diff --git a/.github/workflows/render_site_from_rmd.yml b/.github/workflows/render_site_from_rmd.yml index ab44e3c..48df697 100644 --- a/.github/workflows/render_site_from_rmd.yml +++ b/.github/workflows/render_site_from_rmd.yml @@ -11,7 +11,7 @@ name: render R Markdown files to docs # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages permissions: - contents: read + contents: write pages: write id-token: write diff --git a/ddl/Sql Server/Medical_Imaging_Ext_sql_server_1.0_ddl.rtf b/ddl/Sql Server/Medical_Imaging_Ext_sql_server_1.0_ddl.rtf new file mode 100644 index 0000000..46e3c9e --- /dev/null +++ b/ddl/Sql Server/Medical_Imaging_Ext_sql_server_1.0_ddl.rtf @@ -0,0 +1,34 @@ +{\rtf1\ansi\ansicpg1252\cocoartf2709 +\cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fswiss\fcharset0 Helvetica;} +{\colortbl;\red255\green255\blue255;} +{\*\expandedcolortbl;;} +\margl1440\margr1440\vieww11520\viewh8400\viewkind0 +\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0 + +\f0\fs24 \cf0 --sql server CDM DDL Specification for OMOP CDM Medical Imaging Ext\ +CREATE TABLE image_occurrence(\ + image_occurrence_id integer NOT NULL,\ + person_id integer NOT NULL,\ + procedure_occurrence_id integer NOT NULL,\ + visit_occurrence_id integer,\ + anatomic_site_concept_id integer,\ + wadors_uir varchar(max),\ + local_path varchar(max) NOT NULL,\ + image_occurrence_date date NOT NULL,\ + image_study_uid varchar(max) NOT NULL,\ + image_series_uid varchar(max) NOT NULL,\ + modality varchar(250) NOT NULL);\ +\ +CREATE TABLE image_feature(\ + image_feature_id integer NOT NULL,\ + person_id integer NOT NULL,\ + image_occurrence_id integer NOT NULL,\ + table_concept_id integer NOT NULL,\ + table_row_id integer NOT NULL,\ + image_feature_concept_id integer NOT NULL,\ + image_feature_type_concept_id integer NOT NULL,\ + image_finding_concept_id integer,\ + image_finding_id integer,\ + anatomic_site_concept_id integer,\ + alg_system varchar(max),\ + alg_datetime datetime);} \ No newline at end of file diff --git a/ddl/Sql Server/OMOP_CDM_Medical_Imaging_Ex_Field_Level.csv b/ddl/Sql Server/OMOP_CDM_Medical_Imaging_Ex_Field_Level.csv new file mode 100644 index 0000000..190385b --- /dev/null +++ b/ddl/Sql Server/OMOP_CDM_Medical_Imaging_Ex_Field_Level.csv @@ -0,0 +1,13 @@ +cdmTableName,cdmFieldName,isRequired,cdmDatatype,userGuidance +image_feature,image_feature_id,Yes ,integer ,The unique key is given to an imaging feature. +image_feature,person_id,Yes ,integer,The person_id of the Person table for whom the the procedure is recorded. This can be a system-generated code or adopted from original source. +image_feature,image_occurrence_id,Yes,integer,The unique key of the Image_occurrence table. +image_feature,table_concept_id,Yes,integer,"The concept_id of the domain table that feature is stored in Measurement, Observation, etc. This concept should be used with the table_row_id." +image_feature,table_row_id,Yes,integer,The row_id of the domain table that feature is stored. +image_feature,image_feature_concept_id,Yes,integer,Concept_id of standard vocabulary—often a LOINC or RadLex of image features +image_feature,image_feature_type_concept_id,Yes,integer ,"This field can be used to determine the provenance of the imaging features (e.g., DICOM SR, algorithms used on images)" +image_feature,image_finding_concept_id,No,integer,"RadLex or other terms of the groupings of image feature (e.g., nodule)" +image_feature,image_finding_id,No,integer ,Integer for linking related image features. It should not be interpreted as an order of clinical relevance. +image_feature,anatomic_site_concept_id,No,integer ,This is the site on the body where the feature was found. It maps the ANATOMIC_SITE_SOURCE_VALUE to a Standard Concept in the Spec Anatomic Site domain. +image_feature,alg_system ,No ,varchar(max),"URI of the algorithm that extracted features, including version information" +image_feature,alg_datetime ,No ,datetime ,The date and time of the algorithm processing. \ No newline at end of file diff --git a/ddl/Sql Server/OMOP_CDM_Medical_Imaging_Ext_Field_Level.csv b/ddl/Sql Server/OMOP_CDM_Medical_Imaging_Ext_Field_Level.csv new file mode 100644 index 0000000..f52e742 --- /dev/null +++ b/ddl/Sql Server/OMOP_CDM_Medical_Imaging_Ext_Field_Level.csv @@ -0,0 +1,65 @@ +cdmTableName,cdmFieldName,isRequired,cdmDatatype,userGuidance +image_occurrence,image_occurrence_id,Yes,integer ,The unique key is given to an imaging study record (often referred to as the accession number or imaging order number) +image_occurrence,person_id,Yes,integer,The person_id of the Person for whom the procedure is recorded. This can be a system-generated code or adopted from original source. +image_occurrence,procedure_occurrence_id,Yes,integer ,The unique key is given to a procedure record for a person. Link to the Procedure_occurrence table. +image_occurrence,visit_occurrence_id,No,integer,The unique key is given to the visit record for a person. Link to the Visit_occurrence table. +image_occurrence,anatomic_site_concept_id,No,integer,Anatomical location of the imaging procedure by the medical acquisition device (gross anatomy). It maps the ANATOMIC_SITE_SOURCE_VALUE to a Standard Concept in the Spec Anatomic Site domain. This should be coded at the lowest level of granularity. +image_occurrence,wadors_uri ,No ,varchar (max) ,A Web Access to DICOM Objects via Restful Web Services Uniform Resource Identifier on study level. +image_occurrence,local_path,Yes,varchar (max),"Universal Naming Convention (UNC) path to the folder containing the image object file access via a storage block access protocol. (e.g., \\Server\Directory)" +image_occurrence,image_occurrence_date ,Yes,date ,The date the imaging procedure occurred. +image_occurrence,image_study_UID ,Yes,varchar (250) ,DICOM Study UID +image_occurrence,image_series_UID ,Yes ,varchar (250) ,DICOM Series UID +image_occurrence,modality ,Yes ,varchar (250) ,"DICOM-defined value (e.g., US, CT, MR, PT, DR, CR, NM)" +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, +,,,, \ No newline at end of file