Cap Forms Processed tables
CAP_FORMS
The table cap_forms contains details about the Lung Resection Cap Forms.
Table Columns
| field | type |
|---|---|
| pat_id | STRING |
| pat_mrn_id | STRING |
| stanford_patient_uid | STRING |
| birth_date | DATETIME |
| synoptic_name | STRING |
| concept_hierarchy | STRING |
| parent_element_name | STRING |
| element_name | STRING |
| smrtdta_elem_value | STRING |
| comment | STRING |
| accession_number | STRING |
| order_proc_id | INTEGER |
| pat_enc_csn_id | INTEGER |
| element_id | STRING |
| taken_time | DATETIME |
| result_id | STRING |
| hlv_id | INTEGER |
| res_val_status_c | INTEGER |
| case_id | INTEGER |
| cur_source_lqf_id | STRING |
| line | INTEGER |
| synoptic_id | INTEGER |
Columns Description
pat_id
Unique identifier for the patient in EPIC Clarity
pat_mrn_id
Patient Medical Record Number
stanford_patient_uid
Unique patient identifier within the STARR DataLake that consist on the concatenation of patient MRN and DOB
birth_date
Patient’s date of birth
synoptic_name
For this dataset it is LUNG: RESECTION for all rows
concept_hierarchy
This include the provenance for a particular element in the CAP form
Example
LUNG > MARGINS > Margin Status for Non-Invasive Tumor > All margins negative for non-invasive tumor
parent_element_name
One of the elements of the CAP form. It is in general part of the description of the particular clinical finding from which a report needs to be made.
Example
MARGIN STATUS FOR NON-INVASIVE TUMOR
element_name
One of the elements of the CAP form. It is in general part of the observation of the particular clinical finding from which a report needs to be made.
Example
ALL MARGINS NEGATIVE FOR NON-INVASIVE TUMOR
smrtdta_elem_value
This is in general the same as the information presented on element_name or it could be the actual clinical finding
Examples
Lymphatic invasion present1.2 cm
comment
This in general contains free form clinical findings such as tumor sizes.
Examples
1.4 cm10%
accession_number
This is the accession number linked with the sample from which the report is made.
order_proc_id
This is the order identifier. This links the CAP form with a particular order for the procedure.
pat_enc_csn_id
Encounter identifier. This links the CAP form with a clinical encounter.
element_id
Internal EPIC identifier for the particular CAP form element
taken_time
The DATETIME in which the sample was taken.
result_id
The unique identifier for the result record.
hlv_id
The unique identifier (.1 item) for the value record.
res_val_status_c
Integer representing validation statuses of result records.
case_id
The unique identifier for the case record.
cur_source_lqf_id
The unique ID of the SmartForm that is the source of the current value.
line
Other EPIC identifier for the particular CAP form element or metadata
synoptic_id
The unique identifier for the synoptic result record.
SHC_PATHOLOGY_REPORTS
The table shc_pathology_reports contains the pathology report text and details about them. It only contains pathology reports associated with the Lung Resection CAP forms present on the table cap_forms
Table Columns
| field | type |
|---|---|
| stanford_patient_uid | STRING |
| pat_id | STRING |
| order_proc_id | INTEGER |
| pat_enc_csn_id | INTEGER |
| order_time | DATETIME |
| taken_time | DATETIME |
| result_time | DATETIME |
| order_type | STRING |
| proc_code | STRING |
| proc_name | STRING |
| specimen_accession_numbers | STRING |
| section_name | STRING |
| section_order | INTEGER |
| section_text | STRING |
| load_table_id | STRING |
| trace_id | STRING |
| source_flag | STRING |
Columns Description
stanford_patient_uid
Unique patient identifier within the STARR DataLake that consist on the concatenation of patient MRN and DOB
pat_id
Unique identifier for the patient in EPIC Clarity
order_proc_id
This is the order identifier. This links the pathology report with a particular order for the procedure.
pat_enc_csn_id
Encounter identifier. This links the pathology report with a clinical encounter.
order_time
The DATETIME when the pathology report order was placed.
taken_time
The DATETIME in which the sample was taken.
result_time
The DATETIME when the pathology report result was finalized.
order_type
The type of order that generated this pathology report (e.g., surgical pathology, biopsy).
proc_code
The procedure code associated with the pathology examination.
proc_name
The descriptive name of the procedure that generated the pathology report.
specimen_accession_numbers
The accession number(s) linked with the specimen(s) from which the pathology report was made.
section_name
The name of the specific section within the pathology report (e.g., “Gross Description”, “Microscopic Description”, “Diagnosis”).
section_order
The order/sequence number of this section within the pathology report.
section_text
The actual text content of this specific section of the pathology report.
load_table_id
Internal identifier for the data loading process that brought this record into the system.
trace_id
Unique identifier for tracing the data lineage and processing history of this record.
source_flag
This is shc for this dataset