2009 12 06 - LOINC Workshop

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2009 12 06 - LOINC Workshop

  1. 1. Using RELMA<br />Or…In Search of the Missing LOINC<br />Laboratory LOINC Meeting – December 2009<br />James T. Case MS, DVM, PhD<br />Professor, Clinical Diagnostic Informatics<br />California Animal Health and Food Safety Laboratory<br />University of California, Davis<br />
  2. 2. Acknowledgements<br /><ul><li>RELMA Development Team
  3. 3. John Hook, Mark Fisher, Ryan Phillips, Karen Ahmad, and more!
  4. 4. Kathy Mercer
  5. 5. Clem McDonald
  6. 6. Dan Vreeman
  7. 7. The Lab LOINC Committee
  8. 8. Funding Support
  9. 9. NLM, Regenstrief Institute, NCI, CDC</li></li></ul><li>What will we cover today?<br /><ul><li>Why we are doing this!
  10. 10. Overview of LOINC
  11. 11. Installing RELMA
  12. 12. Setting personal preferences
  13. 13. Loading a Local Observation File (LMOF)
  14. 14. Searching for a LOINC Term
  15. 15. Preparing LMOF for Mapping
  16. 16. Review of Map Screen Functions
  17. 17. Setting Search Limits
  18. 18. Mapping Local Terms to LOINC
  19. 19. Viewing LOINC Term Details
  20. 20. Proposing/Submitting New LOINC Terms
  21. 21. Exporting/Printing Mapped Terms
  22. 22. Mapping your own LMOF data </li></li></ul><li>Why are we doing this?Goals of Health Information Standards<br /><ul><li>Interoperability – the ability to exchange information between organizations
  23. 23. Comparability – the ability to ascertain the equivalence of data from different sources
  24. 24. Data Quality – the measurement of accessibility, completeness, accuracy and precision (and more)</li></li></ul><li>Levels of Interoperability<br /><ul><li>Basic – allows messages to be exchanged between computer systems
  25. 25. Word processing documents, text messages
  26. 26. Functional – describes the standard syntax (format) of the message
  27. 27. Document templates, forms, data structures
  28. 28. Message standards
  29. 29. Semantic – requires use of standard vocabularies within the message</li></li></ul><li>Comparability<br /><ul><li>Meaning of the data is consistent when shared among different parties
  30. 30. Erysipelas – Human skin disease; StreptococcusGrp A
  31. 31. Erysipelas – Animal Septicemia – Erysipelothrixrhusiopathiae
  32. 32. Common terminology required
  33. 33. Should work in the background
  34. 34. Not just words
  35. 35. Codes – uniquely identifies terms
  36. 36. Classification – groups related terms
  37. 37. Vocabulary – specialized, precise terms that remove ambiguity</li></li></ul><li>Potential Uses of Health Data are Constrained by Data Quality Factors<br /><ul><li>Data quality issues
  38. 38. Different for client communications vs. analysis
  39. 39. Often constrained by external forces
  40. 40. E.g. criteria for diagnosis often differs from the criteria for reporting
  41. 41. Unidirectional effect of data consolidation
  42. 42. Detailed → General
  43. 43. General → Detailed</li></li></ul><li>The Problem<br />“In attempting to arrive at the truth, I have applied everywhere for information, but in scarcely an instance have I been able to obtain hospital records fit for any purpose of comparison. If they could be obtained, they would enable us to decide many other questions… They would show [subscribers] how their money was being spent [and] what amount of good was really being done with it…”<br />Florence Nightingale - Notes on a Hospital, 1873<br />
  44. 44. What you see in the order list<br />Test comparisons<br />Lab A<br />Test Name:Lyme Disease Serology<br />Measures:B. burgdorferi Ab IgG<br />Method: ELISA<br />Scale: quantitative<br />e.g.: Titer 1:40<br />Lab B<br />Test Name:Lyme Disease Antibody<br />Measures:B. burgdorferi Ab IgM<br />Method: Immune blot<br />Scale: qualitative<br />e.g.: Positive<br />LOINC Code = 5062-5<br />LOINC Code = 6321-4<br />
  45. 45. Why LOINC?<br />“Within one laboratory, local jargon terms may be used which are usually well understood between colleagues, but would not be sufficiently widely known for communication with the outside world.”<br />U. Forsum et al., Pure Appl. Chem 72:555-745, 2000 Properties and Units in the Clinical Laboratory Sciences Part VII. Properties and Units in Clinical Microbiology<br />
  46. 46. LOINC® 101<br />
  47. 47. Anatomy of a LOINC Term<br />5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA<br />LOINC Code<br />5193-8<br />Hepatitis B virus surface Ab<br />Component<br />ACnc<br />Property Measured<br />Pt<br />Timing<br />Ser<br />System<br />Qn<br />Scale<br />EIA<br />Method<br />There are six major LOINC axes<br />
  48. 48. What is NOT part of a LOINC Name?<br /><ul><li>The instrument used in testing
  49. 49. Specific details about the specimen
  50. 50. Priority (e.g. STAT)
  51. 51. Where testing was done
  52. 52. Who did the test
  53. 53. Test interpretation
  54. 54. Anything that is not an intrinsic part of the name of the result
  55. 55. Other things that are carried in;
  56. 56. The OBR or OBX segment
  57. 57. An HL7 Version 3 Observation Object</li></li></ul><li>Component/Analyte<br />The substance or entity that is measured, evaluated, or observed<br />- Sodium<br />- Glucose<br />- Brucella sp. organism<br />- Influenza A Virus antigen<br /><ul><li>Cytomegalovirus Virus antibody
  58. 58. Lipids.Total</li></ul>5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA<br />
  59. 59. Component/Analyte Structure<br />AnalyteName^Challenge^Adjustments<br /><ul><li>Formal name of Analyte (e.g. Calcium)
  60. 60. Must specify any “subanalyte”
  61. 61. e.g. Coronavirus Ag
  62. 62. May have a subclass – separated by “.”
  63. 63. e.g. Calcium.Free
  64. 64. Challenge - e.g, 1H post 100 gm Glucose PO
  65. 65. Two subparts separated by “post”
  66. 66. <time delay> post <challenge type>
  67. 67. Adjustments/corrections
  68. 68. E.g. Adjusted to pH 7.4</li></li></ul><li>Property<br />the most difficult LOINC axis<br />The characteristic or attribute of the analyte that is measured, evaluated, or observed<br />Major Categories<br /><ul><li>Mass: Observations reported with mass (milligrams, grams, etc.) in the numerator of their units of measure
  69. 69. Substance: Observations reported with moles or milliequivalents in the numerator of their units of measure
  70. 70. Catalytic activity: Observations that report enzymatic activity
  71. 71. Arbitrary: Results that report arbitrary units in the numerator of their units of measure
  72. 72. Number: Counts</li></ul>5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA<br />
  73. 73. Property<br />the most difficult LOINC axis<br />Combine Major Categories with Subtypes for Full Property<br /><ul><li>MCnc – mass concentration (mass/unit vol)
  74. 74. MCnt – mass content (mass/unit mass)
  75. 75. NCnc – number concentration (number/unit vol)
  76. 76. TmStp – time
  77. 77. CCnc – catalytic concentration (activity)
  78. 78. Prid – presence or identity
  79. 79. Imp – impression/interpretation
  80. 80. Find – subjective or objective observation
  81. 81. Type – “Kind-of”</li></ul>5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA<br />
  82. 82. Common Issues with LOINC Properties<br />Fraction (proportion) vs. Ratio<br />a/a+b vs. a/b<br /><ul><li>Fraction = Part/whole
  83. 83. Number fraction (NFr): % Eosinophils
  84. 84. Substance fraction (SFr): % HGB which is A2
  85. 85. Ratio = Measures multiple analytes from the same system (specimen)
  86. 86. Mass concentration ratio - MCrto
  87. 87. e.g., BUN/Creat in urine specimen
  88. 88. Substance ratio-SCrto
  89. 89. Urea/Creatinine expressed as mmol/L (SI units)
  90. 90. Relative Ratio = Measures from different systems
  91. 91. RelRto – multiple of the median
  92. 92. RlTm – time from actual and normal control</li></li></ul><li>Timing*<br />The interval of time over which the observation or measurement was made<br /><ul><li>Pt - at a point in time
  93. 93. 12H - a twelve hour collection
  94. 94. 24H - a twenty four hour collection</li></ul>*non-Pt timings are usually associated with Ratio Property<br />
  95. 95. System<br />The system (context) or specimen type upon which the observation was made.<br />Ser - Serum<br />Bld - Whole blood (RBC)<br />Ur- Urine<br />BldA - Arterial blood<br />Liver - Liver<br />Flu – Body Fluid, unspecified<br />Gast – Gastric fluid/contents<br />Food – Food or feedstuff<br />Tiss – Tissue<br />XXX – To be specified in another part of the message <br />Super System<br />Second subpart (^). When not included, “patient” is the default. Used to indicated blood product unit (BPU), a bone marrow donor, or a fetus.<br />
  96. 96. Scale<br /><ul><li>Qn - quantitative
  97. 97. Continuous numeric (real, integer, ratio)
  98. 98. Optional operator (>, , , <)
  99. 99. When assay detection limits are exceeded
  100. 100. Ord - ordinal
  101. 101. a ranked set of possible values (1+, 2+, 3+)
  102. 102. Nom - nominal
  103. 103. an unranked collection of possible values
  104. 104. a taxonomy (e.g list of bacteria)
  105. 105. Nar - narrative
  106. 106. free text narrative (e.g., visit note)</li></li></ul><li>Scale (Special)<br /><ul><li>OrdQn – Ordinal or Quantitative
  107. 107. Primarily used for antimicrobial observations e.g. MIC reported as resistant, intermediate, susceptible or as the mm diameter of the inhibition zone
  108. 108. Use is discouraged
  109. 109. Multi – structured text “globs”
  110. 110. e.g. chromatography output
  111. 111. Use is discouraged
  112. 112. Doc – Clinical documents
  113. 113. Set – Clinical attachments (headers)</li></li></ul><li>Method<br /><ul><li>Methods only needed if interpretation affected
  114. 114. Different normal ranges
  115. 115. Test Sensitivity
  116. 116. Listed only at the generic level
  117. 117. Agglutination
  118. 118. Immunoassay
  119. 119. Probe with target amplification</li></li></ul><li>Mapping Terms to LOINCThings to Remember<br /><ul><li>The thing ordered is not always the thing measured:
  120. 120. Blood Culture – live organism(s) identified
  121. 121. VDRL – TreponemapallidumAb
  122. 122. Urinalysis – lots of different things
  123. 123. The question (what am I measuring? e.g. Glucose) is not the answer (e.g. 90 mg/dl)
  124. 124. You are mapping the question, not the answer!
  125. 125. You must know the specifics of the component being tested for (what is this test actually measuring?)</li></li></ul><li>RELMA®<br />Regenstrief LOINC Mapping Assistant<br />
  126. 126. Purpose of Tutorial<br /><ul><li>“Eliminate” need to read the User’s Manual
  127. 127. Become familiar with RELMA features
  128. 128. Provide some insight into mapping tips/pitfalls
  129. 129. Help begin the mapping process for your institution
  130. 130. Note: Screen shots from version 3.24(early release)</li></li></ul><li>New in This Version (Rel. 4.2) <br /><ul><li>RELMA converted to Microsoft's .NET technology.
  131. 131. Uses Microsoft Windows Installer 
  132. 132. New “Lookup” Screen
  133. 133. Simplified access to LOINC term lookup
  134. 134. Misspellings have context “suggestions”
  135. 135. Display details now more accessible
  136. 136. Export configuration and printing more flexible
  137. 137. Addition of UCUM units in process</li></li></ul><li>RELMA Functions<br /><ul><li>Manual and automated mapping assistant
  138. 138. Same free use as LOINC (see license)
  139. 139. Comes with the LOINC files and indexes
  140. 140. Now migrated to MS .NET environment.
  141. 141. RELMA tools transform local words in local file
  142. 142. User creates file of local term/name and codes
  143. 143. Assigns LOINC term to local test/battery code
  144. 144. Context sensitive hierarchies for local use.</li></li></ul><li>LOINC Web Site<br />
  145. 145. Highlights<br /><ul><li>Browseable Hierarchies
  146. 146. Display search results in tree view
  147. 147. Enhanced “details” view of terms/parts
  148. 148. References
  149. 149. Descriptions
  150. 150. Sample units
  151. 151. Empirically-derived common test list
  152. 152. Special features for panels/forms
  153. 153. Enhanced export/copy-paste options</li></li></ul><li>RELMA Search logic <br />For a given test:<br /><ul><li>User can select LOINC records containing:
  154. 154. A set of words connected by ANDs or Ors
  155. 155. Additional keyed in words
  156. 156. A particular category of test (e.g. microbiology)
  157. 157. Wild cards of ? and *
  158. 158. Selected classes, systems, components,
  159. 159. Any intersection of the above</li></ul>Note:<br />RELMA assumes exact match on word unless user adds terminal “*” to indicate wild card.<br />
  160. 160. RELMA Logic<br />Not  #&lt;word A&gt;<br />Or  &lt;word A&gt; | &lt;word B &gt;<br />And  &lt;word B&gt; &lt;word A&gt;<br />
  161. 161. Additional RELMA Features <br /><ul><li>User Specified Search Limits
  162. 162. Selectable trees for:
  163. 163. Class
  164. 164. System (specimen)
  165. 165. Component
  166. 166. Method</li></li></ul><li>Installing RELMA®<br />
  167. 167. Installation Steps<br /><ul><li>Make sure you have enough free disk space!
  168. 168. 1Gb is recommended
  169. 169. From CD - Start – Run – D:RELMASetup
  170. 170. Specify installation directory
  171. 171. Life will be easier if you accept the default
  172. 172. Two database files installed
  173. 173. RELMA.MDB – LOINC Terms Database
  174. 174. LMOF3.MDB – Local Master Observation File
  175. 175. Two sample files copied
  176. 176. WinXP: C:Documents and SettingsUsernameMy DocumentsRELMASamples
  177. 177. Vista: C:UsersyouraccountDocumentsRELMASamples
  178. 178. Run from Start – (All) Programs – Regenstrief – RELMA</li></li></ul><li>Running RELMA®<br />Version 4.2<br />
  179. 179. Copyright Screen<br />
  180. 180. Main Menu/Welcome Screen<br />Click File, Set Preferred Language<br />
  181. 181. Select Linguistic Variant(s)<br />
  182. 182. LOINC Terms with Spanish Linguistic Variant<br />Spanish!<br />
  183. 183. Welcome Screen<br />New Feature!<br />
  184. 184. Setting User Preferences<br />
  185. 185. Set User Preferences<br />Select User Preferences<br />From the File Menu<br />...or from Welcome Screen<br />
  186. 186. Set User Preference Dialog<br />New File Locations:<br />Now stored in My Documents<br />Startup Screen Preference<br />
  187. 187. User Map Screen Preferences<br />Click Map Screen Tab<br />Include/Exclude Battery Terms<br />Add comments on Mappings<br />
  188. 188. Importing Local Terms into RELMA<br />
  189. 189. 4 Ways to Load LMOF Files<br /><ul><li>Direct entry into LMOF from within RELMA (painful)
  190. 190. Handy for individual entries/edits
  191. 191. Create an Access table that mimics the LMOF structure (less painful but tedious)
  192. 192. Appendix A: RELMA Manual
  193. 193. Create a delimited ASCII file from your local test catalog (good choice)
  194. 194. Load directly from HL7 v2.x messages
  195. 195. Pulls data from OBR and OBX segments
  196. 196. Stores NTE segment data</li></li></ul><li>Constructing a Local Dataset<br />Create extract of your test catalog with:<br /><ul><li>Battery/Panel Code
  197. 197. Battery/Panel Description or Name
  198. 198. *Local Code
  199. 199. *Test Description or Name
  200. 200. Include Method if Important
  201. 201. Units
  202. 202. Example Values
  203. 203. Laboratory Section</li></li></ul><li>Creating Delimited ASCII File<br /><ul><li>RELMA can’t parse free text
  204. 204. Need to create separate fields
  205. 205. Can use any of these delimiters
  206. 206. Tab, Semicolon, Comma, Space
  207. 207. Can define your own
  208. 208. Fields can be in any order
  209. 209. Minimum required fields
  210. 210. Local Code
  211. 211. Local Description
  212. 212. Units (highly recommended)</li></li></ul><li>Entering New Local Terms <br />into RELMA<br />
  213. 213. Manual Enter/Edit <br />View/Add/Edit Local Terms<br />
  214. 214. Edit Term Dialog<br />Text alignment option<br />EditAddDelete Terms<br />Search Terms by Keyword<br />Print Preview List<br />
  215. 215. Add Local Term<br />MICRO<br />BUBPLAG<br />BUBONIC PLAGUE – RRT PCR<br />Click to Add to Current Working File<br />
  216. 216. Search Local Term File<br />Hematocrit<br />Enter Keyword from any Field<br />Return to Full List<br />
  217. 217. Print Preview Local Term File<br />Must Select Terms you want to appear<br />
  218. 218. Steps to Import Local Terms<br />Click Import Local TermsButton from Main Menu <br />a)File&gt;Import Local Terms from Delimited File<br />Locate your local terms text file<br />Sample file loaded into C:Program FilesRELMA<br />Name your Working Set<br />LMOF database can contain multiple work sets<br />Define default section (Optional)<br />Identify file delimiter <br />Assign fields to LMOF attributes<br />Ignore fields you don’t need<br />Combine fields if needed<br />Check “Case-sensitive” if needed<br />Click Import.<br />
  219. 219. Local Term File Options<br />
  220. 220. Example Tab-Delimited File<br />
  221. 221. Importing Local Files<br />Select Import Local Terms<br />
  222. 222. Navigate to File Location<br />Select File and Click Open<br />Sample files stored in RELMA Directory<br />
  223. 223. Open File in RELMA<br />Name your working set. RELMA allows multiple sets in LMOF database<br />Select your delimiter<br />Import Button<br />
  224. 224. Open File in RELMA<br />
  225. 225. Fields Segregated<br />Assign LMOF Attribute<br />Choose field name<br />
  226. 226. Ready to Import<br />Minimum assignments<br />Now you can click the Import button!<br />
  227. 227. Change Local Term File<br />Select the Working Set<br />
  228. 228. Alternative Pragmatic Way<br /><ul><li>Use large set of HL7 messages
  229. 229. Automatically make dataset of:
  230. 230. OBR ID
  231. 231. OBR description
  232. 232. OBX ID
  233. 233. OBX description
  234. 234. Sample of results with
  235. 235. Real values
  236. 236. Units
  237. 237. Abnormal flags
  238. 238. Normal ranges</li></li></ul><li>Generate Local term file from HL7 messages<br />Select Import Terms from HL7 File<br />
  239. 239. Select File to Import<br />Select HL7 File<br />
  240. 240. Specify HL7 File Name and Sample Size<br />Name the Local Term File (working set)<br />Select the number of sample values<br />Select which codes to store<br />
  241. 241. HL7 Messages Data Statistics<br />
  242. 242. New Terms added to LMOF<br />Click on “Edit Test to see Sample Data<br />New Battery Code<br />
  243. 243. Sample Results for Observation<br />New Test Code<br />Sample Values from Messages<br />
  244. 244. Lenny L’OINC says:<br />“Load the Sample Files<br />Into RELMA now!”<br /><ul><li>Import the two sample files provided
  245. 245. Import_Sample_OBR.txt
  246. 246. Contains battery code and description
  247. 247. Import_Sample_OBX.txt
  248. 248. Contains test code and description
  249. 249. Create 2 working sets</li></li></ul><li>Cleaning your data<br />
  250. 250. Preparing your Data for Mapping<br /><ul><li>Improve mapping success by:
  251. 251. Expanding abbreviations
  252. 252. Standardizing colloquial terms
  253. 253. Ignoring “administrative” terms
  254. 254. Standardizing time references
  255. 255. Can be done prior to importing
  256. 256. Better to use tools built into RELMA</li></li></ul><li>Preparing your Data for Mapping<br /><ul><li>Find local Words not in LOINC
  257. 257. Tools>Concepts in Local Term File Unknown to RELMA
  258. 258. Creates a list of local terms in your file not found in LOINC
  259. 259. Only needs to be run once per working set version
  260. 260. Can be printed or saved as a file
  261. 261. Autosearches LOINC terminology
  262. 262. Global Replace, Interactive Replace, Ignore</li></li></ul><li>RELMA Cleaning Tools<br />Use this tool to find unknown terms<br />
  263. 263. Scanning Local Terms<br />Scan File for Unknown Terms<br />
  264. 264. Replace Local Terms<br />Assign LMOF Attribute<br />ReplacementOptions<br />
  265. 265. RELMA Cleaning Tools<br />Use this tool to make global substitutions<br />
  266. 266. Term Substitution<br />Save this global substitution for only this working set<br />
  267. 267. Searching for LOINC Terms<br />
  268. 268. New Simplified Search Only Tool<br />
  269. 269. Search Window<br />Enter Search Terms <br />Limit to <br />Specific Units<br />Limit to Common <br />Tests<br />
  270. 270. Mapping Local Terms<br />
  271. 271. Mapping Local Terms<br /><ul><li>Select “Map Local Terms to LOINC” from Welcome Screen
  272. 272. Select your Working Set to Map
  273. 273. File>Change Local term File
  274. 274. Select the subset of terms to work with:
  275. 275. All
  276. 276. Mapped
  277. 277. Unmapped
  278. 278. Set your Search Limits
  279. 279. Set Search Limits Button</li></li></ul><li>Standard Mapping Window Features<br /><ul><li>Customizable grid
  280. 280. View details of LOINC term
  281. 281. Sort by column
  282. 282. Click column
  283. 283. Custom Sort
  284. 284. Print or export results grid
  285. 285. Spell check squiggly line to signify words not known to RELMA</li></li></ul><li>Mapping Screen <br />Quick select button list<br />View or edit local term<br />Custom Grid Configuration<br />
  286. 286. Configure Grid<br />Select elements to display<br />Reorder grid elements<br />Visually resize elements<br />Reset Default Configuration<br />
  287. 287. View Local Term Details<br />
  288. 288. Standard Mapping Screen<br />Begin a <br />search<br />
  289. 289. Initial Mapping Results<br />EEK! What’ll I do?!<br />Click to show words used in search<br />
  290. 290. Initial Mapping Results<br />Use term checkbox<br />Number of LOINC terms containing keyword<br />Battery terms included in search<br />
  291. 291. Revised Mapping Results<br />Match units selected by default<br />Number of matching records found<br />
  292. 292. Re-revised Mapping Results<br />Number of matching records found<br />Match units unselected<br />
  293. 293. Standard Mapping Screen<br />Clear all input fields<br />
  294. 294. Cleared Mapping Screen<br />CANINE DISTEMPER VIRUS IF<br />Enter keywords here<br />
  295. 295. Ad hoc term search<br />
  296. 296. Standard Mapping Screen<br />Navigate through the local terms<br />
  297. 297. Tabbed Access to Functions<br />Navigate to Functions from Mapping Page<br />Switch between Grid and Tree Views<br />
  298. 298. Tree View<br />
  299. 299. Tree View<br /><ul><li>Results displayed hierarchically
  300. 300. Defined by the multi-axial hierarchy in search restrictions (covered later)
  301. 301. Map to a term in tree by clicking Map button or double clicking term
  302. 302. Only rows that have LOINC Codes</li></li></ul><li>Tree View<br />Can map to terms with LOINC Codes<br />Cannot map to terms representing LOINC parts<br />Tree Navigation Buttons<br />
  303. 303. Assigning a LOINC Map<br />Click “Map” Button <br />(or doubleclick)<br />Highlight correct term<br />
  304. 304. Adding Mapping Comments<br />Check with Frank in Chemistry <br />If comments option is selected, prompt appears<br />
  305. 305. Assigning a LOINC Map<br />LOINC Term Assigned<br />
  306. 306. View LOINC Term Details<br />View details for a specific LOINC Term<br />Right clicking on a LOINC term brings up a Task Menu<br />
  307. 307. LOINC Term Details<br />Can scroll down a single formatted page<br />Can scroll through returned subset of terms<br />Change to expanded details view <br />Change text size<br />
  308. 308. Configure Export Options<br />Output Options<br />Include <br />column headers<br />Save Configuration and/or Export<br />
  309. 309. Excel Export Format<br />
  310. 310. More on Searching Mapping Screen<br />
  311. 311. Using Wildcards in Searches<br /><ul><li>Substring search supported by default
  312. 312. “Gluc” yields any terms with “gluc” in the component/analyte
  313. 313. “*” replaces any number of characters
  314. 314. GLUC*
  315. 315. *COSE
  316. 316. GLU*SE
  317. 317. “?” replaces a single character
  318. 318. GLUCOS?
  319. 319. ?LUCOSE
  320. 320. GLUC?SE</li></li></ul><li>Other Search Qualifiers<br /><ul><li>“#” represents the “NOT” operator
  321. 321. #GLUCOSE – terms without the Word Glucose
  322. 322. “|” is the “OR” operator
  323. 323. GLUCOSE | LACTOSE
  324. 324. Can have multiple “OR”s per box
  325. 325. Can Mix OR and NOT and Wildcards</li></li></ul><li>Search Qualifiers <br />Includes Glucuronidase, Glucosidase, Glucosylceramidase, etc.<br />
  326. 326. Combining Search Terms<br />Exclude Glucosidase<br />Reduced number of terms<br />
  327. 327. Limiting Searches<br />
  328. 328. Setting Search Limits<br /><ul><li>Narrows search to specific subset of LOINC terms
  329. 329. Reduces number of candidate terms
  330. 330. Limits can be applied to all components
  331. 331. Component attribute can be further restricted by number of words
  332. 332. Tree structure allows for hierarchical constraints</li></li></ul><li>General Search Constraints<br /><ul><li>Controls features including:
  333. 333. Limit to LOINC terms compatible with submitted units
  334. 334. Forced match with any specimen contained in name
  335. 335. Methodless terms only
  336. 336. Limit to components/analytes with N or fewer words in their name
  337. 337. Pop up search timing statistics after each search
  338. 338. Use carefully or search may not be successful</li></ul> (Note parallel control switches at bottom of screen)<br />
  339. 339. Setting Search Limits<br />Click Hierarchy & Search Limits Tab<br />
  340. 340. Setting search limits<br />Can also set most of them by toggling buttons at the bottom of the screen <br />Toggle Buttons<br />
  341. 341. Search Constraints<br />Attribute trees<br />Local Unit Constraint:<br />Now defaults to “ON”<br />Predefined, general search constraints<br />
  342. 342. Terms Consistent with Units<br />Only terms consistent with mmol/L appear<br />
  343. 343. Setting Search Limits<br />Specimen constraints<br />
  344. 344. Terms Consistent with Specimen <br />CSF<br />Enter default Specimen<br />
  345. 345. Terms Consistent with Specimen <br />Only CSF Terms are returned<br />
  346. 346. Setting Search Limits<br />Methodless Terms Restriction<br />Override Methodless Terms Restriction<br />
  347. 347. Limit to Methodless Terms<br />
  348. 348. Limit to Methodless Terms<br />Only Methodless Terms Appear<br />
  349. 349. More on Methodless Terms<br /><ul><li>Some LOINC categories do not have methodless terms
  350. 350. Checking methodless only will remove these from view on results grid
  351. 351. Checking additional box allows these to be seen</li></li></ul><li>Methodless Only Unchecked<br />All terms returned<br />
  352. 352. Methodless Only Checked<br />Differ in one or more components<br />Only Methodless terms returned<br />
  353. 353. Conditional Methodless<br />No methodless term; all shown<br />More terms returned<br />
  354. 354. Setting Search Limits<br />Limit to Lab Tests Only <br />(No Clinical LOINC Terms)<br />
  355. 355. Setting Search Limits<br />Limit to lab tests that comprise 99.8% of INPC volume<br />
  356. 356. Setting Search Limits<br />Limit Number of Words in the Component Attribute<br />
  357. 357. Limit Number of Component Words<br />Without Limit Applied: 800 terms returned<br />
  358. 358. Limit Number of Component Words<br />Restriction appears on Toggle Bar <br />(cannot toggle off)<br />Component limited to 1 word<br />With Limit Applied: <br />67 terms returned<br />
  359. 359. Setting Search Limits<br />Include Deprecated LOINC Codes with Returned Terms<br />
  360. 360. Include Deprecated LOINC Terms<br />You cannot map to deprecated LOINC terms<br />Deprecated LOINC Terms appear as Strikethrough Text with a “Do Not” Symbol <br />
  361. 361. Favor Property Restriction<br />All other components being equal MCnc only will be displayed<br />Favor one type of property over others<br />
  362. 362. Order/Observation Restriction<br />Order or Observation preference<br />
  363. 363. LOINC Hierarchies – Class Tree<br />Three top-level branches<br />Tree Navigation Buttons<br />
  364. 364. Before Class Restriction<br />Most terms have class of “CHAL”<br />Large number of candidate terms<br />
  365. 365. Search Trees<br />chal<br />Restrict eligible tests to non-challenge chemistry tests only<br />
  366. 366. Following Class Restriction<br />Only Non-Challenge Chemistry tests returned<br />
  367. 367. Improvements to Trees<br />Continued reorganization to provide a Specimen hierarchy<br />
  368. 368. Improved Hierarchy for Component<br />Show the LOINC Codes associated with these components<br />
  369. 369. Show Associated LOINCs<br />Click on details for more information about the selection<br />
  370. 370. Details Screen LOINC Part<br />
  371. 371. Details Screen LOINC Term<br />Detailed Information on LOINC Parts<br />
  372. 372. Tree Export Tools<br />Export according to Configuration <br />Configure Export Format <br />
  373. 373. Tree Export Configuration<br />
  374. 374. RELMA - Tree Features<br /><ul><li>All trees operate the same way
  375. 375. Shows terms spelled out
  376. 376. Can expand and collapse parts or all of tree.
  377. 377. Tree is string searchable
  378. 378. Search can be based on one or more branches of a tree with or without other criteria
  379. 379. Use “Clear Most Limits” button on Mapping Screen to remove all tree selections</li></li></ul><li>Navigating through the Mapping Process<br />
  380. 380. LOINC Mapping Tactics<br /><ul><li>Limit effort to one lab section at a time and focus expertise
  381. 381. Chemistry and hematology will be easiest
  382. 382. Consider prioritizing by frequency</li></li></ul><li>Vreeman DJ, Finnell JT, Overhage JM. A Rationale for Parsimonious Laboratory Term Mapping by Frequency. AMIA Annu Symp Proc. 2007;:771-775.<br />
  383. 383. More LOINC Mapping Tactics<br /><ul><li>Try using method-less terms first
  384. 384. Specific methods can be transmitted in:
  385. 385. OBX–17 (v2.x), Observation.methodCode (v3.0)
  386. 386. Examine local units or real results to verify correct properties
  387. 387. Properties are rarely distinguishable in tests
  388. 388. You don’t have to do it all at one sitting
  389. 389. Use the “Unmapped” function to return where you left off
  390. 390. With every release - Update previous mappings to identify deprecated terms</li></li></ul><li>Common Mapping Issues<br /><ul><li>Locally Defined Test Name Ambiguity
  391. 391. Reuse of local test code
  392. 392. “Analyte-free” Local Test Names
  393. 393. Incongruent Value sets (Scale ambiguity)
  394. 394. Result vs. Interpretation
  395. 395. Available LOINC Terms too Specific
  396. 396. Available LOINC Terms too General
  397. 397. Panel vs. Discrete Test
  398. 398. Common in Microbiology</li></li></ul><li>Using your Mapped Terms<br /><ul><li>Print results of LOINC Mapping
  399. 399. Export to File</li></li></ul><li>Configure Export Format<br />Context Sensitive Export Configuration <br />
  400. 400. LMOF Export Configuration<br />Select Export Format <br />Select Fields to Export<br />Save Configuration and Export<br />
  401. 401. Print Mapped Terms from View/Add/Edit Menu<br />Click Print button to Preview output<br />Must highlight terms to be printed<br />
  402. 402. Formatted Report Output<br />Click Print button to output formatted report<br />
  403. 403. Custom Export Configuration<br />Select the Format you wish to Export<br />Select the Fields you wish to Export<br />
  404. 404. Excel™ Export<br />
  405. 405. Intelligent Mapper <br /><ul><li>Run in batch mode to find N- closest terms
  406. 406. Can then use this output to do final mapping
  407. 407. Again units are VERY important
  408. 408. Can pick all limits available to regular mapping
  409. 409. With Radiology can use CPT to help
  410. 410. Intelligent Mapper Radiology References
  411. 411. Vreeman DJ, McDonald CJ. A Comparison of Intelligent Mapper and Document Similarity Scores for Mapping Local Radiology Terms to LOINC. Proc AMIA Symp. 2006;809-813.
  412. 412. Vreeman DJ and McDonald CJ. Automated Mapping of Local Radiology Terms to LOINC. Proc AMIA Symp. 2005;769-773.</li></li></ul><li>Picking the Intelligent Mapper<br />Begin by finding qualifying candidates based on local file attributes<br />
  413. 413. Intelligent Mapper Start Screen<br />Max search time per local term<br />May Apply Hierarchy Restrictions Prior to Run<br />
  414. 414. Intelligent Mapper - Mapping Screen<br />
  415. 415. Exporting Mapped Terms<br />Export Terms to Delimited File<br />Now a button on the Main Window!<br />
  416. 416. Export Terms Dialog<br />Select Term Set<br />Select Delimiter<br />Check Fields you wish to export<br />
  417. 417. Other RELMA® Features<br />
  418. 418. Panels, Forms and Survey Review<br />Review Panels, Forms and Surveys<br />Review Panels, Forms and Surveys<br />
  419. 419. Government Forms<br />Component LOINC terms<br />Form Name<br />
  420. 420. Laboratory panels<br />Expand category to see panels <br />Double-click panel name to see components<br />
  421. 421. Expanded Panel Detail<br />
  422. 422. Expanded Clinical Panel<br />
  423. 423. Clinical Panels<br />35089-2, 35090-0<br />Find where a term has been used<br />
  424. 424. LOINC Term Panel Usage<br />
  425. 425. Other Survey Instruments<br />
  426. 426. HIPAA Attachments<br />View Various HIPAA Attachments <br />
  427. 427. HIPPA Attachment Tree<br />
  428. 428. Expanded Attachment Data<br />
  429. 429. Context Specific Hierarchies<br /><ul><li>Allows local definition of LOINC code hierarchies
  430. 430. Template data base is provided with RELMA
  431. 431. CONTEXT_SPECIFIC_HIERARCHY_TEMPLATE.mdb
  432. 432. Does not support .accdb format
  433. 433. Hierarchies can be displayed (only) in RELMA
  434. 434. Codes and terms may come from multiple code systems</li></li></ul><li>Access Context-Specific Hierarchies<br />Select Context Specific Hierarchies<br />
  435. 435. Context Specific Hierarchies<br />Change schema using the File Menu<br />
  436. 436. Can’t find the term you want?<br />
  437. 437. Search Hints and Tips<br /><ul><li> Keywords with zero frequency are ignored
  438. 438. May need to rephrase – use synonym
  439. 439. Some causes for no returned terms
  440. 440. Too many keywords in search – uncheck some
  441. 441. Limits applied that don’t make sense
  442. 442. E.g. Method-less tests plus Method tree set to EIA
  443. 443. Did not find and revise words not in RELMA
  444. 444. Local units not in RELMA
  445. 445. Units are GREAT discriminators
  446. 446. You may have tests that need to be added to LOINC</li></li></ul><li>Proposing New LOINC Terms<br />
  447. 447. Proposing New Terms<br /><ul><li>Make sure the term is really needed
  448. 448. Think of other names for the same concept
  449. 449. Avoid detailed methods or localizations
  450. 450. Is the distinction really important?
  451. 451. Supply sufficient annotation to justify the new term
  452. 452. Package inserts, sample reports (email to Regenstrief)
  453. 453. The more the better!
  454. 454. Construct new terms within RELMA
  455. 455. File>Propose a LOINC
  456. 456. Linked to the “trees” to allow browsing
  457. 457. Can review and submit them to LOINC from within RELMA</li></li></ul><li>Propose new LOINC terms<br />Select Propose a LOINC<br />
  458. 458. Propose new LOINC terms<br />Required fields<br />Create new term, save current term or Exit form<br />Navigate through proposed terms<br />
  459. 459. Preview Proposed Terms<br />Review your new terms<br />
  460. 460. Preview Proposed Terms<br />Choose whether to send or postpone<br />X<br />X<br />X<br />X<br />All proposed terms fully editable<br />
  461. 461. Use Existing Terms as Template<br />Click the Propose Term button<br />Select your closest match<br />
  462. 462. Use Existing Terms as Template<br />All required components filled in<br />
  463. 463. Using LOINC and SNOMED Together<br />
  464. 464. Where do LOINC and SNOMED Fit?<br /><ul><li>LOINC represents the question:
  465. 465. Is there any Botulism toxin in my specimen? (33708-9)
  466. 466. Organisms identified in specimen? (634-6)
  467. 467. SNOMED represents the answer:
  468. 468. Negative (SCTID 260385009)
  469. 469. E. coli O157:H7 (SCTID 103429008)</li></ul>Remember:<br />
  470. 470. Where do LOINC and SNOMED Fit?<br /><ul><li>In an HL7 message, LOINC may be used:
  471. 471. In OBR-4 (Universal Service Identifier)
  472. 472. In OBX-3 (Observation Identifier
  473. 473. SNOMED may be used:
  474. 474. In OBX-5 (where nominal values are needed)
  475. 475. Almost anyplace else in an HL7 message where coded values are needed</li></li></ul><li>OBX: With a Coded Value<br />A code that identifies the data type in <br />OBX-5 as a<br />coded element<br />The code is<br />from LOINC<br />The code is<br />from SNOMED<br />OBX-3:A code that identifies the data in OBX-5(Listeria culture)<br />OBX-5: Data<br />A code for L. monocytogenes<br />OBX||CE|6609-2^Listeria ID^LN||36094007^L. monocytogenes^SCT<br />
  476. 476. HL7 2.5 Example (ER-7 format)<br />First Result (Culture and ID)<br />First Result (Culture and ID)<br />Second Result(s) <br />OBXs<br />MSH|^~&| LABGL1|| DMCRES|| 199812300100|| ORU^ R01| LABGL1199510221838581| P| 2.3||| NE| NE<br />PID||| 6910828^ Y^ C8|| Newman^ Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^<br />Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090<br />OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult <br />^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^ UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN<br />OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium ^SCT|||||| F||| 199812292128|| CA20837<br />OBR|| 110801^ LABGL| 387209373^ DMCRES| 29567-9^Bacterial Susceptibility Panel^ LN||| 199812300934||||||||Bacterial isolate| IN2973^ Schadow^ Gunther^^^^ MD^ UPIN||||||||| Salmonella typhimurium ||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN<br />OBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006^Intermediate ^SCT|||||| F||| 199812300934|| CA20837<br />OBX|| CE|18967-7^Penicillin^LN||30714006^Resistant^SCT|||||| F||| 199812300934|| CA20837<br />OBX|| CE|18928-2^Gentamicin^ LN||131196009^Susceptible^SCT|||||| F||| 199812300934|| CA20837<br />First Order OBR (Culture and ID)<br />First Result Value (SNOMED)<br />Second Order OBR (Susceptibility)<br />First Result Description OBX (LOINC)<br />
  477. 477. Q and A Session<br />
  478. 478. ExerciseMap your own data<br />

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