Version 26.1 by Robin Huisman on 2024/07/11 10:13
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1 = Exporting lab results to TerraIndex for a customer =
2
3 The file that is used for the examples: [[Example file>>attach:LabResults.xml]]
4
5 {{toc/}}
6
7 {{warning}}
8 SIKB Version 9 is obsolete, and replaced with version 13 or version 14.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]]
9 {{/warning}}
10
11 == What is a Lab result file ==
12
13 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: “idOpdracht, projectCode, idanlmons and anlmons”
14 \\[[image:IMSIKB0101 - Labresults.png]]
15
16
17 == File structure ==
18
19
20 (% class="table-hover" %)
21 |(% colspan="1" rowspan="1" %)**Attribute name**|(% colspan="1" rowspan="1" %)**Description**|(% colspan="1" rowspan="1" %)**Unit**
22 |(% 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
23 |(% 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
24 |(% colspan="1" rowspan="1" %)**Datum**|(% colspan="1" rowspan="1" %)The date on which the lab result file was made|(% colspan="1" rowspan="1" %)(((
25 date
26
27 yyyy-mm-dd
28 )))
29 |(% 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
30 |(% 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
31 |(% colspan="1" rowspan="1" %)**Taal**|(% colspan="1" rowspan="1" %)(((
32 The language of the lab results this depends on the XSD used.
33
34 dut = dutch
35
36 eng = English
37 )))|(% colspan="1" rowspan="1" %)string
38 |(% colspan="1" rowspan="1" %)**Projectgegevens**|(% colspan="1" rowspan="1" %)This section contains all the result information|(% colspan="1" rowspan="1" %)-
39
40 = Questions from Luca to Robin =
41
42 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) ?
43 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."
44 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.
45 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?
46 1. In Validation: ValidationScore. What are STOWA Protocols? is it Stichting Toegepast Onderzoek Waterbeheer?
47 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?
48 1. in the section MeasureUncertainty > link to pdf file in description is invalid. What should it be?
49 1. SIKB 14 Parameter result combinations> first sentence makes no sense to me. Please review so i can translate.
50 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?
51
52
53 (% class="wikigeneratedid" %)
54 ~==== Added by luca: all Classes related to "IMMetingen::Results"
55
56 ==== MeasureResult ====
57
58
59 |**Attribute Name**|**Description**
60 |(((
61 **numericValue** Measure
62 )))|Numeric Value - the numerical value of the observation. When no unit for the measurement is known, the unit 'Dimensionless' should be used.
63 |(((
64 **valueProcessingMethod** GenericName
65 )))|(((
66 Value Processing Method - a mathematical/statistical operation that is applied while the method of value determination/analysis standard remains unchanged.
67
68 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.
69
70 Domain table: Value Processing Method
71 )))
72 |(((
73 **qualityIndicatorType** GenericName
74 )))|(((
75 Quality Indicator/Judgement -> Detection limit, etc.
76
77 Domain table: Quality Judgement
78 )))
79
80 ==== Accuracy ====
81
82
83 |**Attribute Name**|**Description**|**Unit**
84 |(((
85 **recovery** Float
86 )))|(((
87 The part (percentage) of material that is recovered in an analysis.
88 )))|Percentage [%]
89 |(((
90 **spread** Float
91 )))|Spread = the error measured (in %) in multiple repeated measurements of the same sample/situation (and by the same laboratory technician/measuring device).|Percentage [%]
92 |(((
93 **measurementUncertainty** Float
94 )))|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 [%]
95 |(((
96 **zScore** Float
97 )))|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.|
98 |(((
99 **drift** Float
100 )))|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 [%]
101
102 ==== ====
103
104 ==== Validation ====
105
106
107 This DataClass contains optional attributes and indicates which validation steps the measureResult (measurement value) has undergone.
108
109
110 |**Attribute Name**|**Description**
111 |(((
112 **automatedControl** GenericName
113 )))|(((
114 The first-line control is often an automated check of whether the measurement value is correct. It uses a domain table: ValidationSteps.
115
116 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).
117
118 Domain table: ValidationSteps
119 )))
120 |(((
121 **expertControl** GenericName
122 )))|(((
123 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.
124
125 Domain table: ValidationSteps
126 )))
127 |(((
128 **validationScore** GenericName
129 )))|(((
130 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
131
132 Domain table: ValidationScore
133 )))
134
135 ==== ====
136
137 ==== AnalyticResult ====
138
139
140 The analyzed result of an observation, typically originating from a laboratory.
141
142
143 |=**Attribute Name**|=**Description**
144 |(((
145 **limitSymbol** CharacterString
146 )))|(((
147 LimietSymbool, allowed values: '<' en '>'.
148
149 '<' stands for 'less than the lowest threshold'
150
151 '>' stands for 'greater than the highest threshold'
152
153 The boundary for the limit symbol can be specified in the DeterminationLimits (LimitSymbolReferenceCode) as a reference with the actual value of the limit. The value can be included in the exchange in two ways:
154
155 1) as a CData block: <![CDATA[<]]> or <![CDATA[>]]>
156
157 2) as HTML code: '&amp; lt;' or '&amp; gt;'
158 )))
159 |(((
160 **alphanumericValue** CharacterString
161 )))|Textual value associated with an analysis result
162
163 ==== ====
164
165 ==== MeasureUncertainty ====
166
167
168 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]]
169
170
171 |=**Attribute Name**|=**Description**
172 |(((
173 **distributionType** GenericName
174 )))|(((
175 The type of statistical distribution associated with the observation.
176
177 Domain table: ProbabilityDistribution
178 )))
179 |(((
180 **statisticalParameter** Measure
181 )))|(((
182 Parameters that determine the shape and size of the statistical distribution.
183
184 Domain table: StatisticalParameter
185 )))
186
187 ==== ====
188
189 ==== DeterminationLimits ====
190
191
192 |=**Attribute Name**|=**Description**
193 |(((
194 **detectionLimit** Measure
195 )))|(((
196 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%).
197
198
199 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]]
200 )))
201 |(((
202 **reportingLimit** Measure
203 )))|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.
204 |(((
205 **limitSymbolReferenceCode **GenericName
206 )))|(((
207 The threshold value that the limitSymbol of AnalyticResult refers to.
208
209 Domain table: LimitSymbolReference
210 )))
211 |(((
212 **quantitationLimit** Measure
213 )))|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%.
214
215 === ===
216
217 === Structure projectgegevens ===
218
219 (% style="text-align:center" %)
220 [[image:1637656734277-997.png]]
221
222
223 (% class="table-hover" %)
224 |(% colspan="1" rowspan="1" %)**Attribute name**|(% colspan="1" rowspan="1" %)**Description**|(% colspan="1" rowspan="1" %)**Unit**
225 |(% colspan="1" rowspan="1" %)**idopdracht**|(% colspan="1" rowspan="1" %)The TerraIndex id of the lab assignment the result belongs to.|(% colspan="1" rowspan="1" %)-
226 |(% colspan="1" rowspan="1" %)**projectcode**|(% colspan="1" rowspan="1" %)The project code of the project as it was delivered in the lab assignment|(% colspan="1" rowspan="1" %)string
227 |(% colspan="1" rowspan="1" %)**projectnaam**|(% colspan="1" rowspan="1" %)The name of the project as it was delivered in the lab assignment.|(% colspan="1" rowspan="1" %)string
228 |(% colspan="1" rowspan="1" %)**ordernummer**|(% colspan="1" rowspan="1" %)Not relevant. The order in which the lab result could be shown|(% colspan="1" rowspan="1" %)string
229 |(% colspan="1" rowspan="1" %)**projectleider**|(% colspan="1" rowspan="1" %)The project leader of the customer. This needs the be the “contactpersoon” from the lab assignment with the code PL|(% colspan="1" rowspan="1" %)string
230 |(% colspan="1" rowspan="1" %)**status**|(% colspan="1" rowspan="1" %)The status of the lab assignment. See Labstatus Codegroup 76 in the attachments for all the options.|(% colspan="1" rowspan="1" %)integer
231 |(% colspan="1" rowspan="1" %)**datumverwacht**|(% colspan="1" rowspan="1" %)The date on which the lab expects the certificate to be available|(% colspan="1" rowspan="1" %)Date
232 yyyy-mm-dd
233 |(% colspan="1" rowspan="1" %)**certificaatnummer**|(% colspan="1" rowspan="1" %)The number of the certificate that will be send to the user.|(% colspan="1" rowspan="1" %)string
234 |(% colspan="1" rowspan="1" %)(((
235 **analysemonsters**
236
237
238
239 )))|(% colspan="1" rowspan="1" %)A table containing all the analysis sample with their corresponding results|(% colspan="1" rowspan="1" %)-
240
241 == Structure analysemonsters ==
242
243 (% style="text-align:center" %)
244 [[image:1637656914799-534.png]]
245
246 (% class="table-hover" %)
247 |(% colspan="1" rowspan="1" %)**Attribute name**|(% colspan="1" rowspan="1" %)**Description**|(% colspan="1" rowspan="1" %)**Unit**
248 |(% colspan="1" rowspan="1" %)**Idanlmons**|(% colspan="1" rowspan="1" %)The unique identification code of the analyses sample as given in the lab assignment file|(% colspan="1" rowspan="1" %)string
249 |(% colspan="1" rowspan="1" %)**Anlmons**|(% colspan="1" rowspan="1" %)The name of the analyses sample as given in the lab assignment file|(% colspan="1" rowspan="1" %)string
250 |(% colspan="1" rowspan="1" %)**Certificaat**|(% colspan="1" rowspan="1" %)The way the name of the sample should be on the certificate. This is also given in the lab assignment|(% colspan="1" rowspan="1" %)string
251 |(% colspan="1" rowspan="1" %)**Monstersoort**|(% colspan="1" rowspan="1" %)The code referencing the type the sample is. Check the attachment: Sample type codegroup 51 for all the options|(% colspan="1" rowspan="1" %)integer
252 |(% colspan="1" rowspan="1" %)**Status**|(% colspan="1" rowspan="1" %)The status of the sample. See Labstatus Codegroup 76 in the attachments.|(% colspan="1" rowspan="1" %)integer
253 |(% colspan="1" rowspan="1" %)**Datumverwacht**|(% colspan="1" rowspan="1" %)The date on which the results for the sample are expected|(% colspan="1" rowspan="1" %)(((
254 date
255
256 yyyy-mm-dd
257 )))
258 |(% colspan="1" rowspan="1" %)**Volgorde**|(% colspan="1" rowspan="1" %)Is a unused field in TerraIndex|(% colspan="1" rowspan="1" %)integer
259 |(% colspan="1" rowspan="1" %)**analyseresultaten**|(% colspan="1" rowspan="1" %)A table containing all the measurement values of the analysis samples.|(% colspan="1" rowspan="1" %)-
260
261 == Structure analyseresultaten ==
262
263 (% style="text-align:center" %)
264 [[image:1637657248973-790.png]]
265
266 (% class="table-hover" %)
267 |(% colspan="1" rowspan="1" %)**Attribute name**|(% colspan="1" rowspan="1" %)**Description**|(% colspan="1" rowspan="1" %)**Unit**
268 |(% colspan="1" rowspan="1" %)**componentcode**|(% colspan="1" rowspan="1" %)The SIKB component code. See ComponentCode Codegroup 52 in the attachements for all possible options.|(% colspan="1" rowspan="1" %)integer
269 |(% colspan="1" rowspan="1" %)**meetwaarde**|(% colspan="1" rowspan="1" %)What the measured value is for the analyses|(% colspan="1" rowspan="1" %)float
270 |(% colspan="1" rowspan="1" %)**meetwaardeomschrijving**|(% colspan="1" rowspan="1" %)Alpha numerical description of the result|(% colspan="1" rowspan="1" %)string
271 |(% colspan="1" rowspan="1" %)**eenheidcode**|(% colspan="1" rowspan="1" %)The unit of the measured value. See Unit CodeGroup 40 in the attachements for all possible options|(% colspan="1" rowspan="1" %)integer
272 |(% colspan="1" rowspan="1" %)**referentiecode**|(% colspan="1" rowspan="1" %)This defines what the reference for the measurement value is. See ReferenceType CodeGroup 41 for all the possible options|(% colspan="1" rowspan="1" %)integer
273 |(% colspan="1" rowspan="1" %)**analysenorm**|(% colspan="1" rowspan="1" %)Against which standard the analysis has been tested. See Laboratory method Codegroup 57 in the attachments for all the option. I your standard is not in the list leave this empty|(% colspan="1" rowspan="1" %)integer
274 |(% colspan="1" rowspan="1" %)**datummonstervoorbehandeling**|(% colspan="1" rowspan="1" %)The date on which the sample was pre-treated. We don’t do anything with this value|(% colspan="1" rowspan="1" %)(((
275 date
276
277 yyyy-mm-dd
278 )))
279 |(% colspan="1" rowspan="1" %)**opmerking**|(% colspan="1" rowspan="1" %)A remark for this result|(% colspan="1" rowspan="1" %)string
280 |(% colspan="1" rowspan="1" %)**certificering**|(% colspan="1" rowspan="1" %)Under which certificate the analyses has been done. See CertificateCode Codegroup 48 for all the possible options. If you do not find you code leave this field empty|(% colspan="1" rowspan="1" %)integer
281 |(% colspan="1" rowspan="1" %)**status**|(% colspan="1" rowspan="1" %)The status of the labresult in the labassignemnt. See Labstatus Codegroep 76 in the attachments|(% colspan="1" rowspan="1" %)integer
282 |(% colspan="1" rowspan="1" %)**datumverwacht**|(% colspan="1" rowspan="1" %)Date on which the analyses results are expected.|(% colspan="1" rowspan="1" %)date
283
284 = =
285
286 = What to exchange to store the right results? =
287
288 The data stream ‘Lab Result’ is the feedback of analysis results on the requested lab assignment at a laboratory.
289
290 **Important fields:**
291
292 |=Entity|=Fixed value|=Remark
293 |**Project**|lokaalID (GUID)|As submitted in the Lab assignment XML
294 | |projectCode|As submitted in the Lab assignment XML
295 |**Labassignment**|lokaalID (GUID)|As submitted in the Lab assignment XML
296 |**Sample (analysis sample)**|lokaalID (GUID)|As submitted in the Lab assignment XML, if assignment in SIKB<11, but results in >=11; fill with old BISNR/IDANLMONS.
297 | |Name|As submitted in the Lab assignment XML
298 |**Sample (field sample)**|(((
299 lokaalID (GUID)
300 )))|Only if this entity is included, which is optional.
301
302 **Remarks:**
303
304 * The entity ‘Analysis Result’ does not yet have a fixed lokaalID (GUID), connected laboratories cannot yet guarantee that a unique ID will be generated.
305 * 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.
306 * 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.
307
308 **Importing the data can be done based on the following steps:**
309
310 * Search Project with Project.lokaalID (as placed in the Lab assignment XML).
311 * Search Project with Project.ProjectCode (as placed in the Lab assignment XML) if searching on Project.LokaalID yields no results.
312 * Search Project and Lab assignment with Labassignment.LokaalID (as placed in the Lab assignment XML) if the Project has not yet been found.
313 * Search Project (if Project not yet found) and Analysis Sample with Sample.LokaalID as GUID (as placed in the Lab assignment XML, version 11 and higher).
314 * Search Project (if Project not yet found) and Analysis Sample with Sample.LokaalID as BISNR (as placed in the Lab assignment XML, versions lower than 11, 'old' idanlmons/BISNR).
315 * Search Analysis Sample with Sample.Name within the project, if the Analysis Sample has not been found but the project has.
316
317 **What can be imported?**
318
319 * If an Analysis Sample is found, the Analysis Results are always updated or added.
320 * If Project is found, but the analysis sample is not; then this analysis sample is imported as a new analysis sample with all results.
321 * (If it concerns water samples, a new fictional/temporary measuring point and filter could be created.)
322
323 = SIKB 14 Parameter result combinations =
324
325 In the SIKB0101 version 14 exchange of **__labresults is combination needed __**for exchanging the result parameters of the Lab analysis.
326 It's based on PhysicalProperty, the combination of Quantity, Parameter and Condition.
327 \\[[image:1713183008796-215.png]]
328 *small remark, condition will be used as: [0..1]
329
330 The combinations are defined for different compartiments like soil/ground, groundwater, wastewater.
331 Below are some examples, and some attachments included to support all combinations.
332
333 **2 Examples for Soil:**
334
335 |__**Parameter Name**__|__**Parameter ID**__|__**Quantity ID**__|__**Quantity name**__|__**Condition ID**__|__**Condition Name**__
336 |lood|1116|2725|Massafractie|1|t.o.v. drooggewicht
337 |minerale olie|1200|2725|Massafractie|93|koolwaterstoffractie C10-C40 / drooggewicht
338
339 **2 Examples for Groundwater:**
340
341 |__**Parameter Name**__|__**Parameter ID**__|__**Quantity ID**__|__**Quantity name**__|__**Condition ID**__|__**Condition Name**__|
342 |cyanide-complex|2595|2720|(massa)Concentratie|9|opgeloste fractie (bijv. na filtratie)
343 |som 29 dioxines (Bbk, 1-10-2010, als TEQ)|2160|2720|(massa)Concentratie|10|uitgedrukt in Toxiciteit equivalenten
344
345 **2 Examples for Wastewater:**
346
347 |__**Parameter Name**__|__**Parameter ID**__|__**Quantity ID**__|__**Quantity name**__|__**Condition ID**__|__**Condition Name**__|
348 |cyanide-complex|2595|2720|(massa)Concentratie|8|Niet van toepassing
349 |som 29 dioxines (Bbk, 1-10-2010, als TEQ)|2160|2720|(massa)Concentratie|10|uitgedrukt in Toxiciteit equivalenten
350
351 __**Full combinations sheet:  **__[[attach:Full List of AnalysisResult combinations 04-2024.xlsx||rel="noopener noreferrer" target="_blank"]]
352
353
354
355

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