6 votes
Accepted

Why are lab tests splitted into 2 tables: chartevents and labevents?

LABEVENTS data is from the actual hospital wide laboratory data management system. CHARTEVENTS data is from the ICU database that is used as an electronic chart for the patient at the bedside. Since ...
alistairewj's user avatar
6 votes

MIMIC III : Date and Time when Diagnosis Code was determined for the patient, say Septic Shock

It is important to be aware that the ICD-9 codes are assigned to hospital stays primarily for billing purposes. The codes are recorded by a coding team upon patient discharge, following a review of ...
tomp's user avatar
  • 1,446
5 votes

Photoplethysmogram sampling frequency problem

There is a known issue with the PPG signals in the MIMIC II/III waveform database, although I don't know whether this is the same issue as what you're seeing. The issue we've seen is that the PPG ...
Benjamin Moody's user avatar
5 votes
Accepted

MIMIC-III. Select only the first ICU admission

Patients may move between various care units over a single hospital admission. MIMIC-III provides significantly more detail than MIMIC-II about these movements thanks to the addition of the transfers ...
tomp's user avatar
  • 1,446
5 votes
Accepted

MIMIC-III: Negative cultures and microbiologyevents

Negative cultures were added to the microbiologyevents table in version 1.4 of MIMIC-III: http://mimic.physionet.org/about/releasenotes/ #188 - Negative microbiology cultures are now recorded in ...
alistairewj's user avatar
4 votes
Accepted

MIMIC-II Introduction document: errors in example code?

I am new to SQL and am trying to explore the MIMIC-II dataset using the query builder so the logical step seemed to be follow the tutorials within the introduction document [1]. The current version ...
tomp's user avatar
  • 1,446
4 votes

MIMIC-III severity score

Adding more severity scores is in the todo list: APACHE score or similar #28: We plan to release code for calculating severity scores as soon as we have time to! On the list are SAPS, SOFA, APS ...
Franck Dernoncourt's user avatar
4 votes

MIMIC-III Elixhauser comorbidity table

Code for deriving an Elixhauser comorbidity table for the MIMIC-III Critical Care Database has been developed by Alistair Johnson and shared via the MIMIC Code Repository. The repository can be found ...
tomp's user avatar
  • 1,446
4 votes
Accepted

MIMIC-III inputevents MV or CV

Two different ICU data management systems were in operation over the period of data collection: Philips Carevue (pre ~2008) and IMDSoft Metavision (post ~2008). The structure of the data collected by ...
tomp's user avatar
  • 1,446
4 votes
Accepted

Looking for admitting SAPS score for first hospitalization of patients in MIMICIII

Code for severity scores and other related clinical concepts can be found in the mimic-code repository: https://github.com/MIT-LCP/mimic-code
alistairewj's user avatar
4 votes
Accepted

Looking for equivalence of MIMIC-II v2.6 dataset in MIMIC-III v1.3

You're correct - the category type "PROCEDURE" in the mimic2v26.d_codeditems table refers to ICD-9 procedure codes. These have been more explicitly delineated in MIMIC-III: the equivalent definitions ...
alistairewj's user avatar
4 votes

Time of death in-hospital?

On MIMIC-III v1.1 and v1.3: SELECT DEATHTIME FROM mimiciii.admissions WHERE DEATHTIME IS NOT NULL ORDER BY DEATHTIME ASC LIMIT 500 ; Maybe you use MIMIC-II.
Franck Dernoncourt's user avatar
4 votes
Accepted

How much did MIMIC have to pay hospitals to get access to their data?

While hospitals charging for data access is a disappointing trend, I don't think MIMIC paid for access in the sense implied by the question. The research and development of MIMIC is the product of ...
Tristan's user avatar
  • 116
3 votes

Pulse transit time values (PTT)

I will assume you are using the MIMIC-II v3 Waveform database. If you look at section 5.4 of the MIMIC-II user guide (warning, 2.3 MB PDF), you will see the following: Inter-waveform alignment ...
alistairewj's user avatar
3 votes
Accepted

Meaning of SEQ_NUM in DIAGNOSES_ICD table and missing values in ICD9_CODE field

For Q1 see diagnoses_icd.sequence in MIMIC-III: does the order matter aside from the primary diagnosis? and Priority sequence column in diagnosis_icd. (#156 - The SEQUENCE column in DIAGNOSES_ICD and ...
Franck Dernoncourt's user avatar
3 votes

loading MIMIC III into SQL Server

The data files conform to the RFC 4180 specification, which is as close as CSVs get to a formal standard. Loading a RFC 4180 formatted CSV is trivial for many database systems. For example, the load ...
tomp's user avatar
  • 1,446
3 votes

MIMIC-III prescription problem

dose_val_rx is a varchar column that contains non-numerical values (for example, sometimes a range is specified such as '1-2' tablets). It isn't clear how you would sum these values, so most database ...
tomp's user avatar
  • 1,446
3 votes
Accepted

How to map MIMIC-II's SUBJECT_ID and HADM_ID with MIMIC-III's SUBJECT_ID and HADM_ID?

The SUBJECT_IDs in MIMIC-II are the same as SUBJECT_IDs in MIMIC-III. HADM_IDs are different because MIMIC-II used an ICU database to define hospital admission and discharge (and only had dates), ...
alistairewj's user avatar
3 votes
Accepted

MIMIC-III: When exactly was MIMIC-III v1.3 released?

When was 1.3 officially released? When was 1.2 officially released? MIMIC-III v1.3 was released on 10 December 2015. MIMIC-III v1.2 was released on 20 November 2015. What is the release history ...
tomp's user avatar
  • 1,446
3 votes

Want to understand MIMIC III warning in table Chartevents

The chartevents table of MIMIC-III is populated with data that has been archived by Metavision ICU, a clinical information system that integrates charted data from various sources, for example heart ...
tomp's user avatar
  • 1,446
3 votes

The unit for blood cell number is different in labevent. How could I unify them?

You've actually found a bug in MIMIC-III v1.3. Some of the CD counts were muddled - actual counts (#/uL) were merged with percentages, and vice versa. If you look at the LOINC code for percent CD8 (...
alistairewj's user avatar
2 votes

Memory consumption MIMIC-III

It really depends on the kind of queries you need to run. Looking at the size of the tables you need to join is the most important. Also, DBMS allow to set the maximum memory (e.g. postgresql.conf in ...
Franck Dernoncourt's user avatar
2 votes

Memory consumption MIMIC-III

The MIMIC III datasets can be downloaded as comma separated value (CSV) files. This means you can either (i) load the data into your favourite database and query it through that, or, (ii) load the ...
user9695's user avatar
2 votes

Start and stop times for non-invasive mechanical ventilation in MIMIC

I'm also new to MIMIC and not an expert, but I recently discovered that it is possible to find start and stop times for mechanical ventilation in the procedureevents_mv table.
zss's user avatar
  • 121
2 votes
Accepted

Are the APACHE scores available somewhere?

"Acute Physiology and Chronic Health Evaluation" (APACHE) scores are rarely recorded by caregivers, so they are not well documented in the core MIMIC dataset. Several APACHE-related itemids appear in ...
tomp's user avatar
  • 1,446
2 votes

(mimic-iii) Why D_LABITEMS doesn't have reference range while D_ITEMs has?

Ideally the D_ITEMS and D_LABITEMS tables would include reference ranges, but this data was not made available to the MIT Laboratory for Computational Physiology. As a result, it was not possible to ...
tomp's user avatar
  • 1,446
2 votes

How to map WFDB_Annotation().getTime() to actual timestamps?

I believe (based on work in June 2015 using MIMIC II v2.6) that the waveforms and the EMR were time-shifted separately, meaning that while some of the patient IDs have been matched, you cannot match ...
user10452's user avatar
2 votes
Accepted

MIMIC-III severity score

While you might find itemids for various severity scores such as APACHE IV in the hospital data, there will be few associated values. This is because the scores are rarely calculated or recorded by ...
tomp's user avatar
  • 1,446
2 votes
Accepted

Relation of MIMIC-II v2.6 and MIMIC-III v1.3 patients records

The vast majority of patients who appear in MIMIC-II v2.6 also appear in MIMIC-III v1.3. These patients retain the same subject_id and can be selected across versions of the database using the ...
tomp's user avatar
  • 1,446
2 votes
Accepted

Inquiry about number of adults in MIMIC-III v1.3

The following query confirms that there are 46,520 distinct patients in MIMIC-III v1.3: SELECT count(distinct subject_id) FROM admissions; -- returns 46520. The following query confirms that the ...
tomp's user avatar
  • 1,446

Only top scored, non community-wiki answers of a minimum length are eligible