Urgent: Vocabulary Release for the upcoming Covid-19 Study-a-thon

Vocabulary Users
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Friends:

The Vocab team just finished the latest update on the Standardized Vocabularies. As usual, turned out a LOT more work that anticipated. Here is what you need to know:

  1. If you are getting your data ready for the study-a-thon, or for the subsequent activities, please:
  • Download the latest from Athena.
  • Read the instructions carefully. Covid-19 is happening rapidly, and the representation in source data is developing equally rapidly.
  1. If you are working on cohorts to apply to the studies please
  • Read the instructions to make sure you develop the right conceptsets and criteria
  • Have your Atlas refreshed with a database built or refreshed through 1).
  • If you don’t have that, use Athena to browse the vocabularies

All questions welcome, as usual.

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But, why would things be easy, if they can be complicated. Turns out we made a booboo. If you are working with the new LOINC concepts for Coronavirus 2 detection you will find them in the Vocabularies, but unfortunately as non-standard. You have two choices:

  • You wait for the hot fix on Monday (which will also fix the hierarchy)
  • You make your own hot fix and set the field standard_concept to “S” in the CONCEPT table for concept_ids 706154, 706155, 706156, 706157, 706158, 706159, 706160, 706161, 706162, 706163, 706164, 706165, 706166, 706167, 706168, 706169, 706170, 706171, 706172, 706173, 706174, 706175, 706176, 706177, 706178, 706179, 706180, 706181.

Or in SQL:

update concept set standard_concept='S' where concept_id in (706154, 706155, 706156, 706157, 706158, 706159, 706160, 706161, 706162, 706163, 706164, 706165, 706166, 706167, 706168, 706169, 706170, 706171, 706172, 706173, 706174, 706175, 706176, 706177, 706178, 706179, 706180, 706181)
;

If you don’t have such codes disregard this. Sorry for the craziness.

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Favipiravir, an approved drug in Japan for influenza, is undergoing clinical trials for Covid-19. There isn’t a standard drug code in Athena yet.

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Awesome @Christian_Reich Thank you so much!

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Friends: No booboo anymore. Please disregard the message above and just download from Athena. You will need it to be able to participate in the study-a-thon.

You got it. Will add to the next hot release. For all other folks not having data with this drug - don’t wait for that release.

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Hi @CSung,

We added this ingredient to the vocabularies. Will be available through Athena on the earliest release.

concept_id concept_name domain_id vocabulary_id concept_class_id standard_concept concept_code valid_start_date valid_end_date invalid_reason
32765 Favipiravir Drug RxNorm Extension Ingredient S OMOP4873976 01-01-70 31-12-99 NULL
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We added some more Drug ingredients. Already available with the latest release in Athena:
Tagging @CSung

concept_id concept_name domain_id vocabulary_id concept_class_id standard_concept concept_code valid_start_date valid_end_date invalid_reason
32764 Umifenovir Drug RxNorm Extension Ingredient S OMOP4873975 01-01-70 31-12-99 NULL
32765 Favipiravir Drug RxNorm Extension Ingredient S OMOP4873976 01-01-70 31-12-99 NULL
32766 Middle East Respiratory Syndrome heterologous combined adenoviral-based vector vaccine Drug RxNorm Extension Ingredient S OMOP4873977 01-01-70 31-12-99 NULL
32767 Carrimycin Drug RxNorm Extension Ingredient S OMOP4873978 01-01-70 31-12-99 NULL
32768 CD24 Extracellular Domain-IgG1 Fc Domain Recombinant Fusion Protein CD24Fc Drug RxNorm Extension Ingredient S OMOP4873979 01-01-70 31-12-99 NULL
32769 Tetrandrine Drug RxNorm Extension Ingredient S OMOP4873980 01-01-70 31-12-99 NULL
32770 Xiyanping Drug RxNorm Extension Ingredient S OMOP4873981 01-01-70 31-12-99 NULL
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These were drugs we added for the CIEL dictionary (code is the CIEL concept ID). I’d be interested if people are using the other ones added by Alexander? Should they be added to CIEL for the open source EHR community?

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-1a Drug Misc

Here is a link to Open Concept Lab for a starter set of mapped concepts around COVID-19. It was released prior to some additional concepts including those above: https://openconceptlab.org/orgs/CIEL/collections/COVID-19-Starter-Set/concepts/

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We keep adjusting to the way COVID-related facts are described in the data. Addressing such things as suspected vs real Conditions, Emergency codes, Timing context, Lab tests hierarchy, pre-coordinations and many others, we’re happy to announce COVID-19 v2.0 Vocabulary Release that is already in Athena.

If you are involved in ETL or data analysis, please make sure to take a look at the changes. After the first version we updated some rules. It’s highly recommended to re-run ETL with the recent version since the interim vocabulary versions are not supported by current or initial instructions.

Instructions are available here

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