bgsi-registry / openehr-registry-template

Variable Management System for BGSI

This repository is intended to contain all OpenEHR archetypes and templates used in Biomedical and Genomic Science Initiative (BGSI), a research-driven clinical initiative led by the Ministry of Health of the Republic of Indonesia. In this repository, we store all OpenEHR objects that we work on using Archetype Designer within the local directory. In the hubs directory, we stashed the template which we use in the production. We are open to discussion, and you will find the latest information on this project in the Discussion segment.

openehr-registry-template's Issues

Preparing `*OPT` and `*JSON` template for RSCM

Continuing from #4:

1. Separate each variable group as a different sub-template
2. Use the pre-specified naming convention from group-nomenclature
3. If you need to add more group name, record it to the group-nomenclature sheet

SMEO-8: Map DM-Dewasa

Mapping registry variables from RSPI Sulianto Saroso to OpenEHR archetype

1. Extract variables from registri-tb-rspiss to variables-all-registries > rspi
2. Map each variable to its respective OpenEHR archetype
3. Maximize the use of general archetype to capture all variables
4. If devising a new archetype was necessary, please discuss prior to creating a new one

Output ➡️ A spreadsheet containing the following column:

1. Groups
2. SNOMED-CT Name
3. SNOMED-CT ID
4. Varname
5. OpenEHR (Archetype)
6. OpenEHR_field
7. FHIR
8. Type
9. Content
10. Cardinality
11. Notes

SMEO-7: Map DM-Anak

Mapping registry variables of healthy controls to OpenEHR archetype

1. Extract variables from registri-healthy-control to variables-all-registries > healthy
2. Map each variable to its respective OpenEHR archetype
3. Maximize the use of general archetype to capture all variables
4. If devising a new archetype was necessary, please discuss prior to creating a new one

Output ➡️ A spreadsheet containing the following column:

1. Groups
2. SNOMED-CT Name
3. SNOMED-CT ID
4. Varname
5. OpenEHR (Archetype)
6. OpenEHR_field
7. FHIR
8. Type
9. Content
10. Cardinality
11. Notes

SMEO-3: Map Cancer disesase with OpenEHR CKM

long task.
ada update2 terbaru bisa dimasukkan didalam komentar.

• misal: sudah done mapping 20 dari 120 variabel klinis

SMEO-4: Map Demographic Registry

long task.
ada update2 terbaru bisa dimasukkan didalam komentar.

• misal: sudah done mapping 20 dari 120 variabel klinis

SMEO-13 [Form tb - tab Follow up] Status meninggal agar tidak mandatory

Task :
Ada beberapa field yang mungkin nampaknya tidak perlu mandatory

1. Tanggal Meninggal *
2. Tempat Kematian - Negara *
3. Tempat Kematian - Lokasi *

Expected :
Agar template di buat non mandatory

SMEO-11 tidak bisa add TB ketika Hasil foto toraks bernilai SELAIN `Tidak Dilakukan`

Secara OPT, seharusnya field Pemeriksaan yang tidak dikerjakan bersifat OPSIONAL, bukan mandatory

Kondisi sekarang, jika Hasil foto toraks dipilih value Negative atau Positive, maka akan terdapat error dikarenakan logic di OPT:

2022-11-26 20:10:46.876  WARN [traceId=c3a659ad-a0f0-4c58-afa6-4bd6648f9b81] 9 --- [nio-8080-exec-8] o.e.r.ehrscape.EhrScapeExceptionHandler  : /content[openEHR-EHR-SECTION.adhoc.v1, 1]/items[openEHR-EHR-ACTION.service.v0, 4]/description: Attribute description of class ACTION does not match existence 1..1

dimana openEHR-EHR-ACTION.service.v0, 4]/description yang dimaksud disini adalah field untuk Pemeriksaan yang tidak dikerjakan yang bersifat lower bound = 1

Output:

• Informasi berikut WAJIB BERSIFAT OPSIONAL dari OPT

        "tuberculosis-adm.v4/admisi/service/pemeriksaan_yang_tidak_dikerjakan|code": "SCTID::399208008",
        "tuberculosis-adm.v4/admisi/service/pemeriksaan_yang_tidak_dikerjakan|value": "Foto toraks",
        "tuberculosis-adm.v4/admisi/service/pemeriksaan_yang_tidak_dikerjakan|terminology": "SNOMED-CT",

TODO:

• Form Admisi > Hasil Foto Toraks bagian alasan dikerjakan, butuh untuk di set sebagai OPSIONAL
• Form Lab > Hasil pemeriksaan mikroskopis * blm optional, butuh untuk di set sebagai OPSIONAL

Mapping registry variable from RSCM to OpenEHR archetypes

1. Extract variables from registri-diabetes-rscm to variables-all-registries > rscm
2. Map each variable to its respective OpenEHR archetype
3. Maximize the use of general archetype to capture all variables
4. If devising a new archetype was necessary, please discuss prior to creating a new one

Output ➡️ A spreadsheet containing the following column:

1. Groups
2. SNOMED-CT Name
3. SNOMED-CT ID
4. Varname
5. OpenEHR (Archetype)
6. OpenEHR_field
7. FHIR
8. Type
9. Content
10. Cardinality
11. Notes

Create AQL Query sample blood pressure untuk cari data composition by nama rumah sakit

Create AQL Query sample blood pressure untuk cari data composition by nama hub

SMEO-6: Map TBC registry

SMEO-2: Explore variable mapping with FHIR Variables

Mismatched error when creating a template

Story:
I want to create dedicated slots for drug resistance so the frontend team can readily deploy the web template only with minor adjustments.

Error:

Could not parse template [local/tuberculosis-lab-v.0.0.0.t.json] in format t_json: RuntimeException: com.fasterxml.jackson.databind.exc.MismatchedInputException: No content to map due to end-of-input at [Source: (byte[])""; line: 1, column: 0]

How to reproduce the error:

1. Go to https://tools.openehr.org/
2. Connect to this GitHub repository (if haven't)
3. Open the template: tuberculosis-lab-v.0.0.0
4. Click Pemeriksaan GeneXpert
5. Add Laboratory analyte result in the Test result slot
6. An error will occur after filling >6 additional slots

Mapping registry variables from RS Sangla to OpenEHR archetype

1. Extract variables from registri-psoriasis-rssangla to variables-all-registries > rssangla
2. Map each variable to its respective OpenEHR archetype
3. Maximize the use of general archetype to capture all variables
4. If devising a new archetype was necessary, please discuss prior to creating a new one

Output ➡️ A spreadsheet containing the following column:

1. Groups
2. SNOMED-CT Name
3. SNOMED-CT ID
4. Varname
5. OpenEHR (Archetype)
6. OpenEHR_field
7. FHIR
8. Type
9. Content
10. Cardinality
11. Notes

SMEO-9 bikin form demografis lengkap

excel:
https://docs.google.com/spreadsheets/d/1YW8Hy0G6F-euJj9HdRJZgcgKlsOVZJhj0dP-tyDDjG8/edit#gid=0

Mapping registry variables from RS Dharmais to OpenEHR archetype

1. Extract variables from registri-asd-ph-sardjito to variables-all-registries > dharmais
2. Map each variable to its respective OpenEHR archetype
3. Maximize the use of general archetype to capture all variables
4. If devising a new archetype was necessary, please discuss prior to creating a new one

Output ➡️ A spreadsheet containing the following column:

1. Groups
2. SNOMED-CT Name
3. SNOMED-CT ID
4. Varname
5. OpenEHR (Archetype)
6. OpenEHR_field
7. FHIR
8. Type
9. Content
10. Cardinality
11. Notes

SMEO-1: Explore variable mapping with OpenEHR CKM

Renaming diabetes mellitus template

  # Background

As per #17, I'm proposing renaming the DM templates to make them more concise. As I evaluated the template, I saw that there's several inconsistencies between template name, templateId, and the semver. Thus, I request renaming these templates to prevent issues with the backend. The file names I'm proposing are as follow:

DM Dewasa:

• diabetesMellitus-vascularSurgery-v0
• diabetesMellitus-endocrinology-v0
• diabetesMellitus-gastroEnteroHepatology-v0
• diabetesMellitus-neurologi-v0
• diabetesMellitus-physExam-v.0
• diabetesMellitus-nephrologyHypertension-v0
• diabetesMellitus-cardiology-v0
• diabetesMellitus-ophthalmology-v0
• diabetesMellitus-psychiatry-v0
• diabetesMellitus-otolaringology-v0
• diabetesMellitus-urologyMale-v0
• diabetesMellitus-urologyFemale-v0

DM Anak

• diabetesMellitusAdolescent-vascularSurgery-v0
• diabetesMellitusAdolescent-endocrinology-v0
• diabetesMellitusAdolescent-gastroEnteroHepatology-v0
• diabetesMellitusAdolescent-neurologi-v0
• diabetesMellitusAdolescent-physExam-v.0
• diabetesMellitusAdolescent-nephrologyHypertension-v0
• diabetesMellitusAdolescent-cardiology-v0
• diabetesMellitusAdolescent-ophthalmology-v0
• diabetesMellitusAdolescent-psychiatry-v0
• diabetesMellitusAdolescent-otolaringology-v0
• diabetesMellitusAdolescent-urologyMale-v0
• diabetesMellitusAdolescent-urologyFemale-v0
• diabetesMellitusAdolescent-social-v0

CC: dok @mnardisasmita

Originally posted by @lamurian in #28

Mapping registry variables from RS Sardjito to OpenEHR archetype

1. Extract variables from registri-asd-ph-sardjito to variables-all-registries > sardjito
2. Map each variable to its respective OpenEHR archetype
3. Maximize the use of general archetype to capture all variables
4. If devising a new archetype was necessary, please discuss prior to creating a new one

Output ➡️ A spreadsheet containing the following column:

1. Groups
2. SNOMED-CT Name
3. SNOMED-CT ID
4. Varname
5. OpenEHR (Archetype)
6. OpenEHR_field
7. FHIR
8. Type
9. Content
10. Cardinality
11. Notes

Create AQL Query sample blood pressure untuk cari data composition by contextID dari enumerator/admin hub

SMEO-5: Sample Cancer registry