericName
  )))|(((
--The second-line control (ExpertControl) is often a specialist check of whether the measurement value is correct. It also uses a domain table: ValidationSteps. Here, different steps can be distinguished as well. This analysis usually does not follow immediately after arrival but is performed periodically. Controls on correlation between measurement stations, history, correlations between parameters, and specialist expertise belong to the second-line control. The control can be approved or disapproved (see quality judgment). Different possible values are described in the domain table ValidationSteps.
++Value Processing Method - a mathematical/statistical operation that is applied while the method of value determination/analysis standard remains unchanged.
--Domain table: ValidationSteps
++The operation can be applied to a series of measurement values with the same parameter (quantity/component or typing or taxon or object) or to a series of measurement values with the same analysis method that are summed up to a sum parameter.
++\\Default the value '5' meaning 'Not available' can and should be used, besides leaving it empty.
++
++Domain table: [[Value Processing Method>>https://codes.sikb.nl/tablet/domain-table-details/a2310c26-065f-4aec-9440-74892ec77753]]
  )))
  |(((
--**validationScore** GenericName
++**qualityIndicatorType** GenericName
  )))|(((
--Score of the validation steps followed, according to the __**STOWA protocols**__. The attribute uses the domain table ValidationScore. The score value ranges from 0 to 5
++Quality Indicator/Judgement -> Detection limit, etc.
++\\Default the value '0' meaning 'Not available' can and should be used, besides leaving it empty.
++If there is a detectionlimit/reportinglimit, use: '4', meaning 'determenated with full detection limit'
--Domain table: ValidationScore
++Domain table: [[Quality Judgement>>https://codes.sikb.nl/tablet/domain-table-details/1e17d9e6-4e0e-4f88-8fe5-c71f6a7931db]]
  )))
--====   ====
--
--==== AnalyticResult ====
--
--
--The analyzed result of an observation, typically originating from a laboratory.
--
--
--|=**Attribute Name**|=**Description**
  |(((
  **limitSymbol** CharacterString
  )))|(((
@@ -166,6 +166,8 @@
 ) as a CData block: <![CDATA[<]]> or <![CDATA[>]]>
 ) as HTML code: '&amp; lt;' or '&amp; gt;'
++\\Default the value is leaving it empty.
++If there is a detectionlimit/reportinglimit, use: '<'
  )))
  |(((
  **alphanumericValue** CharacterString
@@ -173,64 +173,11 @@
  ====   ====
--==== MeasureUncertainty ====
--
--
--Measurement uncertainty in the result. This is the expanded measuring uncertainty as described in the document: [[http:~~/~~/www.nordicinnovation.net/nordtestfiler/tec537.pdf>>http://www.nordicinnovation.net/nordtestfiler/tec537.pdf]]
--
--
--|=**Attribute Name**|=**Description**
--|(((
--**distributionType** GenericName
--)))|(((
--The type of statistical distribution associated with the observation.
--
--Domain table: ProbabilityDistribution
--)))
--|(((
--**statisticalParameter** Measure
--)))|(((
--Parameters that determine the shape and size of the statistical distribution.
--
--Domain table: StatisticalParameter
--)))
--
  ====   ====
--==== DeterminationLimits ====
--
--
--|=**Attribute Name**|=**Description**
--|(((
--**detectionLimit** Measure
--)))|(((
--The smallest value of the measured content or the observed value of the parameter in a sample, which can still be determined with a certain reliability by the laboratory. Conventionally, this is the amount that corresponds to three times the standard deviation at that level (thus, relative standard deviation is 33%).
--
--
--The standard deviation is established under (intra-lab) reproducibility. Also known in English as 'LOD' (Limit of Detection). See also: [[Wikipedia on Detection Limit>>url:https://en.wikipedia.org/wiki/Detection_limit]]
--)))
--|(((
--**reportingLimit** Measure
--)))|The smallest value of the measured content or the observed value of the parameter in a sample, agreed upon with the client by the executing laboratory, which is reported to the client. The reporting limit is at least the detection limit and is sometimes specified in an accreditation scheme like AS3000.
--|(((
--**limitSymbolReferenceCode **GenericName
--)))|(((
--The threshold value that the limitSymbol of AnalyticResult refers to.
--
--Domain table: LimitSymbolReference
--)))
--|(((
--**quantitationLimit** Measure
--)))|The smallest value of the measured content or the observed value of the parameter in a sample, which can still be determined with a certain reliability by the laboratory. Conventionally, this is the amount that corresponds to ten times the standard deviation at that level (thus, relative standard deviation is 10%). Also known in English as 'LOQ' (Limit of Quantitation). At this value, the rate of 'false negatives' is less than 1%.
--
--===   ===
--
  === Structure projectgegevens ===
--(% style="text-align:center" %)
--[[image:1637656734277-997.png]]
--
  (% class="table-hover" %)
  |(% colspan="1" rowspan="1" %)**Attribute name**|(% colspan="1" rowspan="1" %)**Description**|(% colspan="1" rowspan="1" %)**Unit**
  |(% colspan="1" rowspan="1" %)**idopdracht**|(% colspan="1" rowspan="1" %)The TerraIndex id of the lab assignment the result belongs to.|(% colspan="1" rowspan="1" %)-
@@ -294,10 +294,12 @@
  =   =
--= What to exchange to store the right results? =
++= What to exchange to bind the right results to the right sample? =
--The data stream ‘Lab Result’ is the feedback of analysis results on the requested lab assignment at a laboratory.
++The data stream ‘Lab Result’ is the feedback of analysis results on the requested lab assignment at a laboratory. At import we need to bind it onto the correct sample.
++This requires importand field to match the samples in the xml to the samples in our database.
++
  **Important fields:**
  |=Entity|=Fixed value|=Remark
@@ -316,7 +316,7 @@
  * For Asbestos and Asphalt, new samples are also created at the Lab, which are therefore fed back with a reference to the sample from which they are derived.
  * There is still a desire to feedback from a lab whether an analysis sample has been modified at the lab in terms of sub-samples. For example, if a jar has broken and been replaced with another jar. This has not yet been included in current practices.
--**Importing the data can be done based on the following steps:**
++**Importing the data will be done based on the following steps:**
  * Search Project with Project.lokaalID (as placed in the Lab assignment XML).
  * Search Project with Project.ProjectCode (as placed in the Lab assignment XML) if searching on Project.LokaalID yields no results.
@@ -330,6 +330,7 @@
  * If an Analysis Sample is found, the Analysis Results are always updated or added.
  * If Project is found, but the analysis sample is not; then this analysis sample is imported as a new analysis sample with all results.
  * (If it concerns water samples, a new fictional/temporary measuring point and filter could be created.)
++*
  = SIKB 14 Parameter result combinations =
@@ -338,6 +338,12 @@
  \\[[image:1713183008796-215.png]]
  *small remark, condition will be used as: [0..1]
++Domaintables bound to these fields:
++
++* Quantity -[[ Parameter, but only group/groep: Grootheid (Quantity)>>https://codes.sikb.nl/tablet/domain-table-details/0eafa483-2875-4c94-890d-66258a6b4d88]]
++* Parameter -[[ Parameter, but mainly group/groep: Chemische Stof (Chemical substance)>>https://codes.sikb.nl/tablet/domain-table-details/0eafa483-2875-4c94-890d-66258a6b4d88]]
++* Condition - Condition, but not group/groeps that refer to Chemical substance.
++
  The combinations are defined for different compartiments like soil/ground, groundwater, wastewater.
  Below are some examples, and some attachments included to support all combinations.
@@ -344,23 +344,31 @@
  **2 Examples for Soil:**
  |__**Parameter Name**__|__**Parameter ID**__|__**Quantity ID**__|__**Quantity name**__|__**Condition ID**__|__**Condition Name**__
--|lood|1116|2725|Massafractie|1|t.o.v. drooggewicht
--|minerale olie|1200|2725|Massafractie|93|koolwaterstoffractie C10-C40 / drooggewicht
++|lood
++(lead)|1116|2725|Massafractie
++(Massfraction)|1|t.o.v. drooggewicht
++(relative to dry weight)
++|minerale olie
++(minerale oil)|1200|2725|Massafractie
++(Massfraction)|93|koolwaterstoffractie C10-C40 / drooggewicht
++(hydrocarbon fraction C10-C40 / dry weight)
  **2 Examples for Groundwater:**
  |__**Parameter Name**__|__**Parameter ID**__|__**Quantity ID**__|__**Quantity name**__|__**Condition ID**__|__**Condition Name**__|
  |cyanide-complex|2595|2720|(massa)Concentratie|9|opgeloste fractie (bijv. na filtratie)
--|som 29 dioxines (Bbk, 1-10-2010, als TEQ)|2160|2720|(massa)Concentratie|10|uitgedrukt in Toxiciteit equivalenten
++|som 29 dioxines (TEQ)|2160|2720|(massa)Concentratie|10|uitgedrukt in Toxiciteit equivalenten
  **2 Examples for Wastewater:**
  |__**Parameter Name**__|__**Parameter ID**__|__**Quantity ID**__|__**Quantity name**__|__**Condition ID**__|__**Condition Name**__|
  |cyanide-complex|2595|2720|(massa)Concentratie|8|Niet van toepassing
--|som 29 dioxines (Bbk, 1-10-2010, als TEQ)|2160|2720|(massa)Concentratie|10|uitgedrukt in Toxiciteit equivalenten
++|som 29 dioxines (TEQ)|2160|2720|(massa)Concentratie|10|uitgedrukt in Toxiciteit equivalenten
  __**Full combinations sheet:  **__[[attach:Full List of AnalysisResult combinations 04-2024.xlsx||rel="noopener noreferrer" target="_blank"]]
++We can help you with the right combinations and mappings to your own codes.
++

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