Skip to content

Commit 93ce031

Browse files
alistairewjalistairewj
committed
fix links and add sidebar
1 parent 8442a84 commit 93ce031

File tree

14 files changed

+469
-11
lines changed

14 files changed

+469
-11
lines changed

‎jekyll-site/_docs/iii/tables/index.md‎

Lines changed: 46 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,46 @@
1+
---
2+
title: "MIMIC-III Tables"
3+
layout: default
4+
parent: "MIMIC-III documentation"
5+
nav_order: 20
6+
has_children: true
7+
permalink: /docs/iii/tables/
8+
---
9+
10+
# MIMIC-III Tables
11+
12+
MIMIC-III contains 26 tables covering different aspects of patient care in the ICU and hospital setting.
13+
14+
## Table Categories
15+
16+
### Patient Demographics and Admissions
17+
- **patients** - Patient demographics
18+
- **admissions** - Hospital admissions
19+
- **icustays** - ICU stays
20+
- **transfers** - Patient transfers between units
21+
22+
### Clinical Events
23+
- **chartevents** - Charted observations and vital signs
24+
- **labevents** - Laboratory test results
25+
- **microbiologyevents** - Microbiology culture results
26+
- **noteevents** - Clinical notes
27+
- **datetimeevents** - Date/time events
28+
- **inputevents_mv** - Fluid inputs (MetaVision)
29+
- **inputevents_cv** - Fluid inputs (CareVue)
30+
- **outputevents** - Patient outputs
31+
32+
### Medications and Procedures
33+
- **prescriptions** - Medication prescriptions
34+
- **procedureevents_mv** - Procedures (MetaVision)
35+
- **services** - Clinical services
36+
- **cptevents** - CPT codes for procedures
37+
38+
### Reference Tables
39+
- **caregivers** - ICU caregiver information
40+
- **d_cpt** - CPT code dictionary
41+
- **d_icd_diagnoses** - ICD diagnosis code dictionary
42+
- **d_icd_procedures** - ICD procedure code dictionary
43+
- **d_items** - Item dictionary for charted events
44+
- **d_labitems** - Laboratory item dictionary
45+
46+
Each table includes detailed documentation about structure, relationships, and usage patterns.

‎jekyll-site/_docs/iii/tutorials/index.md‎

Lines changed: 48 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,48 @@
1+
---
2+
title: "MIMIC-III Tutorials"
3+
layout: default
4+
parent: "MIMIC-III documentation"
5+
nav_order: 40
6+
has_children: true
7+
permalink: /docs/iii/tutorials/
8+
---
9+
10+
# MIMIC-III Tutorials
11+
12+
Tutorials and examples for working with MIMIC-III data.
13+
14+
## Available Tutorials
15+
16+
This section contains step-by-step tutorials covering:
17+
18+
- Basic data exploration
19+
- Common analysis patterns
20+
- SQL query examples
21+
- Data extraction techniques
22+
- Visualization methods
23+
- Research methodologies
24+
25+
## Getting Started with MIMIC-III
26+
27+
MIMIC-III is the predecessor to MIMIC-IV and contains ICU data from 2001-2012. While we recommend new research projects use MIMIC-IV, these tutorials remain valuable for:
28+
29+
- Working with existing MIMIC-III datasets
30+
- Understanding legacy analysis approaches
31+
- Comparative studies between MIMIC-III and MIMIC-IV
32+
- Historical data analysis
33+
34+
## Tutorial Categories
35+
36+
### Basic Queries
37+
Introduction to querying MIMIC-III tables and understanding the data structure.
38+
39+
### Clinical Analysis
40+
Examples of common clinical research questions and how to answer them using MIMIC-III.
41+
42+
### Data Processing
43+
Techniques for cleaning, preprocessing, and preparing MIMIC-III data for analysis.
44+
45+
### Advanced Topics
46+
Complex queries, machine learning applications, and advanced analytics.
47+
48+
For new users, we recommend starting with the [Getting Started]({{ "/docs/gettingstarted/" | relative_url }}) section and the [MIMIC-III About]({{ "/docs/iii/about/" | relative_url }}) pages before diving into these tutorials.

‎jekyll-site/_docs/iv/about/concepts.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -73,7 +73,7 @@ For events which occur over a period of time, `starttime` and `endtime` provide
7373

7474
### `dod`
7575

76-
`dod` is the patient's date of death sourced from one of two sources: the hospital database or a state death database. See the [*patients*](/docs/iv/modules/hosp/patients) documentation for more detail.
76+
`dod` is the patient's date of death sourced from one of two sources: the hospital database or a state death database. See the [*patients*]({{ "/docs/iv/modules/hosp/patients" | relative_url }}) documentation for more detail.
7777

7878
### `transfertime`
7979

‎jekyll-site/_docs/iv/index.md‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -26,36 +26,36 @@ MIMIC-IV is organized into modules based on the source of the data:
2626
### Core Module
2727
Patient demographics, admission tracking, and stay information.
2828

29-
[Explore Core Module →](/docs/iv/modules/core/){: .btn .btn-outline }
29+
[Explore Modules →]({{ "/docs/iv/modules/" | relative_url }}){: .btn .btn-outline }
3030

3131
### Hospital (Hosp) Module
3232
Data from the hospital-wide electronic health record including lab results, medications, diagnoses, and procedures.
3333

34-
[Explore Hosp Module →](/docs/iv/modules/hosp/){: .btn .btn-outline }
34+
[Explore Hosp Module →]({{ "/docs/iv/modules/hosp/" | relative_url }}){: .btn .btn-outline }
3535

3636
### ICU Module
3737
Highly granular data from the ICU including vital signs, fluid balance, and charted observations.
3838

39-
[Explore ICU Module →](/docs/iv/modules/icu/){: .btn .btn-outline }
39+
[Explore ICU Module →]({{ "/docs/iv/modules/icu/" | relative_url }}){: .btn .btn-outline }
4040

4141
### Emergency Department (ED) Module
4242
Emergency department data including triage, vital signs, and treatment information.
4343

44-
[Explore ED Module →](/docs/iv/modules/ed/){: .btn .btn-outline }
44+
[Explore ED Module →]({{ "/docs/iv/modules/ed/" | relative_url }}){: .btn .btn-outline }
4545

4646
### Chest X-Ray (CXR) Module
4747
Chest X-ray images and associated radiology reports.
4848

49-
[Explore CXR Module →](/docs/iv/modules/cxr/){: .btn .btn-outline }
49+
[Explore CXR Module →]({{ "/docs/iv/modules/cxr/" | relative_url }}){: .btn .btn-outline }
5050

5151
### Note Module
5252
De-identified clinical notes and reports.
5353

54-
[Explore Note Module →](/docs/iv/modules/note/){: .btn .btn-outline }
54+
[Explore Note Module →]({{ "/docs/iv/modules/note/" | relative_url }}){: .btn .btn-outline }
5555

5656
## Getting Started with MIMIC-IV
5757

58-
1. **Understand the structure** - Review the [modular organization](/concepts/mimic-iv-structure/)
59-
2. **Learn about identifiers** - Understand how patients are [linked across modules](/concepts/patient-linking/)
60-
3. **Try the tutorials** - Start with [basic queries](/tutorials/first-query/)
61-
4. **Explore use cases** - See [example analyses](/tutorials/analysis-examples/)
58+
1. **Understand the structure** - Review the [modular organization]({{ "/docs/iv/modules/" | relative_url }})
59+
2. **Learn about identifiers** - Understand how patients are [linked across modules]({{ "/docs/iv/about/" | relative_url }})
60+
3. **Try the tutorials** - Start with [MIMIC-IV tutorials]({{ "/docs/iv/tutorials/" | relative_url }})
61+
4. **Explore concepts** - See [core concepts]({{ "/docs/iv/about/concepts/" | relative_url }})

‎jekyll-site/_docs/iv/modules/cxr/index.md‎

Lines changed: 31 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,31 @@
1+
---
2+
title: "Chest X-Ray Module"
3+
layout: default
4+
parent: "MIMIC-IV Modules"
5+
grand_parent: "MIMIC-IV"
6+
nav_order: 4
7+
has_children: true
8+
permalink: /docs/iv/modules/cxr/
9+
---
10+
11+
# Chest X-Ray Module
12+
13+
MIMIC-CXR provides chest X-ray images and radiology reports for a subset of patients admitted to the emergency department. This module contains:
14+
15+
- High-resolution chest X-ray images
16+
- Associated radiology reports
17+
- Study metadata and timing
18+
- Image processing information
19+
20+
## Tables in this Module
21+
22+
The CXR module contains tables for:
23+
24+
- **mimic_cxr_studies** - Study-level metadata
25+
- **mimic_cxr_metadata** - Image metadata
26+
- **mimic_cxr_reports** - Radiology reports
27+
- **mimic_cxr_sectioned** - Sectioned radiology reports
28+
- **mimic_cxr_chexpert** - CheXpert labels
29+
- **mimic_cxr_negbio** - NegBio labels
30+
31+
This module enables research combining medical imaging with clinical data from the same patients.

‎jekyll-site/_docs/iv/modules/ecg/index.md‎

Lines changed: 29 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,29 @@
1+
---
2+
title: "ECG Module"
3+
layout: default
4+
parent: "MIMIC-IV Modules"
5+
grand_parent: "MIMIC-IV"
6+
nav_order: 6
7+
has_children: true
8+
permalink: /docs/iv/modules/ecg/
9+
---
10+
11+
# ECG Module
12+
13+
The ECG module contains electrocardiogram waveform data and measurements. This includes:
14+
15+
- High-frequency ECG waveforms
16+
- Automated measurements
17+
- Clinical annotations
18+
- Study metadata
19+
20+
## Tables in this Module
21+
22+
The ECG module contains:
23+
24+
- **record_list** - List of available ECG records
25+
- **machine_measurements** - Automated ECG measurements
26+
- **annotations** - Clinical annotations and interpretations
27+
- **diagnosis** - ECG diagnoses and findings
28+
29+
This module enables cardiovascular research using high-quality ECG data linked to comprehensive clinical information.

‎jekyll-site/_docs/iv/modules/ed/index.md‎

Lines changed: 32 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,32 @@
1+
---
2+
title: "Emergency Department Module"
3+
layout: default
4+
parent: "MIMIC-IV Modules"
5+
grand_parent: "MIMIC-IV"
6+
nav_order: 3
7+
has_children: true
8+
permalink: /docs/iv/modules/ed/
9+
---
10+
11+
# Emergency Department Module
12+
13+
The Emergency Department (ED) module contains data for emergency department patients including:
14+
15+
- Triage assessments
16+
- Nurse-validated vital signs
17+
- Medicine reconciliation
18+
- Treatment information
19+
- Disposition and discharge planning
20+
21+
## Tables in this Module
22+
23+
The ED module contains tables for:
24+
25+
- **edstays** - Emergency department stay information
26+
- **triage** - Triage assessment data
27+
- **vitalsign** - Vital signs recorded in the ED
28+
- **medrecon** - Medication reconciliation
29+
- **diagnosis** - ED diagnoses
30+
- **pyxis** - Medication dispensing information
31+
32+
Each table is documented with structure details, data definitions, and usage examples.

‎jekyll-site/_docs/iv/modules/hosp/index.md‎

Lines changed: 38 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,38 @@
1+
---
2+
title: "Hospital Module"
3+
layout: default
4+
parent: "MIMIC-IV Modules"
5+
grand_parent: "MIMIC-IV"
6+
nav_order: 2
7+
has_children: true
8+
permalink: /docs/iv/modules/hosp/
9+
---
10+
11+
# Hospital Module
12+
13+
The Hospital module provides all data acquired from the hospital-wide electronic health record. This includes:
14+
15+
- Laboratory measurements
16+
- Microbiology cultures
17+
- Medication information
18+
- Services provided
19+
- Billed diagnoses and procedures
20+
- Transfers between hospital units
21+
- Discharge information
22+
23+
## Tables in this Module
24+
25+
The Hospital module contains tables for:
26+
27+
- **admissions** - Hospital admission information
28+
- **patients** - Patient demographics
29+
- **transfers** - Patient transfers between units
30+
- **services** - Clinical services
31+
- **diagnoses_icd** - ICD diagnosis codes
32+
- **procedures_icd** - ICD procedure codes
33+
- **prescriptions** - Medication prescriptions
34+
- **labevents** - Laboratory test results
35+
- **microbiologyevents** - Microbiology culture results
36+
- **provider** - Healthcare provider information
37+
38+
Documentation for each table includes structure details, relationships, and usage examples.

‎jekyll-site/_docs/iv/modules/icu/index.md‎

Lines changed: 33 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,33 @@
1+
---
2+
title: "ICU Module"
3+
layout: default
4+
parent: "MIMIC-IV Modules"
5+
grand_parent: "MIMIC-IV"
6+
nav_order: 1
7+
has_children: true
8+
permalink: /docs/iv/modules/icu/
9+
---
10+
11+
# ICU Module
12+
13+
The ICU module contains data collected from the clinical information system used within the Intensive Care Unit. This includes highly granular information such as:
14+
15+
- Hour-to-hour vital signs
16+
- Fluid management information
17+
- Charted clinical observations
18+
- Medication administration
19+
- Procedures performed
20+
- Caregiver information
21+
22+
## Tables in this Module
23+
24+
The ICU module contains the following tables:
25+
26+
- **caregiver** - Information about ICU caregivers
27+
- **chartevents** - Charted observations and vital signs
28+
- **datetimeevents** - Date/time events
29+
- **inputevents** - Fluid inputs and medications
30+
- **outputevents** - Patient outputs (urine, drainage, etc.)
31+
- **procedureevents** - Procedures performed in the ICU
32+
33+
Each table is documented with its structure, relationships, and usage examples.

‎jekyll-site/_docs/iv/modules/index.md‎

Lines changed: 34 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,34 @@
1+
---
2+
title: "MIMIC-IV Modules"
3+
layout: default
4+
parent: "MIMIC-IV"
5+
nav_order: 2
6+
has_children: true
7+
permalink: /docs/iv/modules/
8+
---
9+
10+
# MIMIC-IV Modules
11+
12+
MIMIC-IV is organized into modules that reflect the different data sources and clinical areas:
13+
14+
## Available Modules
15+
16+
### ICU Module
17+
Intensive Care Unit data including vital signs, medications, and clinical observations.
18+
19+
### Hospital Module
20+
Hospital-wide data including laboratory results, medications, diagnoses, and procedures.
21+
22+
### Emergency Department Module
23+
Emergency department visits, triage assessments, and treatment information.
24+
25+
### Chest X-Ray Module
26+
Chest X-ray images and associated radiology reports.
27+
28+
### Note Module
29+
Clinical notes and documentation from patient care.
30+
31+
### ECG Module
32+
Electrocardiogram waveform data and measurements.
33+
34+
Each module contains multiple tables with detailed documentation about the structure and content of the data.

0 commit comments

Comments
 (0)