Metadata Server Management

Guidelines for concept management

• Use one central OpenMRS server for "golden" metadata (concepts, etc)
• When possible, use the CIEL dictionary for new concepts instead of recreating a new one.
• Use the Maternal Concept Lab (MCL) for viewing the CIEL, PIH, AMPATH dictionaries.  
• Use Metadata sharing (MDS) for getting existing concepts.  
  • Use MCL to generate an export package with concepts for import into your local "golden" server  OR
  • Use the CIEL dropbox to get the latest mysqldump of the CIEL concept* tables.  Install this on a local OpenMRS server along with the MDS module.  Export packages from this server for your local "golden" server.
• Create a concept source for this server (ie.  Rwanda, PIH) where the concept_ids will be used for mappings (ie.  PIH: 12)
• Add unique mappings terms for use with forms and reports (ie. "PIH: 12", "PIH: Anemia", "CIEL:123456", "Rwanda: 388").  The names must be unique.
• These mappings should have a concept reference map type of "SAME-AS"
• Add terminology mappings where useful (ie. SNOMED, ICD10, RxNORM, ICPC2, LOINC). These are helpful for standardizing diagnoses, procedures, and billing.  These are already populated in CIEL and PIH.
  • The Systematized Nomenclature of Medicine (SNOMED) is a systematic, computer-processable collection of medical terms, in human and veterinary medicine, to provide codes, terms, synonyms and definitions which cover anatomy, diseases, findings, procedures, microorganisms, substances, etc.
  • ICD-10 is the 10th revision of the International Statistical Classification of Diseases and Related Health Problems (ICD), a medical classification list by the World Health Organization (WHO). It contains codes for diseases, signs and symptoms, abnormal findings, complaints, social circumstances, and external causes of injury or diseases.
  • RxNorm is a name of a US-specific terminology in medicine that contains all medications available on US market.
  • The International Classification of Primary Care (ICPC) is a classification method for primary care encounters. It allows for the classification of the patient’s reason for encounter (RFE), the problems/diagnosis managed, primary or general health care interventions.
    
  • Logical Observation Identifiers Names and Codes (LOINC) is a database and universal standard for identifying medical laboratory observations. 
• Locale - Concepts should be in appropriate language:  English, French, Spanish, Haitian Kreyol, Kinyarwanda, etc.
• Validate the following with the validation module:
  • concepts
  • concept names
  • concept description
• Confirm that all user fields in concept* tables have existing users.  A variety of fields (creator, voided_by, changed_by, and retired_by) are on the concept* tables and correspond to the user_id in the users table.  If concept* tables have been directly updated via mysql (mysqldump and source), then users might not exist for concept* tables.
• Cleanup and possibly delete unused concepts
• Delete or retire duplicate concepts.  If a concept is retired, it can still be used in the system for past or future obs; however, it will not appear by default in concept dictionary searches or htmlform dropdowns.  Retiring a concept doesn't cause any problems.  Deleting a concept when it's used is a problem.  If a form uses the concept, it will break the form.  If an obs used the concept, that will also produce an error.
• Check for appropriate classes and datatypes 
  • diagnosis, symptom, finding, program, workflow, state or misc should have a datatype of N/A
  • LabSet, MedSet, and ConvSet should have set members
  • questions should not have a datatype of N/A

Guidelines for htmlforms

• Maintain the latest forms on the metadata server
• Use mds to create htmlform packages which include all the concepts, program, drugs, locations, etc.
• Forms and reports should use mappings to a concept dictionary (ie. CIEL or Rwanda) and not uuids or concept_ids

• <htmlform>
      <macros>
                  <!-- Hemoglobin 3ccc7158-26fe-102b-80cb-0017a47871b2 21 -->
          <at:var at:name="HEMOGLOBIN" />=RWANDA:21
      </macros>
   
     <p>Hb: <obs conceptId="$<at:var at:name="HEMOGLOBIN" />" /></p>
  
  

  Add concept mappings within macro in the htmlform

Tools

• Groovy module - Can be used with sync or non-sync environments to make changes to the OpenMRS database. The groovy modules allows for groovy scripts to be saved and managed within OpenMRS.
  • Script for deleting concept terms, maps, sources (ie. local, AMPATH, etc)
  • Script for adding new concept terms, maps, source (ie. Rwanda)
  • Script for renaming a concept source (ie. MVP/CIEL)
• Metadata Sharing (mds) - Used to copy all metadata (concept and forms) between systems. Works well with sync and helps to propagate changes to all servers.
• Validation module - Checks the concept dictionary for duplicate concept names, concept descriptions with null descriptions, Locations, etc.
• Github repo for scripts (TBD)
  •  Add scripts (mysql and groovy) to public repo for sharing.  
    • Concept cleanup
    • Helper scripts for OpenMRS migration
    • Maintenance tools for propagating software (war and modules)
    • De identifying scripts
    • Adding new concept terms, maps, source
    • Check for duplicate mappings (when a reference term from PIH, CIEL, or Rwanda should not be on multiple concepts)