reorg for nicer nav bar

Author: alistairewj

jekyll-site/_config.yml

@@ -24,7 +24,7 @@ collections:
   overview:
     permalink: /:collection/:path/
     output: true
-  databases:
+  docs:
     permalink: /:collection/:path/
     output: true
   tutorials:
@@ -62,7 +62,7 @@ just_the_docs:
     overview:
       name: "Overview"
       nav_order: 1
-    databases:
+    docs:
       name: "Databases"
       nav_order: 2
     tutorials:
@@ -125,7 +125,7 @@ defaults:
       nav_exclude: false
   - scope:
       path: ""
-      type: "databases"
+      type: "docs"
     values:
       layout: "default"
       nav_exclude: false

jekyll-site/_docs/cxr/index.md

@@ -0,0 +1,29 @@
+---
+title: "Chest X-Ray (CXR)"
+layout: default
+nav_order: 24
+has_children: true
+permalink: /docs/cxr/
+---
+
+# Chest X-Ray Module
+
+MIMIC-CXR provides chest X-ray images and radiology reports for a subset of patients admitted to the emergency department. This module contains:
+
+- High-resolution chest X-ray images
+- Associated radiology reports
+- Study metadata and timing
+- Image processing information
+
+## Tables in this Module
+
+The CXR module contains tables for:
+
+- **mimic_cxr_studies** - Study-level metadata
+- **mimic_cxr_metadata** - Image metadata  
+- **mimic_cxr_reports** - Radiology reports
+- **mimic_cxr_sectioned** - Sectioned radiology reports
+- **mimic_cxr_chexpert** - CheXpert labels
+- **mimic_cxr_negbio** - NegBio labels
+
+This module enables research combining medical imaging with clinical data from the same patients.

jekyll-site/_docs/ed/index.md

@@ -0,0 +1,30 @@
+---
+title: "Emergency Department (ED)"
+layout: default
+nav_order: 25
+has_children: true
+permalink: /docs/ed/
+---
+
+# Emergency Department Module
+
+The Emergency Department (ED) module contains data for emergency department patients including:
+
+- Triage assessments
+- Nurse-validated vital signs
+- Medicine reconciliation
+- Treatment information
+- Disposition and discharge planning
+
+## Tables in this Module
+
+The ED module contains tables for:
+
+- **edstays** - Emergency department stay information
+- **triage** - Triage assessment data
+- **vitalsign** - Vital signs recorded in the ED
+- **medrecon** - Medication reconciliation
+- **diagnosis** - ED diagnoses
+- **pyxis** - Medication dispensing information
+
+Each table is documented with structure details, data definitions, and usage examples.

jekyll-site/_docs/ii/index.md

@@ -0,0 +1,14 @@
+---
+title: "MIMIC-II"
+layout: default
+nav_order: 23
+has_children: true
+permalink: /docs/ii/
+---
+
+# MIMIC-II documentation
+
+MIMIC-II is an older version of the MIMIC database, now replaced by [MIMIC-III](/docs/iii/about/) and [MIMIC-IV](/docs/iv/about). The following information may still be helpful however:
+
+- MIMIC-II documentation: [mimic-ii-guide.pdf](mimic-ii-guide.pdf)
+- Introduction to MIMIC-II: [introduction-mimic-ii.pdf](introduction-mimic-ii.pdf)

jekyll-site/_docs/ii/introduction-mimic-ii.pdf

@@ -0,0 +1,234 @@
+---
+title: MIMIC-II v2.6
+parent: MIMIC-II documentation
+nav_order: 2
+---
+
+# MIMIC-II v2.6
+
+## Changelog
+
+- Merge the last year of the ISM database
+
+The last year of ISM, through September 2008, has been added, including indications of matches to waveforms.
+
+- New dateshifts
+
+We have given all subjects a new, random dateshift.
+
+- Add overall SOFA score as total of each organ system's score
+
+The individual-system SOFA scores are in CHARTEVENTS, with itemids 20002 through 20007; a new itemid, 20009, has been added, and it s for the total score. The relevant columns in ICUSTAY\_DETAIL (sofa\_first, sofa\_min, sofa\_max) indicate this total score.
+
+- Add a column to ICUSTAY\_DETAIL indicating number of matched waveforms
+
+A new column, matched\_waveforms\_num, has been added to ICUSTAY\_DETAIL; it gives the number of waveforms matched to the patient.
+
+- Add waveform statistics
+
+Basic waveform statistics and metadata have been added to the database; these are essentially the organized output of what one would see by running the WFDB utility wfdbdesc (over all of the
+waveforms).
+
+- Add LOINC codes for hospital labs
+
+D\_LABITEMS contains two new columns, loinc\_code and loinc\_description, giving the LOINC codes and descriptions respectively.
+
+- Add diagnosis-related groups (DRGs)
+
+A new table, DRGEVENTS, maps subject IDs and hospital-admission IDs to DRG itemids, which are defined in D\_CODEDITEMS.
+
+- Add procedures
+
+PROCEDUREEVENTS contains indications of procedures performed on patients, for given hospital-admission IDs. The itemids for procedures are defined in D\_CODEDITEMS. Exact times for procedures
+are not given; however, their dates are given in the proc\_dt column, and the order in which a patient's procedures are performed, for a given day, are indicated by consecutive numbers (integers) in the sequence\_num column.
+
+- Add demographic information
+
+DEMOGRAPHICEVENTS contains indications of marital status, type and source of admission, ethnicity, overall payor group, and religion as recorded for each patient upon admission to the hospital. The
+definitions of the itemids are given in D\_CODEDITEMS.
+
+- Add microbiology information
+
+MICROBIOLOGYEVENTS contains information on microbiology tests performed on patients: specimen, organism, and antibacterium are indicate in the spec\_itemid, org\_itemid, and ab\_itemid columns
+respectively; these itemids are defined in D\_CODEDITEMS.
+
+- Remove duplicate mappings of waveform case IDs to subject IDs in PARAMETER\_MAPPING
+
+- Fix the icustay\_expire\_flg in ICUSTAY\_DETAIL
+
+icustay\_expire\_flg indicates whether the given patient died during the given ICU stay. For some patients, this column was 'Y' for all of his/her ICU stays, rather than just the last; this has been fixed.
+
+- Fix case of hospital admission ID not unique to subject ID
+
+Hospital admission 15449 was mapped to two different patients; this has been fixed.
+
+- Add Exlihauser comorbidity scores
+
+The Exlihauser comorbidity scores (calculated from DRG and ICD-9 codes) can be found in COMORBIDITY\_SCORES
+
+## Known limitations, bugs.
+
+- Missing data
+
+Newly added data: DRGs, Demographics, Microbiology tests and procedures were not available for all subjects. Therefore, you will find that this data is missing for some subjects.
+
+We were unable to complete the import of some of the text
+data. Radiology, Echo and ECG reports are missing from NOTEEVENTS.
+
+- Waveform dates
+
+The waveform metadata contains dates from the current waveforms available on PhysioNet:
+
+https://archive.physionet.org/physiobank/database/mimic2db/
+
+The dates found here will not match those found elsewhere in the
+database.
+
+# MIMIC-II v2.5
+
+## Changelog
+
+Major changes since version 2.4 :
+
+- Date of death after hospital discharge
+
+Patients have been matched against the Social Security death tapes, and the date of death has been imported into MIMIC-II.  For patients who died in the hospital, their respective dates of discharge were used as their dates of death. Two additional columns have been added to the D\_PATIENTS table:
+
+- DOD                            = Date of Death
+- HOSPITAL\_EXPIRE\_FLG  = Whether or not the patient deid in the hospital
+
+The column EXPIRE\_FLG in the ADMISSION table has been removed.
+
+- New Waveform case ID matches
+
+A first round of waveforms with up to 8 simultaneous channels have been matched to SUBJECT\_IDs. The matches can be found in the PARAMETER\_MAPPING table where CATEGORY is "SUBJECT\_ID\_TO\_CASE\_ID", the columns PARAM1\_NUM (for the SUBJECT\_ID) and PARAM2\_STR (for the waveform case ID).
+
+- Merge NOTEEVENTS into REPORTEVENTS
+
+REPORTEVENTS has been merged into NOTEEVENTS. Categories have been extracted into D\_REPORTITEMS, with the ITEMID column as the foreign key, but not completely; the D\_* tables will be combined into a complete dictionary in a later release.
+
+- New ICUSTAY\_DAYS materialized view
+
+The ICUSTAY\_DAYS materialized view was added to divide each ICU stays into daily periods. This greatly helps computation of cumulative queries.
+
+- Daily SOFA scores
+
+New entries in D\_CHARTITEMS were added to represent SOFA scores (itemid = 20002), and corresponding scores were added in CHARTEVENTS.
+
+- Daily SAPS I calculations
+
+For each ICU stay, a daily SAPS I was added into the CHARTEVENTS table, with ITEMID 20001.
+
+- Add a view for summarizing the D\_CHARTITEMS table
+
+It was somewhat troublesome for users of the database to collect statistics for the parameters (ITEMIDs) in D\_CHARTITEMS. Therefore, a summarizing materialized view, D\_CHARTITEMS\_DETAIL, was added as a first introduction of all charted parameters; it describes how many patients each parameter was charted from, and various statistics such as min., max., and average.
+
+- Clean "value1" and "value2" columns in CHARTEVENTS for numeric itemids
+
+Some ITEMIDs in the CHARTEVENTS table that are supposed to be only numeric (such as ABP, HR) had repeated values in columns VALUE1/VALUE2 (which are VARCHAR columns) and VALUE1NUM/VALUE2NUM (NUMBER columns); VALUE1 and VALUE2 were cleaned accordingly.
+
+- Reorganized ICUSTAY\_DETAIL materialized view
+
+The ICUSTAY\_DETAIL view has been used as a key component in  many of computation for several researches. We added/changed some columns to reflect:
+
+- EXPIRE\_FLG                 = Flag to indicate if the paitent is dead, either in the hospital or after discharge
+- HOSPITAL\_EXPIRE\_FLG = If the patient deid in the hospital
+- ICUSTAY\_EXPIRE\_FLG   = If the patient deid in the ICU
+- HEIGHT                       = Patient height
+- WEIGHT\_FIRST            = The first measured weight for the patient in the ICU stay 
+- WEIGHT\_MIN               = The minimum weight for the ICU stay
+- WEIGHT\_MAX              = The maximum weight for the ICU stay
+- SAPSI\_FIRST               = The first measured SAPS-I score for the patient in the ICU stay 
+- SAPSI\_MIN                  = The minimum SAPS-I score for the ICU stay
+- SAPSI\_MAX                 = The maximum SAPS-I score for the ICU stay
+- SOFA\_FIRST                = The first measured SOFA score for the patient in the ICU stay 
+- SOFA\_MIN                   = The minimum SOFA score for the ICU stay
+- SOFA\_MAX                  = The maximum SOFA score for the ICU stay
+
+- Add an ICUSTAY\_ID column to all event tables
+
+To facilitate queries and other computations, the ICUSTAY\_ID column has been added to event tables: CHARTEVENTS, IOEVENTS, MEDEVENTS, LABEVENTS and TOTALBALEVENTS.
+
+- Clean duplicates in D\_CAREUNITS
+
+There were duplicate names in the table D\_CAREUNITS that needed to be merged, and their foreign keys updated.
+
+- Remove entries from item tables which contain no records in event tables
+
+292 unused rows have been removed from D\_MEDITEMS; 3544 from D\_CHARTITEMS.
+
+- Fix problems with duplicate hospital admissions
+
+Six patients had hospital admissions with overlapping admission-to-discharge date intervals. These were fixed by examining the discharge summaries.
+
+- Add missing foreign key for POE\_ORDER
+
+For POE\_ORDER, columns SUBJECT\_ID and HADM\_ID were properly made to be foreign keys for the tables D\_PATIENTS and ADMISSIONS, respectively.
+
+## Database statistics (adult records summary)
+
+| | N* | #cases** (%unit) | mean ±std | median | IQR (Q1,Q3) |
+|---- | ---- | ---- | ---- | ---- | ---- |
+|Hospital admissions | 22,870 | | | | |
+|ICU Stays | 25,328 | | | | |
+|Age (years) | 25,328 | | 63.3 ±17.7 | 65.20 | 26.1 (51.3,77.4)|
+|Gender (male) | 25,328 | 14,259 (56.3%) | | | |
+|ICU Los (days) | 25,328 | | 4.7 ±11 | 2.20 | 3.3 (1.1,4.4)|
+|Hospital Los (days) | 22,870 | | 10.7 ±13 | 7.00 | 9 (4,13)|
+|SAPS I - day 1 *** | 20,142 | | 13.4 ±5.3 | 13.00 | 7 (10,17)|
+|Mechanical ventilation | 25,328 | 11,969 (47.3%) | | | |
+|Invasive Swan-Ganz hemodynamic monitoring | 25,328 | 5,637 (22.3%) | | | |
+|Invasive arterial blood pressure monitoring | 25,328 | 14,054 (55.5%) | | | |
+|Use of vaso-active medications | 25,328 | 8,693 (34.3%) | | | |
+|Hospital mortality | 22,870 | 2,666 (11.7%) | | | |
+
+\* N = The number of ICUStays or Hospitalizations. that were included in the calculation for the given ICU Unit.
+
+** #cases = The number of ICUStays orHospitalizations that match the category criteria. For example: In Gender, #cases will be the number of male ICUStays in a unit.
+
+*** Only ICUStays where they have all 14 SAPS parameters were included
+
+# MIMIC-II v2.4
+
+## Changelog
+
+- Bug #5: Fix problems with icustay generation
+- Bug #13: Fix in "Unknown" service type in icustay\_detail
+- Bug #21: Rename ORDER column in PARAMETER\_MAPPING table
+- Bug #26: Make event date fields consistent
+- Bug #27: Rename d\_labitems.lab\_category to category for consistency with other item tables
+- Bug #40: Modify SAPS I calculation to correctly account for ventilated patients
+- Feature #11: Delete the materialized view VITAL\_SIGNS\_RAW, because this was just a temporal data  to  be used by some statistics calculations.
+- Feature #12: Add indices on cgid, itemid to chartevents
+- Feature #14: Add AKI materialized view
+- Feature #15: Add organ system failure materialized view
+- Feature #16: Restore the Physionet 2009 challenge patients
+- Feature #34: Re-generate SAPS scores after fixing Icustay problems
+- Change request #36: Make the "Length Of Stay" columns consistent in minutes
+- Change request #37: Replace ICUSTAY materialized view with ICUSTAYEVENTS table
+- Change request #38: Make consistent some column names in ICUSTAY_DETAIL
+
+## Database statistics (adult records summary)
+
+| | N* | #cases** (%unit) | mean ±std | median | IQR (Q1,Q3) |
+|---- | ---- | ---- | ---- | ---- | ----|
+|Hospital admissions | 22,870 | | | | |
+|ICU Stays | 25,328 | | | | |
+|Age (years) | 25,328 | | 63.3 ±17.7 | 65.20 | 26.1 (51.3,77.4)|
+|Gender (male) | 25,328 | 14,259 (56.3%) |  |  |  |
+|ICU Los (days) | 25,328 | |  4.7 ±11 | 2.20 | 3.3 (1.1,4.4)|
+|Hospital Los (days) | 22,870 | |  10.7 ±13 | 7.00 | 9 (4,13)|
+|SAPS I - day 1 *** | 20,142 | |  13.4 ±5.3 | 13.00 | 7 (10,17)|
+|SAPS I - day 2 *** | 13,495 | |  11.8 ±4.6 | 11.00 | 6 (9,15)|
+|SAPS I - day 3 *** | 9,070 | |  12.2 ±4.5 | 12.00 | 6 (9,15)|
+|Mechanical ventilation | 25,328 | 11,969 (47.3%) | | | |
+|Invasive Swan-Ganz hemodynamic monitoring | 25,328 | 5,637 (22.3%) | | ||
+|Invasive arterial blood pressure monitoring | 25,328 | 14,054 (55.5%) | | ||
+|Use of vaso-active medications | 25,328 | 8,693 (34.3%) | | ||
+|Hospital mortality | 22,870 | 2,666 (11.7%) | | ||
+
+\* N = The number of ICUStays or Hospitalizations. that were included in the calculation for the given ICU Unit.
+
+** #cases = The number of ICUStays orHospitalizations that match the category criteria. For example: In Gender, #cases will be the number of male ICUStays in a unit.
+
+*** Only ICUStays where they have all 14 SAPS parameters were included. 2nd and 3rd day data comes from version 2.5 of the database.