1. Using RELMA Or…In Search of the Missing LOINC Laboratory LOINC Meeting – December 2009 James T. Case MS, DVM, PhD Professor, Clinical Diagnostic Informatics California Animal Health and Food Safety Laboratory University of California, Davis

3. John Hook, Mark Fisher, Ryan Phillips, Karen Ahmad, and more!

4. Kathy Mercer

5. Clem McDonald

6. Dan Vreeman

7. The Lab LOINC Committee

8. Funding Support

10. Overview of LOINC

11. Installing RELMA

12. Setting personal preferences

13. Loading a Local Observation File (LMOF)

14. Searching for a LOINC Term

15. Preparing LMOF for Mapping

16. Review of Map Screen Functions

17. Setting Search Limits

18. Mapping Local Terms to LOINC

19. Viewing LOINC Term Details

20. Proposing/Submitting New LOINC Terms

21. Exporting/Printing Mapped Terms

23. Comparability – the ability to ascertain the equivalence of data from different sources

25. Word processing documents, text messages

26. Functional – describes the standard syntax (format) of the message

27. Document templates, forms, data structures

28. Message standards

30. Erysipelas – Human skin disease; StreptococcusGrp A

31. Erysipelas – Animal Septicemia – Erysipelothrixrhusiopathiae

32. Common terminology required

33. Should work in the background

34. Not just words

35. Codes – uniquely identifies terms

36. Classification – groups related terms

38. Different for client communications vs. analysis

39. Often constrained by external forces

40. E.g. criteria for diagnosis often differs from the criteria for reporting

41. Unidirectional effect of data consolidation

42. Detailed → General

44. What you see in the order list Test comparisons Lab A Test Name:Lyme Disease Serology Measures:B. burgdorferi Ab IgG Method: ELISA Scale: quantitative e.g.: Titer 1:40 Lab B Test Name:Lyme Disease Antibody Measures:B. burgdorferi Ab IgM Method: Immune blot Scale: qualitative e.g.: Positive LOINC Code = 5062-5 LOINC Code = 6321-4

45. Why LOINC? “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.” 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

46. LOINC® 101

47. Anatomy of a LOINC Term 5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA LOINC Code 5193-8 Hepatitis B virus surface Ab Component ACnc Property Measured Pt Timing Ser System Qn Scale EIA Method There are six major LOINC axes

49. Specific details about the specimen

50. Priority (e.g. STAT)

51. Where testing was done

52. Who did the test

53. Test interpretation

54. Anything that is not an intrinsic part of the name of the result

55. Other things that are carried in;

56. The OBR or OBX segment

58. Lipids.Total5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA

60. Must specify any “subanalyte”

61. e.g. Coronavirus Ag

62. May have a subclass – separated by “.”

63. e.g. Calcium.Free

64. Challenge - e.g, 1H post 100 gm Glucose PO

65. Two subparts separated by “post”

67. Adjustments/corrections

69. Substance: Observations reported with moles or milliequivalents in the numerator of their units of measure

70. Catalytic activity: Observations that report enzymatic activity

71. Arbitrary: Results that report arbitrary units in the numerator of their units of measure

72. Number: Counts5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA

74. MCnt – mass content (mass/unit mass)

75. NCnc – number concentration (number/unit vol)

76. TmStp – time

77. CCnc – catalytic concentration (activity)

78. Prid – presence or identity

79. Imp – impression/interpretation

80. Find – subjective or objective observation

81. Type – “Kind-of”5193-8:Hepatitis B virus surface Ab:ACnc:Pt:Ser:Qn:EIA

83. Number fraction (NFr): % Eosinophils

84. Substance fraction (SFr): % HGB which is A2

85. Ratio = Measures multiple analytes from the same system (specimen)

86. Mass concentration ratio - MCrto

87. e.g., BUN/Creat in urine specimen

88. Substance ratio-SCrto

89. Urea/Creatinine expressed as mmol/L (SI units)

90. Relative Ratio = Measures from different systems

91. RelRto – multiple of the median

93. 12H - a twelve hour collection

94. 24H - a twenty four hour collection*non-Pt timings are usually associated with Ratio Property

95. System The system (context) or specimen type upon which the observation was made. Ser - Serum Bld - Whole blood (RBC) Ur- Urine BldA - Arterial blood Liver - Liver Flu – Body Fluid, unspecified Gast – Gastric fluid/contents Food – Food or feedstuff Tiss – Tissue XXX – To be specified in another part of the message Super System Second subpart (^). When not included, “patient” is the default. Used to indicated blood product unit (BPU), a bone marrow donor, or a fetus.

97. Continuous numeric (real, integer, ratio)

98. Optional operator (>, , , <)

99. When assay detection limits are exceeded

100. Ord - ordinal

101. a ranked set of possible values (1+, 2+, 3+)

102. Nom - nominal

103. an unranked collection of possible values

104. a taxonomy (e.g list of bacteria)

105. Nar - narrative

107. Primarily used for antimicrobial observations e.g. MIC reported as resistant, intermediate, susceptible or as the mm diameter of the inhibition zone

108. Use is discouraged

109. Multi – structured text “globs”

110. e.g. chromatography output

111. Use is discouraged

112. Doc – Clinical documents

114. Different normal ranges

115. Test Sensitivity

116. Listed only at the generic level

117. Agglutination

118. Immunoassay

120. Blood Culture – live organism(s) identified

121. VDRL – TreponemapallidumAb

122. Urinalysis – lots of different things

123. The question (what am I measuring? e.g. Glucose) is not the answer (e.g. 90 mg/dl)

124. You are mapping the question, not the answer!

127. Become familiar with RELMA features

128. Provide some insight into mapping tips/pitfalls

129. Help begin the mapping process for your institution

131. Uses Microsoft Windows Installer

132. New “Lookup” Screen

133. Simplified access to LOINC term lookup

134. Misspellings have context “suggestions”

135. Display details now more accessible

136. Export configuration and printing more flexible

138. Same free use as LOINC (see license)

139. Comes with the LOINC files and indexes

140. Now migrated to MS .NET environment.

141. RELMA tools transform local words in local file

142. User creates file of local term/name and codes

143. Assigns LOINC term to local test/battery code

146. Display search results in tree view

147. Enhanced “details” view of terms/parts

148. References

149. Descriptions

150. Sample units

151. Empirically-derived common test list

152. Special features for panels/forms

154. A set of words connected by ANDs or Ors

155. Additional keyed in words

156. A particular category of test (e.g. microbiology)

157. Wild cards of ? and *

158. Selected classes, systems, components,

159. Any intersection of the aboveNote: RELMA assumes exact match on word unless user adds terminal “*” to indicate wild card.

160. RELMA Logic Not  #&lt;word A&gt; Or  &lt;word A&gt; | &lt;word B &gt; And  &lt;word B&gt; &lt;word A&gt;

162. Selectable trees for:

163. Class

164. System (specimen)

165. Component

168. 1Gb is recommended

169. From CD - Start – Run – D:ELMAetup

170. Specify installation directory

171. Life will be easier if you accept the default

172. Two database files installed

173. RELMA.MDB – LOINC Terms Database

174. LMOF3.MDB – Local Master Observation File

175. Two sample files copied

176. WinXP: C:ocuments and Settingssernamey DocumentsELMAamples

177. Vista: C:sersouraccountocumentsELMAamples

179. Copyright Screen

180. Main Menu/Welcome Screen Click File, Set Preferred Language

181. Select Linguistic Variant(s)

182. LOINC Terms with Spanish Linguistic Variant Spanish!

183. Welcome Screen New Feature!

184. Setting User Preferences

185. Set User Preferences Select User Preferences From the File Menu ...or from Welcome Screen

186. Set User Preference Dialog New File Locations: Now stored in My Documents Startup Screen Preference

187. User Map Screen Preferences Click Map Screen Tab Include/Exclude Battery Terms Add comments on Mappings

188. Importing Local Terms into RELMA

190. Handy for individual entries/edits

191. Create an Access table that mimics the LMOF structure (less painful but tedious)

192. Appendix A: RELMA Manual

193. Create a delimited ASCII file from your local test catalog (good choice)

194. Load directly from HL7 v2.x messages

195. Pulls data from OBR and OBX segments

197. Battery/Panel Description or Name

198. *Local Code

199. *Test Description or Name

200. Include Method if Important

201. Units

202. Example Values

204. Need to create separate fields

205. Can use any of these delimiters

206. Tab, Semicolon, Comma, Space

207. Can define your own

208. Fields can be in any order

209. Minimum required fields

210. Local Code

211. Local Description

213. Manual Enter/Edit View/Add/Edit Local Terms

214. Edit Term Dialog Text alignment option Editddelete Terms Search Terms by Keyword Print Preview List

215. Add Local Term MICRO BUBPLAG BUBONIC PLAGUE – RRT PCR Click to Add to Current Working File

216. Search Local Term File Hematocrit Enter Keyword from any Field Return to Full List

217. Print Preview Local Term File Must Select Terms you want to appear

218. Steps to Import Local Terms Click Import Local TermsButton from Main Menu a)File&gt;Import Local Terms from Delimited File Locate your local terms text file Sample file loaded into C:rogram FilesELMA Name your Working Set LMOF database can contain multiple work sets Define default section (Optional) Identify file delimiter Assign fields to LMOF attributes Ignore fields you don’t need Combine fields if needed Check “Case-sensitive” if needed Click Import.

219. Local Term File Options

220. Example Tab-Delimited File

221. Importing Local Files Select Import Local Terms

222. Navigate to File Location Select File and Click Open Sample files stored in RELMA Directory

223. Open File in RELMA Name your working set. RELMA allows multiple sets in LMOF database Select your delimiter Import Button

224. Open File in RELMA

225. Fields Segregated Assign LMOF Attribute Choose field name

226. Ready to Import Minimum assignments Now you can click the Import button!

227. Change Local Term File Select the Working Set

229. Automatically make dataset of:

230. OBR ID

231. OBR description

232. OBX ID

233. OBX description

234. Sample of results with

235. Real values

236. Units

237. Abnormal flags

239. Select File to Import Select HL7 File

240. Specify HL7 File Name and Sample Size Name the Local Term File (working set) Select the number of sample values Select which codes to store

241. HL7 Messages Data Statistics

242. New Terms added to LMOF Click on “Edit Test to see Sample Data New Battery Code

243. Sample Results for Observation New Test Code Sample Values from Messages

245. Import_Sample_OBR.txt

246. Contains battery code and description

247. Import_Sample_OBX.txt

248. Contains test code and description

251. Expanding abbreviations

252. Standardizing colloquial terms

253. Ignoring “administrative” terms

254. Standardizing time references

255. Can be done prior to importing

257. Tools>Concepts in Local Term File Unknown to RELMA

258. Creates a list of local terms in your file not found in LOINC

259. Only needs to be run once per working set version

260. Can be printed or saved as a file

261. Autosearches LOINC terminology

263. Scanning Local Terms Scan File for Unknown Terms

264. Replace Local Terms Assign LMOF Attribute ReplacementOptions

265. RELMA Cleaning Tools Use this tool to make global substitutions

266. Term Substitution Save this global substitution for only this working set

267. Searching for LOINC Terms

268. New Simplified Search Only Tool

269. Search Window Enter Search Terms Limit to Specific Units Limit to Common Tests

270. Mapping Local Terms

272. Select your Working Set to Map

273. File>Change Local term File

274. Select the subset of terms to work with:

275. All

276. Mapped

277. Unmapped

278. Set your Search Limits

280. View details of LOINC term

281. Sort by column

282. Click column

283. Custom Sort

284. Print or export results grid

286. Configure Grid Select elements to display Reorder grid elements Visually resize elements Reset Default Configuration

287. View Local Term Details

288. Standard Mapping Screen Begin a search

289. Initial Mapping Results EEK! What’ll I do?! Click to show words used in search

290. Initial Mapping Results Use term checkbox Number of LOINC terms containing keyword Battery terms included in search

291. Revised Mapping Results Match units selected by default Number of matching records found

292. Re-revised Mapping Results Number of matching records found Match units unselected

293. Standard Mapping Screen Clear all input fields

294. Cleared Mapping Screen CANINE DISTEMPER VIRUS IF Enter keywords here

295. Ad hoc term search

296. Standard Mapping Screen Navigate through the local terms

297. Tabbed Access to Functions Navigate to Functions from Mapping Page Switch between Grid and Tree Views

298. Tree View

300. Defined by the multi-axial hierarchy in search restrictions (covered later)

301. Map to a term in tree by clicking Map button or double clicking term

303. Assigning a LOINC Map Click “Map” Button (or doubleclick) Highlight correct term

304. Adding Mapping Comments Check with Frank in Chemistry If comments option is selected, prompt appears

305. Assigning a LOINC Map LOINC Term Assigned

306. View LOINC Term Details View details for a specific LOINC Term Right clicking on a LOINC term brings up a Task Menu

307. LOINC Term Details Can scroll down a single formatted page Can scroll through returned subset of terms Change to expanded details view Change text size

308. Configure Export Options Output Options Include column headers Save Configuration and/or Export

309. Excel Export Format

310. More on Searching Mapping Screen

312. “Gluc” yields any terms with “gluc” in the component/analyte

313. “*” replaces any number of characters

314. GLUC*

315. *COSE

316. GLU*SE

317. “?” replaces a single character

318. GLUCOS?

319. ?LUCOSE

321. #GLUCOSE – terms without the Word Glucose

322. “|” is the “OR” operator

323. GLUCOSE | LACTOSE

324. Can have multiple “OR”s per box

326. Combining Search Terms Exclude Glucosidase Reduced number of terms

327. Limiting Searches

329. Reduces number of candidate terms

330. Limits can be applied to all components

331. Component attribute can be further restricted by number of words

333. Limit to LOINC terms compatible with submitted units

334. Forced match with any specimen contained in name

335. Methodless terms only

336. Limit to components/analytes with N or fewer words in their name

337. Pop up search timing statistics after each search

338. Use carefully or search may not be successful (Note parallel control switches at bottom of screen)

339. Setting Search Limits Click Hierarchy & Search Limits Tab

340. Setting search limits Can also set most of them by toggling buttons at the bottom of the screen Toggle Buttons

341. Search Constraints Attribute trees Local Unit Constraint: Now defaults to “ON” Predefined, general search constraints

342. Terms Consistent with Units Only terms consistent with mmol/L appear

343. Setting Search Limits Specimen constraints

344. Terms Consistent with Specimen CSF Enter default Specimen

345. Terms Consistent with Specimen Only CSF Terms are returned

346. Setting Search Limits Methodless Terms Restriction Override Methodless Terms Restriction

347. Limit to Methodless Terms

348. Limit to Methodless Terms Only Methodless Terms Appear

350. Checking methodless only will remove these from view on results grid

352. Methodless Only Checked Differ in one or more components Only Methodless terms returned

353. Conditional Methodless No methodless term; all shown More terms returned

354. Setting Search Limits Limit to Lab Tests Only (No Clinical LOINC Terms)

355. Setting Search Limits Limit to lab tests that comprise 99.8% of INPC volume

356. Setting Search Limits Limit Number of Words in the Component Attribute

357. Limit Number of Component Words Without Limit Applied: 800 terms returned

358. Limit Number of Component Words Restriction appears on Toggle Bar (cannot toggle off) Component limited to 1 word With Limit Applied: 67 terms returned

359. Setting Search Limits Include Deprecated LOINC Codes with Returned Terms

360. Include Deprecated LOINC Terms You cannot map to deprecated LOINC terms Deprecated LOINC Terms appear as Strikethrough Text with a “Do Not” Symbol

361. Favor Property Restriction All other components being equal MCnc only will be displayed Favor one type of property over others

362. Order/Observation Restriction Order or Observation preference

363. LOINC Hierarchies – Class Tree Three top-level branches Tree Navigation Buttons

364. Before Class Restriction Most terms have class of “CHAL” Large number of candidate terms

365. Search Trees chal Restrict eligible tests to non-challenge chemistry tests only

366. Following Class Restriction Only Non-Challenge Chemistry tests returned

367. Improvements to Trees Continued reorganization to provide a Specimen hierarchy

368. Improved Hierarchy for Component Show the LOINC Codes associated with these components

369. Show Associated LOINCs Click on details for more information about the selection

370. Details Screen LOINC Part

371. Details Screen LOINC Term Detailed Information on LOINC Parts

372. Tree Export Tools Export according to Configuration Configure Export Format

373. Tree Export Configuration

375. Shows terms spelled out

376. Can expand and collapse parts or all of tree.

377. Tree is string searchable

378. Search can be based on one or more branches of a tree with or without other criteria

381. Chemistry and hematology will be easiest

384. Specific methods can be transmitted in:

385. OBX–17 (v2.x), Observation.methodCode (v3.0)

386. Examine local units or real results to verify correct properties

387. Properties are rarely distinguishable in tests

388. You don’t have to do it all at one sitting

389. Use the “Unmapped” function to return where you left off

391. Reuse of local test code

392. “Analyte-free” Local Test Names

393. Incongruent Value sets (Scale ambiguity)

394. Result vs. Interpretation

395. Available LOINC Terms too Specific

396. Available LOINC Terms too General

397. Panel vs. Discrete Test

400. LMOF Export Configuration Select Export Format Select Fields to Export Save Configuration and Export

401. Print Mapped Terms from View/Add/Edit Menu Click Print button to Preview output Must highlight terms to be printed

402. Formatted Report Output Click Print button to output formatted report

403. Custom Export Configuration Select the Format you wish to Export Select the Fields you wish to Export

404. Excel™ Export

406. Can then use this output to do final mapping

407. Again units are VERY important

408. Can pick all limits available to regular mapping

409. With Radiology can use CPT to help

410. Intelligent Mapper Radiology References

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.

413. Intelligent Mapper Start Screen Max search time per local term May Apply Hierarchy Restrictions Prior to Run

414. Intelligent Mapper - Mapping Screen

415. Exporting Mapped Terms Export Terms to Delimited File Now a button on the Main Window!

416. Export Terms Dialog Select Term Set Select Delimiter Check Fields you wish to export

417. Other RELMA® Features

418. Panels, Forms and Survey Review Review Panels, Forms and Surveys Review Panels, Forms and Surveys

419. Government Forms Component LOINC terms Form Name

420. Laboratory panels Expand category to see panels Double-click panel name to see components

421. Expanded Panel Detail

422. Expanded Clinical Panel

423. Clinical Panels 35089-2, 35090-0 Find where a term has been used

424. LOINC Term Panel Usage

425. Other Survey Instruments

426. HIPAA Attachments View Various HIPAA Attachments

427. HIPPA Attachment Tree

428. Expanded Attachment Data

430. Template data base is provided with RELMA

431. CONTEXT_SPECIFIC_HIERARCHY_TEMPLATE.mdb

432. Does not support .accdb format

433. Hierarchies can be displayed (only) in RELMA

435. Context Specific Hierarchies Change schema using the File Menu

436. Can’t find the term you want?

438. May need to rephrase – use synonym

439. Some causes for no returned terms

440. Too many keywords in search – uncheck some

441. Limits applied that don’t make sense

442. E.g. Method-less tests plus Method tree set to EIA

443. Did not find and revise words not in RELMA

444. Local units not in RELMA

445. Units are GREAT discriminators

448. Think of other names for the same concept

449. Avoid detailed methods or localizations

450. Is the distinction really important?

451. Supply sufficient annotation to justify the new term

452. Package inserts, sample reports (email to Regenstrief)

453. The more the better!

454. Construct new terms within RELMA

455. File>Propose a LOINC

456. Linked to the “trees” to allow browsing

458. Propose new LOINC terms Required fields Create new term, save current term or Exit form Navigate through proposed terms

459. Preview Proposed Terms Review your new terms

460. Preview Proposed Terms Choose whether to send or postpone X X X X All proposed terms fully editable

461. Use Existing Terms as Template Click the Propose Term button Select your closest match

462. Use Existing Terms as Template All required components filled in

463. Using LOINC and SNOMED Together

465. Is there any Botulism toxin in my specimen? (33708-9)

466. Organisms identified in specimen? (634-6)

467. SNOMED represents the answer:

468. Negative (SCTID 260385009)

469. E. coli O157:H7 (SCTID 103429008)Remember:

471. In OBR-4 (Universal Service Identifier)

472. In OBX-3 (Observation Identifier

473. SNOMED may be used:

474. In OBX-5 (where nominal values are needed)

476. HL7 2.5 Example (ER-7 format) First Result (Culture and ID) First Result (Culture and ID) Second Result(s) OBXs MSH|^~amp;| LABGL1|| DMCRES|| 199812300100|| ORU^ R01| LABGL1199510221838581| P| 2.3||| NE| NE PID||| 6910828^ Y^ C8|| Newman^ Alfred^ E|| 19720812| M|| W| 25 Centscheap Ave^^ Whatmeworry^ UT^ 85201^^ P||( 555) 777- 6666|( 444) 677- 7777|| M|| 773789090 OBR|| 110801^ LABGL| 387209373^ DMCRES|634-6^Bacteria XXX Aerobe Cult ^LN||| 199812292128||||||||Stool| IN2973^ Schadow^ Gunther^^^^ MD^ UPIN|||||||||||||||| CA20837^ Spinosa^ John^^^^ MD^ UPIN OBX|| CE| 634-6^Bacteria XXX Aerobe Cult^ LN||50136005^Salmonella typhimurium ^SCT|||||| F||| 199812292128|| CA20837 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 OBX|| CE|23631-5^Trimethoprim/Sulfasoxazole^ LN||264841006^Intermediate ^SCT|||||| F||| 199812300934|| CA20837 OBX|| CE|18967-7^Penicillin^LN||30714006^Resistant^SCT|||||| F||| 199812300934|| CA20837 OBX|| CE|18928-2^Gentamicin^ LN||131196009^Susceptible^SCT|||||| F||| 199812300934|| CA20837 First Order OBR (Culture and ID) First Result Value (SNOMED) Second Order OBR (Susceptibility) First Result Description OBX (LOINC)

477. Q and A Session

478. ExerciseMap your own data