update menu

.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
 

ddl/Sql Server/Medical_Imaging_Ext_sql_server_1.0_ddl.rtf

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+{\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);}

ddl/Sql Server/OMOP_CDM_Medical_Imaging_Ex_Field_Level.csv

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+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.

ddl/Sql Server/OMOP_CDM_Medical_Imaging_Ext_Field_Level.csv

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+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)"
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