Vocab Tools and Processes

Owned by Amanda Payne
Last updated: Sept 16, 2021
11 min read

Contents

1.0 Links to Important SharePoint Libraries and Documents

1.1 APHL Informatics Consulting Site

1.2 Vocab Workspace

1.2.1 Vocab Core Group Library

1.3 Outside the Vocab Workspace

1.3.1 Templates

1.3.2 TA Manual

1.3.3 Config Management

1.3.4 Vocab Issues

1.3.5 Vocab Guiding Principles and Decisions

1.3.6 Archived site

1.4 Vocab Specific Documents by Project

1.4.1 Public Health Laboratory Interoperability Project (PHLIP)

1.4.2 ELSM for Vaccine-Preventable Diseases (VPD)

1.4.3 Rabies

1.4.4 NNDSS Modernization Initiative (NMI)

1.4.5 Electronic Laboratory Reporting (ELR)

1.4.6 Antimicrobial Resistance Laboratory Network (ARLN)

1.4.7 Laboratory Messaging Community of Practice (LabMCoP)

1.5 Message validation process Step-by-Step

1.5.1 Validating test message

2.0 General Resources

2.1 CDC Resources

2.2 HL7 Resources

2.3 LOINC & SNOMED Resources

1.0 Links to Important SharePoint Libraries and Documents

All of APHL’s vocabulary resources, including general working documents, references, and project-related work files, are stored on SharePoint.

1.1 APHL Informatics Consulting Site

This page serves as the unofficial home page for the TA Team. In addition to team calendars and conference lines, templates, and workspaces for the major functional areas (i.e., project management, technical architecture, and vocabulary), this site includes jurisdiction-specific working documents for the ELSM for Influenza and ELRTA projects.

https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/SitePages/Home.aspx

1.2 Vocab Workspace

This page provides links to several important libraries that the vocabulary team uses to organize its work files, presentations, and resources.

https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/SitePages/Vocab_Core_Group_Work_Space.aspx

1.2.1 Vocab Core Group Library

This library contains many of the vocabulary team’s work files. It is grouped into the following categories; note that this list is presented in order of the page, not importance. Important folders/files to review are highlighted.

We are looking for new tooling for maintenance here, these code systems are both published 2x per year in PHINvads and synched with LOINC and US edition of SCT

  • ELSM – Any Influenza ELSM related documents prepared by the vocab team, including older versions of the documents published via the Config Management tab (also accessible via left side link ELSM 2.5.1) – most of the documents now are just for historical purposes, except this one: https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/Vocab%20Core%20Group%20Library/Influenza%20PCR%20CDC%20test.xls

  • ELRTA – Any ELR TA-related documentation. The contents of this group are rather old actually and include info on the ELR R2 guide ballot, etc.

  • eLEXNET – Information about the data elements used in eLEXNET, the data exchange format used, and the manual on how to map local to FDFA terms.

  • Database – Contains the specimencrossmapping dB (collection of terms describing different specimen types with definitions, collection methods, and SNOMED CT mapping) and some metadata around it.

  • Centralized ELR -

  • ARLN -

1.3 Outside the Vocab Workspace

In addition to the Vocab workspace, the following libraries or documents on SharePoint are of relevance for the vocab team.

1.3.1 Templates

1.3.2 TA Manual

Description of TA services https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/Templates/APHL%20INFORMATICS%20SERVICES%20GUIDANCE%20MANUAL.docx

1.3.3 Config Management

The Configuration Management site on SharePoint contains standards documents for all projects, as well as tools and materials relevant to the APHL-managed Change Control Board (CCB). So far, the CCB manages ELSM for Influenza and VPD. There are plans to add ELR for Animal Rabies soon. The Configuration Management site includes:

1.3.4 Vocab Issues

This tracking list is not high in use, since we have started using ZenDesk. Previously, we used it to track longer-term issues, so we wouldn’t forget about them. We review the issues 3 times a year on a vocab call now, but it is open for discussion if the team wants to make this a more active tool. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/Vocab_Issues/Lists/Vocab%20Issues/Status.aspx

1.3.5 Vocab Guiding Principles and Decisions

This Wiki library is a collection of definitions and decisions documented over time since PHLIP started in 2006. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/Vocab_Guiding_Principles/SitePages/Home.aspx

1.3.6 Archived site

APHL retired an old SharePoint site at the end of 2012. Occasionally, the vocab team may need to reference the documentation on this archived site.

1.4 Vocab Specific Documents by Project

1.4.1 Public Health Laboratory Interoperability Project (PHLIP)

1.4.2 ELSM for Vaccine-Preventable Diseases (VPD)

1.4.3 Rabies

  • Main tooling page - maybe a table with the link and description of what it’s for (do we need to state who has access?):

this would have links to Symedical, NIST IGAMT and TCAMT, OID master sheet (should migrate to smartsheet), specimen CMT, PLT/PLR codes (as long as we need to still use the spreadsheet) etc

1.4.4 NNDSS Modernization Initiative (NMI)

  • References:

  • MMGs and Additional Resources – this link takes you to the list of final MMGs and their associated resources: https://ndc.services.cdc.gov/message-mapping-guides/ Click on the condition of interest to access to following documents:

    • MMG and Test Case Scenarios - provides data elements and their expected answers with info on usage, cardinality, etc. Each condition-specific MMG should be used in conjunction with the GenV2 MMG to create a complete case notification message.

      • The TCSW tab provides the test case scenarios that PHAs must complete prior to onboarding.

    • Implementation spreadsheet – a tool intended to aid PHAs in conducting and documenting their gap analysis. It combines the PHIN guide information with the data elements for the conditions described in the GenV2 and condition-specific MMG.

    • Test message package - a zip file containing sample messages created by CDC for each test case scenario.

    • Annotated case report form (if applicable) - a pdf that maps the data elements in the MMG to the case report form.

    • Other resources - the CDC program may choose to add additional resources for implementation, such as FAQs or crosswalks to previous methods of data transmission.

  • APHL documents (internal use only) - NMI project deliverables can be found on the APHL Sharepoint site here: https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/NMI/NMI Deliverables/Forms/AllItems.aspx. These include compiled test scenarios, implementation spreadsheets, local mapping templates, technical architecture documentation and validation templates.

1.4.5 Electronic Laboratory Reporting (ELR)

1.4.6 Antimicrobial Resistance Laboratory Network (ARLN)

We use ELRR1 for Candida, GC and in the future for CRE, CRPA, Activity2 (and for labs that are not using an order entry portal also for CRE colonization), LOI, and LRI from June 2018

1.4.7 Laboratory Messaging Community of Practice (LabMCoP)

Call notes and documents for the community to discuss and come up with recommendations for messaging problems (we often then take these to HL7 or IHE to have them vetted more broadly and then implemented either in base standards or at least in implementation profiles)

https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/LabMCoP/SitePages/Home.aspx

1.5 Message validation process Step-by-Step

1.5.1 Validating test message

  • Structural validation of the message in the respective tool:

  • If NO errors there, then:

    • Eyeball the message in “notepad++” for:

      • carriage return use = “CR”; any other entry at the end of the line indicating the start of the next segment should be noted as an error to be fixed

      • Check MSH-21 for proper use of all respective profile IDs

      • Check MSH-3/MSH-4 for proper OID use by the sending jurisdiction

      • Check MSH-5/MSH-6 for proper OID use identifying the receiver

  • Test Scenario Content validation:

    • For each project, we have created an excel based test case validation tool, that, once you copy-paste the parsed HL7 message to the tab for the described test case will do a lookup against expected codes and highlight issues (this could use improvement)

Here is an example for NMI: https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/NMI/NMI%20Deliverables/NMI_Validation_Template_20170719_GenV2.xlsx

  • Ensure that any lab-specific algorithms are tested when preparing the test scenario file for the lab

  • For each test case review the expected values in the scenario document (where used) against the values in the message and identify any issues, in particular:

    • Review OBX-2 data type = should match what is actually sent in OBX-5

    • Review codes used in OBX-3 / OBX-5 against the rules document (encoding guideline for PHLIP, OBR-4-OBX-3-OBX-5 rules for VPD and rabies) and in the implementation spreadsheet for NMI

    • Check for any other codes in the OBX segment (OBX-8, OBX-11)

    • Check dates to see if they make sense in order (listed as early to last)

      • Date of Birth = PID-7 (UNLESS this is testing of the fetal specimen)

      • Specimen Collection = OBR-7/OBX-14 (for test results)/SPM-17

      • Specimen Received in Lab = SPM-18

      • Clinically relevant Observation date = OBX-14 (for anything else, but test results)

      • Analysis Date = OBX-19 (for test results)

      • Report Date = OBR-22

    • Status Code in OBR-25 follows these rules:

      • If all OBX-11 = ‘F’, then ‘F’

      • If at least one OBX-11 = ‘C’, then ‘C’ (some systems cannot do this, so document if that is the case in the notes column)

      • For most of the projects we only support F or C, though ELR will sometimes allow P, in which case at least one OBX-11 = ‘P’, then ‘P’ or ‘A’, in which case there is an expectation that some OBX are still missing

    • For the corrected scenario compare the OBR-22 date to the OBR-22 date in the first message for the same specimenID/PatientID/OrderID – if OBR-22 in the corrected message is later than in the first message pass, else error

    • Check that all the specimen types in use at the lab for the project are used at least once across test cases

    • Check that all race/ethnicity codes are used at least once across messages

    • Check that all EPI questions supported by the lab are tested at least once across messages

    • For NMI the expected data MUST MATCH EXACTLY as this document will be used for validation with CDC programs, so the jurisdiction will be asked to provide the data as entered into their system for IDs, dates, etc. and to document that

2.0 General Resources

2.1 CDC Resources

  • PHIN Messaging System: CDC’s home page for PHINMS, with installation instructions and support

  • METS (Message Evaluation and Testing Service) validates the structure and content of an HL7 message in EDI text format. SPHLs can use the MQF to validate PHLIP messages (must use for 2.3.1) during staging.

  • PHIN VADS Value Sets – PHIN VADS is the CDC repository that contains value sets for PHLIP ELSM value sets, as well as ELR HL7 v.2.5.1 and many other message guides

  • PHIN VADS RCMT contains a list of LOINCs and SNOMED codes for reportable conditions

2.2 HL7 Resources

2.3 LOINC & SNOMED Resources