Contents

1.0 Links to Important SharePoint Libraries and Documents

2.0 General 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.

• S&I LOINC Order – Documents related to a joint project (now finished) with ONC’s Standards & Interoperability (S&I) Framework and the Regenstrief Institute to define rules for common test names that are short enough for use in EHR-S but clear enough to not be dangerous. THe S&I Framework documents are no longer available, but here is a PHI conference slide set: https://www.cdc.gov/labhit/paper/2016-standardization-of-laboratory-test-coding---phi-conference.pdf

• RCMT Alert – Related to work on the Reportable Condition Knowledge Management System (RCKMS).

• Package Inserts – All SOPs or package inserts we have collected. If you obtain a new one, please add it here.

• General folder – Includes APHL maintained code system, notes from Vocab-related meetings (NLM, LOINC, IHTSDO), an APHL tool inventory, SDO participation call schedule, reference documentation (JLAC10, HL70487 to SCT mapping for specimen, ELR R2 value sets) – specifically:

  • PLT_PLRMaster:

    • https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/_layouts/15/WopiFrame.aspx?sourcedoc=/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/Vocab Core Group Library/PLT_PLR_Master_January_2021.xlsx&action=default

  • APHL maintained code system for:

    • Lab tests or anything that will be submitted for a LOINC via Regenstrief = PLT

    • Lab results, specimen types, or anything that will be submitted for a SNOMED CT code via NLM = PLR

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

• All TAT – This grouping in the Templates library contains documents that can be used regardless of the project, including:

  • Presentation explaining Interoperability need and a brief intro to standards: https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/Templates/HL7_and_Interoperability.ppt

• Presentation explaining How to LOINC and SNOMED: https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/Templates/How_to_LOINC_and_SNOMED.ppt

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:

• An explanation of the Change Control Process https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/SitePages/CCB.aspx

• Meeting minutes from Change Control Board (CCB) calls https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/SitePages/CCB_Document_Library.aspx

• Change Requests for managed Projects https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Lists/ChangeRequest/Default.aspx

• Standards documents for all projects https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/SitePages/Home.aspx

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.

• Old Glossary and primer document https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/Informatics_Program/Projects/PHLIP/PrimerWG/Wiki%20Pages/Home.aspx

• Old Harmonization work products by condition https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/Informatics_Program/Projects/PHLIP/VMWG/VM Wiki Glossary/Home.aspx

1.4 Vocab Specific Documents by Project

• Underlying HL7 specification = ELR R1 v2.5.1 https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/Vocab%20Core%20Group%20Library/V251_IG_LB_LABRPTPH_R1_INFORM_2010FEB.pdf
  and related documents: https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/Vocab%20Core%20Group%20Library/ELR_IG_R1_Additional_Errata_and_Guidance.docx
  (not on SharePoint, but please review) NIST tooling: ELR Validation Tool @ NIST

1.4.1 Public Health Laboratory Interoperability Project (PHLIP)

• ELSM for Influenza 2.3.1

  • HL7 Implementation guide (legacy connections – working on migrating folks over) https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/HL7%20v231%20APHL%20Influenza%20Msg%20Guide%20ORU%20v1.0.2.doc

  • Message mapping template (2.3.1) – local to HL7 fields, configuration, Epi important information, all HL7 related vocab, country, state, county codes, gender vocab, specimen vocab, OBR-4, OBX-3, OBX-5 https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/AIC/Vocab%20Core%20Group%20Library/PHLIP_Template_Message_Spec_20110802.xls

• ELSM for Influenza 2.5.1

  • Business Rule document describes any additional constraints on the national ELR R1 guide. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/BUSINESS%20RULES%20DOCUMENT%20FOR%20PHLIP%20ELSM2.doc

  • Message mapping template (2.5.1) – local to HL7 fields, configuration, Epi important information, all HL7 related vocab, country, state, county codes, gender vocab, specimen vocab, OBR-4, OBX-3, OBX-5. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/251_PHLIP_Message_Spec_MappingTemplate.xls

• Both 2.3.1 and 2.5.1

  • Encoding Guidelines – describes ALL the available codes for OBR-4, OBX-3, OBX-5, organized into value sets as they apply for the respective tests used – gets updated after Change Requests are approved and released maybe once a year before the beginning of the flu season. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/Flu%20Test%20Encoding%20Guideline%20Aug2016.xls

  • Deprecated code list – provides a list of deprecated codes with their replacement codes, if applicable - we give folks at least 6 months after deprecation to migrate over to replacement codes while both codes are usually valid – tabs list codes with dates after which they are no longer supposed to be messaged. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/Deprecated%20Codes_Flu.xlsx

  • Validation spreadsheet (Test Scenarios) – provides several testing scenarios that labs have to produce as part of the validation process and includes example data – this document is the template to be customized for each laboratory getting onboarded and will be used for validation feedback.
    https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/PHLIP_Validation_Test_Cases_Template.xls

  • Link to the CDC site explaining how to map their PCR tests: http://www.cdc.gov/flu/professionals/diagnosis/rtpcr-test-kits.htm

1.4.2 ELSM for Vaccine-Preventable Diseases (VPD)

• Business Rule document – describes any additional constraints on the national ELR R1 guide. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/VPD_Business_Rules_v2.2.docx

• Message Specification – applied the business rules to the underlying 2.5.1 ELR guide. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/VPD_Message_Spec_20150630.xlsx

• Message mapping template (2.5.1) – local to HL7 fields, configuration, Epi important information, all HL7 related vocab, country, state, county codes, gender vocab, specimen vocab, OBR-4, OBX-3, OBX-5, Specimen reject reason, specimen condition.

• OBR-4-OBX-3-OBX-5 rules – describes ALL the available codes for OBR-4, OBX-3, OBX-5, organized into value sets as they apply for the respective tests used. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/VPD_CodeCombinations.xlsx

• Deprecated code list – identifies the effective time of the codes in the list – when added, when deprecated and provides replacement codes, where applicable. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/Deprecated_Codes_VPD.xlsx

• Submitting Labs – list of submitting labs, their POC, and the assigned reference centers. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/VPD_SubmittingLabs.accdb

1.4.3 Rabies

• Business Rule document – describes any additional constraints on the national ELR R1 guide. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/251_ELR_Animal_Rabies_Business_Rules_Document.docx

• Message mapping template (2.5.1) – local to HL7 fields, configuration, all HL7 related vocab, country, state, county codes, gender vocab, specimen vocab, OBR-4, OBX-3, OBX-5, OBR-4-OBX-3-OBX-5 rules are included in this file. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/251_ELR_Animal_Rabies_Message_Mapping_Template.xls

• Validation spreadsheet (Test Scenarios) – provides several testing scenarios that labs have to produce as part of the validation process and includes example data – this document is the template to be customized for each laboratory getting onboarded and will be used for validation feed. https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/Rabies_TestScenarios_ValidationTool.xlsx

• Published Test Stories – in readable format for sharing https://www.aphlweb.org/aphl_departments/Strategic_Initiatives_and_Research/IPMG/ConfigMgt/Standards%20Document%20Library/Published%20Rabies%20Test%20Stories.html

• 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:

  • NMI PHIN specification – HL7 guide for properly creating a message and defined datatypes. PHIN Messaging Specification for Case Notification v3

  • Event Codes & Other Surveillance Resources - annual event code lists and other resources for sending case notifications to CDC