Vocabulary landscape assessment

[aostropolets (Anna Ostropolets)]

Dear OHDSI Community:

We ask you to participate in the landscape assessment of the needs for the OHDSI Standardized Vocabularies.

You feedback on the Vocabularies use and problems will directly inform which vocabularies and activities we prioritize in 2023.

We ask you to fill two forms:

1. Overall form for people who use the Vocabularies for research, ETL, software development or else.

Link: bit.ly/3iTnyco

2. ETL-specific form for those who perform ETL or have an OMOP CDM instance at their disposal. Please fill it for each data source you have as we will use this information to prioritize the vocabularies we work on.

Link: bit.ly/3R7rYcm

Filling the forms should take you around 10 minutes. We are asking about the vocabularies you use, what you think about their quality, challenges you encountered and what we can do to improve the content and the process of distribution and update.

A link to the video from the recent Community Call for more detail:

Collaborating Towards Standardized Vocabularies (Anna Ostropolets, 24Jan2023 Community Call)

The survey is due February 23rd. The results of the survey are absolutely crucial for further Vocabularies development.

Please give us your thoughts so we can together create more robust, transparent and sustainable Vocabularies!

[Dymshyts (Dmytry Dymshyts)]

Here’s the query for question
“Which tables and fields do you populate with the non-zero concepts from the Vocabularies (check all that apply)?”
from the ETL specific form

with fields as (
select top 1 'person.race_concept_id' as col_name from person where race_concept_id !=0 union all
select top 1 'person.ethnicity_concept_id' from person where ethnicity_concept_id !=0 union all
select top 1 'visit_occurrence.visit_type_concept_id' from	visit_occurrence		 where visit_occurrence.visit_type_concept_id !=0 union all
select top 1 'condition_occcurrence.condition_concept_id' from	condition_occurrence		where condition_occurrence.condition_concept_id !=0 union all
select top 1 'condition_occcurrence.condition_status_concept_id' from	condition_occurrence		where condition_occurrence.condition_status_concept_id !=0 union all
select top 1 'drug_exposure.drug_concept_id' from	drug_exposure		where drug_exposure.drug_concept_id !=0 union all
select top 1 'drug_exposure.route_concept_id' from	drug_exposure		where drug_exposure.route_concept_id !=0 union all
select top 1 'device_exposure.device_concept_id' from	device_exposure		where device_exposure.device_concept_id !=0 union all
select top 1 'measurement.measurement_concept_id' from	measurement		where measurement.measurement_concept_id !=0 union all
select top 1 'measurement.unit_concept_id' from	measurement		where measurement.unit_concept_id !=0 union all
select top 1 'procedure_occurrence.procedure_concept_id' from	procedure_occurrence		where procedure_occurrence.procedure_concept_id !=0 union all
select top 1 'procedure_occurrence.modifier_concept_id' from	procedure_occurrence		where procedure_occurrence.modifier_concept_id !=0 union all
select top 1 'observation.observation_concept_id' from	observation		where observation.observation_concept_id !=0 union all
select top 1 'note.note_type_concept_id' from	note		where note.note_type_concept_id !=0 union all
select top 1 'note.note_class_concept_id' from	note		where note.note_class_concept_id !=0 union all
select top 1 'note.language_concept_id' from	note		where note.language_concept_id !=0 union all
select top 1 'specimen.specimen_concept_id' from	specimen		where specimen.specimen_concept_id !=0 union all
select top 1 'specimen.anatomic_site_concept_id' from	specimen		where specimen.anatomic_site_concept_id !=0 union all
select top 1 'specimen.disease_status_concept_id' from	specimen		where specimen.disease_status_concept_id !=0 union all
--select top 1 'survey_conduct.survey_concept_id' from	survey_conduct		where survey_conduct.survey_concept_id !=0 union all
select top 1 'care_site.place_of_service_concept_id' from	care_site		where care_site.place_of_service_concept_id !=0 union all
select top 1 'provider.specialty_concept_id' from	provider		where provider.specialty_concept_id !=0 union all
select top 1 'payer_plan_period.payer_concept_id' from	payer_plan_period		where payer_plan_period.payer_concept_id !=0 
--select top 1 'cost.cost_concept_id' from	cost		where cost.cost_concept_id !=0 
),
 anna_list as (
select 'person.race_concept_id' as col_name, '1' as rnk union all
select 'person.ethnicity_concept_id' as col_name, '2' as rnk union all
select 'visit_occurrence.visit_type_concept_id' as col_name, '3' as rnk union all
select 'condition_occcurrence.condition_concept_id' as col_name, '4' as rnk union all
select 'condition_occcurrence.condition_status_concept_id' as col_name, '5' as rnk union all
select 'drug_exposure.drug_concept_id' as col_name, '6' as rnk union all
select 'drug_exposure.route_concept_id' as col_name, '7' as rnk union all
select 'device_exposure.device_concept_id' as col_name, '8' as rnk union all
select 'measurement.measurement_concept_id' as col_name, '9' as rnk union all
select 'measurement.unit_concept_id' as col_name, '10' as rnk union all
select 'procedure_occurrence.procedure_concept_id' as col_name, '11' as rnk union all
select 'procedure_occurrence.modifier_concept_id' as col_name, '12' as rnk union all
select 'observation.observation_concept_id' as col_name, '13' as rnk union all
select 'note.note_type_concept_id' as col_name, '14' as rnk union all
select 'note.note_class_concept_id' as col_name, '15' as rnk union all
select 'note.language_concept_id' as col_name, '16' as rnk union all
select 'specimen.specimen_concept_id' as col_name, '17' as rnk union all
select 'specimen.anatomic_site_concept_id' as col_name, '18' as rnk union all
select 'specimen.disease_status_concept_id' as col_name, '19' as rnk union all
select 'survey_conduct.survey_concept_id' as col_name, '20' as rnk union all
select 'care_site.place_of_service_concept_id' as col_name, '21' as rnk union all
select 'provider.specialty_concept_id' as col_name, '22' as rnk union all
select 'payer_plan_period.payer_concept_id' as col_name, '23' as rnk union all
select 'cost.cost_concept_id' as col_name, '24' as rnk 
)
select * from anna_list a
left join fields b on a.col_name =b.col_name 
order by rnk::int