Covid-19 Concept metadata package for Reference Application 2.10

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Following this Talk thread OpenMRS COVID-19 Response , We decided to update reference Application Metadata Packages with Covid-19 related Concepts , that have been added to the CIEL of recent.

I have built a new Concept Metadata package (Covid-19_concepts) to include in the Reference application Metadata module .

  • Note , to build the package , i simply did a text search for “covid” and “corona” on the MDSBuilder, and included all the Concepts in the result-set into the package.

  • Part of the result set is concept 165858 “COVID-19 diagnoses for PIH”, should we aslo include it in the reference application metadata package ?

  • Are there other concepts we would want to add to this package?.

see PR

cc @dkayiwa @ibacher @mksd @jennifer @burke @ssmusoke @akanter @ball

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I think you would want to use the COVID subset on OCL for that… although there would be overlaps with existing concepts in the Ref App. Somehow I think we need to be more careful about differentiating from the Ref App concept package and the COVID additions. ideas beyond text searching?

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Thanks @mozzy

@akanter created a COVID-19 starter set “collection” (see OCL https://www.openconceptlab.org/orgs/CIEL/collections/COVID-19-Starter-Set/). If we want to add COVID-19 concepts to the RefApp, this might be the right set of concepts for the RefApp. I defer to @akanter about this.

I created concept 165858 (“COVID-19 diagnoses for PIH”) which includes many of the new diagnoses added for COVID-19, but likely not complete for others. This was created on mdsbuilder for PIH and to bring into our dictionary, but I don’t expect others to use it. It’s not a CIEL concept.

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@mozzy I’ve create a list of all the concept ids in the CIEL COVID starter set not in the RefApp (at least for the last version of 2.10). I think that’s roughly the set of concepts we want in the COVID metadata package.

This is awesome Ian. I will continue to release additional terms in the next day or so which are not in the current release (and won’t be in the ref app):

165858 Sweating Finding N/A
165859 Abbott RealTime SARS-CoV-2 test Test Coded
165860 Centers for Disease Control and Prevention (CDC) 2019-Novel Coronavirus (2019-nCoV) Real-Time Reverse Transcriptase (RT)-PCR Diagnostic Panel Test N/A
165861 Hologic Panther Fusion® SARS-CoV-2 test Test Coded
165862 Sequential organ failure assessment score Finding Numeric
165863 National early warning score Finding Numeric
165864 History of supplemental oxygen therapy Finding Coded
165865 Xpert® Xpress SARS-CoV-2 antigen test Test Coded
165866 History of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease Diagnosis Coded
165867 Acute respiratory distress syndrome (ARDS) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Diagnosis N/A
165868 Lower respiratory tract infection due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Diagnosis N/A
165869 Acute bronchitis caused by severe acute respiratory syndrome coronavirus 2 Diagnosis N/A
159640 Patient health status Question Coded
165870 Patient condition resolved Finding N/A
165871 Patient condition unresolved Finding N/A
160432 Dead Misc N/A
1067 Unknown Misc N/A
165872 Tocilizumab Drug Misc
165873 Sarilumab Drug Misc
165874 Baricitinib Drug Misc
165875 Boceprevir Drug Misc
165876 Siltuximab Drug Misc
165877 Favilavir Drug Misc
165878 Remdesivir Drug Misc
165879 Pegylated interferon alfa-2b Drug Misc
165880 Pegylated interferon alfa-2a Drug Misc
165881 Pegylated interferon beta-1b Drug Misc
165882 History of positive test for SARS-CoV-2 Finding Coded
165883 Myocarditis due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Diagnosis N/A
165884 Encephalopathy due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Diagnosis N/A
165885 Gastroenteritis due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Diagnosis N/A
165886 Otitis media due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Diagnosis N/A
165887 Bronchitis due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Diagnosis N/A
165888 Venous blood specimen Misc N/A
165889 Capillary blood specimen specimen Misc N/A
163362 Oropharyngeal swab specimen Misc N/A
163363 Nasal swab specimen Misc N/A
165890 Capillary filling function Finding Coded
165891 Normal capillary filling Finding N/A
162512 Prolonged capillary refill time Finding N/A
165893 Provide supplemental oxygen via nasal cannula Procedure N/A
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Thanks so much @ibacher
So i will simply take that list . Great work :grinning:

cc @dkayiwa

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