============================================================================= Run Date: SEP 24, 2013 Designation: LA*5.2*82 Package : LA - AUTOMATED LAB INSTRUMENTS Priority: EMERGENCY Version : 5.2 SEQ #58 Status: Released Compliance Date: OCT 04, 2013 ============================================================================= Subject: UPDATE PROCEDURES FOR SNOMED CT LABORATORY MAPPINGS Category: - Informational Description: ============ This patch is an information patch containing the procedures for updating the SNOMED CT (Systemized Nomenclature of Medicine Clinical Terms) laboratory mappings. 1. SNOMED CT codes are used in the Laboratory application and are mapped to the following files: TOPOGRAPHY FIELD file (#61), ETIOLOGY FIELD file (#61.2), and COLLECTION SAMPLE file (#62). SNOMED CT mappings are local to each facility and may need to periodically be updated (for example, an update might be needed due to a site adding new entries to the above mentioned files, or if existing entries need to be mapped to new SNOMED CT codes). When an update is available for a site, Standards & Terminology Services (STS) will send an email to the Laboratory Information Manager (LIM) to notify the site that there is a new mapping file for them to download and process. It is the responsibility of local or regional Office of Information and Technology (OI&T) personnel (aka, Information Resource Management (IRM)) to download the SNOMED CT mapping file for their facility. Communication needs to be in place between OI&T and Laboratory Service with respect to the process and who will be installing this SNOMED CT file. The SNOMED CT mapping files are stored on the Hines Office of Information (OI) Field Office File Transfer Protocol (FTP) server, under the ANONYMOUS.LAB_SNOMED_CT directory. This directory is NOT replicated to the Albany or Salt Lake City OI Field Office FTP servers. FTP server: ftp.fo-hines.domain.ext Username: anonymous Directory: ANON$:[ANONYMOUS.LAB_SNOMED_CT] File Name*: SITEID_SCT_MM_DD_YY.TXT *For the file name, "SITEID" is your three digit site ID, and "MM_DD_YY" is the date the file was created. Example: 581_SCT_07_04_13.txt Make sure you only download the file for your site. 2. When an updated SNOMED CT mapping file is available, IRM staff will need to FTP the file to an appropriate directory on the local Veterans Health Information Systems and Technology Architecture (VistA) server. Ensure the file is downloaded in the correct format (ASCII). IRM staff must communicate with the Laboratory Information Manager (LIM) to coordinate an acceptable time in which the update can be installed. 3. The option Load SNOMED SCT Mapping [LA7S LOAD MAPPING SCT] will be used to load and process the SNOMED CT mapping file after the file is downloaded to a local directory on the Vista system. This option should be run by IRM staff, because access to the directory level of a system is a security issue and access is usually limited to IRM personnel. (Note: for more information about this option, see the LEDI IV User Manual, section 5.3.20, entitled "Load SNOMED SCT Mapping [LA7S LOAD MAPPING SCT]"). 4. When running the option, the user will be prompted with the following prompts: a. "Host File Directory: xxxx$:[xxxx]//" - Enter the directory where you downloaded the file to (Note: do not enter the file name here - just enter the directory name). b. "Select FILE:" - Enter a double question mark ("??") to get a list of '.txt' files that are in the selected directory. Select FILE: 1// ?? 1 581_SCT_4_25_12.TXT;1 2 581_SCT_6_25_13.TXT;1 Select a file by number from the list The file to load can be selected by number reference. c. Processing Action: Select one of the following: 0 Quit - no action 1 Process SNOMED CT mappings directly 2 Task processing SNOMED CT mappings Processing Action: 0// Select option 1 to process the SNOMED CT mappings directly. Example of executing steps #3 and #4: ------------------------------------- Select Lab liaison menu Option: SMGR Lab Shipping Management Menu Select Lab Shipping Management Menu Option: LSCT Load SNOMED SCT Mapping HOST FILE DIRECTORY: USER$:[TEMP]// Using filespec *.TXT Select FILE: 1// ?? 1 581_SCT_12-14-10.TXT;2 2 HUNT_CORRECT_3-31-11.TXT;1 3 LEDI_LEDI COTS_IP_PORT_CONFIGURATION.TXT;1 4 RELNOTES.TXT;3 5 WORKLOAD_TO_VISTA_201012.TXT;1 Select a file by number from the list Select FILE: 1// 1 Directory: USER$:[TEMP] File.....: 581_SCT_12-14-10.TXT;2 Loading file into TMP global ...SORRY, LET ME THINK ABOUT THAT A MOMENT... Processing file data and storing in file #95.4 ...SORRY, JUST A MOMENT PLEASE... Records added: 13685 Select one of the following: 0 Quit - no action 1 Process SNOMED CT mappings directly 2 Task processing SNOMED CT mappings Processing Action: 0// 1 Process SNOMED CT mappings directly Loading files with National SNOMED CT Codes ********************************************** Loading file #61 [TOPOGRAPHY FIELD] **********************************************....... Lexicon SCT lookup error STS alert sent.. Lexicon SCT lookup error STS alert sent.... No such entry: File #61 IEN:8830 STS alert sent. ************************************************ Loading file #61.2 [ ETIOLOGY FIELD ] ************************************************ Lexicon SCT lookup error STS alert sent. Names do not match: [CLOSTRIDIUM DIFFICILE TOXIN A/B POSITIVE < - > CLOSTRIDIUM DIFFICILE TOXIN B DNA DETECTED] STS alert sent. Lexicon SCT lookup error STS alert sent. ************************************************ Loading file #62 [ COLLECTION SAMPLE ] ************************************************ Lexicon SCT lookup error STS alert sent. Lexicon SCT lookup error STS alert sent. 5. After the SNOMED CT Mapping file is loaded, it should be deleted from the local directory. 6. In conjunction with this patch release, an updated mapping file is being released for all sites. This file should be downloaded and loaded by IRM staff using the process outlined above. In the future, updated mapping files will be made available on a site-by-site basis. When a mapping file is ready for a site to load, a member of the STS team will contact the site to notify them that a new mapping file is ready for them to download and process. Test Sites ========== Bedford VAMC Biloxi VAMC Boston HCS Hines, IL VAMC Houston VAMC Madison, WI VAMC Milwaukee VAMC Minneapolis VA HCS Shreveport VAMC St. Cloud VA HCS Upstate New York HCS VA Heartland-West HCS We would also like to thank the following site who participated in the testing of this patch: Oklahoma City VAMC Routine Information: ==================== No routines included. ============================================================================= User Information: Entered By : ANZALDUA,CAROL Date Entered : JUN 06, 2013 Completed By: DERBES-MURPHY,ELISA Date Completed: SEP 17, 2013 Released By : BELSCHWINDER,MICHAEL Date Released : SEP 24, 2013 ============================================================================= Packman Mail Message: ===================== No routines included