From a8fd7f83ed72ec87d771ff7b26faddefdf7888c0 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Fri, 22 Sep 2023 16:39:51 -0400 Subject: [PATCH 01/23] mimicfed-initial-documentation --- content/en/docs/mimic-nw/_index.md | 24 +++ content/en/docs/mimic-nw/modules/_index.md | 10 ++ .../en/docs/mimic-nw/modules/hosp/_index.md | 12 ++ .../docs/mimic-nw/modules/hosp/admissions.md | 145 ++++++++++++++++++ .../mimic-nw/modules/hosp/d_icd_diagnoses.md | 77 ++++++++++ .../docs/mimic-nw/modules/hosp/d_labitems.md | 57 +++++++ .../mimic-nw/modules/hosp/diagnoses_icd.md | 43 ++++++ content/en/docs/mimic-nw/modules/hosp/emar.md | 72 +++++++++ .../docs/mimic-nw/modules/hosp/labevents.md | 94 ++++++++++++ .../en/docs/mimic-nw/modules/hosp/patients.md | 50 ++++++ .../mimic-nw/modules/hosp/prescriptions.md | 116 ++++++++++++++ .../en/docs/mimic-nw/modules/icu/_index.md | 10 ++ .../docs/mimic-nw/modules/icu/chartevents.md | 71 +++++++++ .../en/docs/mimic-nw/modules/icu/d_items.md | 77 ++++++++++ .../en/docs/mimic-nw/modules/icu/icustays.md | 75 +++++++++ .../mimic-nw/modules/icu/procedureevents.md | 100 ++++++++++++ 16 files changed, 1033 insertions(+) create mode 100644 content/en/docs/mimic-nw/_index.md create mode 100644 content/en/docs/mimic-nw/modules/_index.md create mode 100644 content/en/docs/mimic-nw/modules/hosp/_index.md create mode 100644 content/en/docs/mimic-nw/modules/hosp/admissions.md create mode 100644 content/en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md create mode 100644 content/en/docs/mimic-nw/modules/hosp/d_labitems.md create mode 100644 content/en/docs/mimic-nw/modules/hosp/diagnoses_icd.md create mode 100644 content/en/docs/mimic-nw/modules/hosp/emar.md create mode 100644 content/en/docs/mimic-nw/modules/hosp/labevents.md create mode 100644 content/en/docs/mimic-nw/modules/hosp/patients.md create mode 100644 content/en/docs/mimic-nw/modules/hosp/prescriptions.md create mode 100644 content/en/docs/mimic-nw/modules/icu/_index.md create mode 100644 content/en/docs/mimic-nw/modules/icu/chartevents.md create mode 100644 content/en/docs/mimic-nw/modules/icu/d_items.md create mode 100644 content/en/docs/mimic-nw/modules/icu/icustays.md create mode 100644 content/en/docs/mimic-nw/modules/icu/procedureevents.md diff --git a/content/en/docs/mimic-nw/_index.md b/content/en/docs/mimic-nw/_index.md new file mode 100644 index 00000000..648b7b8e --- /dev/null +++ b/content/en/docs/mimic-nw/_index.md @@ -0,0 +1,24 @@ +--- +title: MIMIC-Fed documentation +linktitle: MIMIC-Fed +weight: 50 + +cascade: +- type: "docs" + _target: + path: "/**" +--- +MIMIC-Fed is a large, freely avaliable federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NHMC) from 2020 to 2022. The federated database adopts a similar data structure as MIMIC-IV v2.2. + +Notably, Northwestern Memorial Health Center (NHMC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). + +The NM EDW tables are categorized into two primary categories, Fact and Dimension, following data warehousing conventions. As implemented in the NM EDW, Fact tables primarily contain events (such as encounters, admissions, diagnosis events, procedure orders, and medication orders), while Dimension tables describe persistent attributes of entities (patients, procedure names, the medication formulary). + +The NM EDW also includes auxiliary tables not directly related to patient care, such as a list of International Classification of Disease codes (ICD-9 and ICD-10). In response to the COVID-19/SARS-COV-2 pandemic, a COVID-19 data mart was created within the EDW to provide convenient access to information on COVID-19 patients, lab results, medications and treatments. + +MIMIC-Fed is currently organized into two distinct modules to highlight the source of the data: + +- [hosp](/docs/mimic-nw/modules/hosp/) - Hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. +- [icu](/docs/mimic-nw/modules/icu/) - ICU level data including icu stays, procedure events, chartevents (vital signs). + +The tables structures adopted to align with MIMIC's data structure for each module are detailed in the respective sections. \ No newline at end of file diff --git a/content/en/docs/mimic-nw/modules/_index.md b/content/en/docs/mimic-nw/modules/_index.md new file mode 100644 index 00000000..0f374cbf --- /dev/null +++ b/content/en/docs/mimic-nw/modules/_index.md @@ -0,0 +1,10 @@ +--- +title: "Modules" +linkTitle: "Modules" +weight: 3 +date: 2023-09-18 +description: > + Description of the data contained in each of the MIMIC-Fed modules. +--- + +Data within the modules will be made available on PhysioNet. diff --git a/content/en/docs/mimic-nw/modules/hosp/_index.md b/content/en/docs/mimic-nw/modules/hosp/_index.md new file mode 100644 index 00000000..f36bd30e --- /dev/null +++ b/content/en/docs/mimic-nw/modules/hosp/_index.md @@ -0,0 +1,12 @@ +--- +title: "Hosp" +linkTitle: "Hosp" +date: 2023-09-18 +weight: 20 +description: > + The Hosp module comprises data sourced from the comprehensive Electronic Health Record (EHR) systems of both BIDMC and NMHC hospitals. Information covered includes patient and admission information, laboratory measurements, billed diagnoses, prescriptions, and electronic medication administration records. +--- + +The hosp module contains data derived from the hospital wide EHR. These measurements are predominantly recorded during the hospital stay, though some tables include data from outside the hospital as well (e.g. outpatient laboratory tests in labevents). Information includes patient and admission details (patients, admissions), laboratory measurements (labevents, d_labitems), hospital billing information (diagnoses_icd, d_icd_diagnoses), medication prescription (prescriptions), and electronic medication administration records (emar). + + diff --git a/content/en/docs/mimic-nw/modules/hosp/admissions.md b/content/en/docs/mimic-nw/modules/hosp/admissions.md new file mode 100644 index 00000000..a36a107e --- /dev/null +++ b/content/en/docs/mimic-nw/modules/hosp/admissions.md @@ -0,0 +1,145 @@ +--- +title: "admissions table" +linktitle: "admissions" +date: 2023-09-18 +weight: 1 +description: > + Detailed information about hospital stays, including admission, discharge, and death times, as well as admission type, admission location, and discharge location; additionally, patient details such as insurance, language, marital status, and race are recorded at the hospital stay level. +--- + +The *admissions* table gives information regarding a patient's admission to the hospital. + +### Links to + +* *patients* on `subject_id` + +## Table columns + +Name | Postgres data type +---- | ---- +`subject_id` | INTEGER NOT NULL +`hadm_id` | INTEGER NOT NULL +`admittime` | TIMESTAMP NOT NULL +`dischtime` | TIMESTAMP +`deathtime` | TIMESTAMP +`admission_type` | VARCHAR(40) NOT NULL +`admission_location` | VARCHAR(60) +`discharge_location` | VARCHAR(60) +`insurance` | VARCHAR(255) +`language` | VARCHAR(10) +`marital_status` | VARCHAR(30) +`race` | VARCHAR(80) +`ethnicity` | VARCHAR(80) +`edregtime` | TIMESTAMP +`edouttime` | TIMESTAMP +`hospital_expire_flag` | SMALLINT + +## Detailed description + +The *admissions* table defines all hospitalizations in the database. Hospitalizations are assigned a unique random integer known as the `hadm_id`. + +### `subject_id` + +`subject_id` is unique identifier for each patient. `subject_id` is unique to each row and can be used to identify data associated with a specific patient. It is a cryptographic random number and each patient has a `subject_id` which is consistent across tables. + +### `hadm_id` + +Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the PATIENTS table using `subject_id`. + +### `admittime` + +`admittime` provides the date and time the patient was admitted to the hospital. + +### `dischtime` + +`dischtime` provides the date and time the patient was discharged from the hospital. + +### `deathtime` + +`deathtime` provides the time of in-hospital death for the patient. Note that `deathtime` is only present if the patient died in-hospital, and if present is almost always the same as the patient’s dischtime. However, there may be some discrepancies. + +### `admission_type` + +`admission_type` is useful for classifying the urgency of the admission. There are 6 distinct additional admission types sourced from the NW EDW database: 'Emergency', 'Urgent', 'Elective', 'Elective-Routine', and 'Trauma'. + +### `admission_location` + +`admission_location` provides information about the hospital department into which the patient was initially admitted. There are 24 admission locations from NW EDW, including 'Neurology', 'Radiation Oncology', 'Pediatrics', 'Medicine', 'Respiratory Therapy', 'Cardiology', 'Cardiac Rehabilitation', 'Pre-Admission Testing', 'Neurological Intensive Care', 'Orthopaedic Surgery', 'Sleep Medicine', 'Gastroenterology', 'Unknown', 'Obstetrics and Gynecology', 'Emergency Medicine', 'Research', 'Intensive Care', 'Gynecology', 'Pediatric Intensive Care', 'Radiology', 'Pathology', 'Obstetrics', and 'Surgery'. Note, 'Pediatrics' is the name of the unit or room, which is not necessarily exclusively for pediatric patients. The data being shared pertains to the adult hospital, with patients aged 18 and above. + + +## `discharge_location` + +Similarly, `discharge_location` is the disposition of the patient after they are discharged from the hospital. There are 33 discharge locations from NW EDW. Some of the 33 discharge locations are suppressed under 'Other Facility' for privacy. + +NHMC discharge locations: + +| Discharge Location | Full Abbreviation (for clarity) | +| ------------------------------------------------------- | --------------------------------- | +| Expired | Died | +| Planned Readmission - DC/transferred to acute inpatient rehab | | +| ED Dismissed-Never Arrived | | +| Home with Equipment or O2 | | +| Shelter | | +| Expired - Hospice | Died in Hospice | +| Home with Home Health Care | | +| Planned Readmission - DC/transferred to skilled nursing facility | | +| Acute Inpatient Rehabilitation | | +| Home or Self Care | | +| Group Home | | +| Planned Readmission - Discharged to home/self-care | | +| Left Against Medical Advice | | +| Inpatient Hospice | | +| Admitted to L&D | Admitted to Labor and Delivery | +| Planned Readmission - DC/transferred to nursing home (custodial) | | +| unknown | | +| Cancer Center or Children's Hospital | | +| Home with Outpatient Services | | +| Critical Access Hospital | | +| Planned Readmission - DC/transferred to other type of healthcare institution | | +| Gift of Hope / Still a Patient | | +| Nursing Home (Custodial) | | +| Home with Hospice | | +| VA System Facility | | +| Planned Readmission - DC/transferred to Long-term Acute Care Hospital (LTAC) | | +| Swing Bed | | +| Against Medical Advice (AMA) or Elopement | | +| Skilled Nursing Facility or Subacute Rehab Care | | +| Designated Disaster Alternative Care Site | | +| Acute Care Hospital | | +| Long-Term Acute Care Hospital (LTAC) | | + + +### `insurance`, `language`, `marital_status`, `race`, `ethnicity` + +The `insurance`, `language`, `marital_status`, and `race` and `ethnicity` columns provide information about patient demographics for the given hospitalization. Note, in BIDMC there is only one column for `race`, however we have added `ethnicity` column to federate NHMC's data. + +The race column in NHMC includes: + +- American Indian or Alaska Native +- Other +- Unknown +- 2 or more races +- Unable to Answer +- Native Hawaiian or Other Pacific Islander +- Asian +- White +- Declined +- Black or African American + +The ethnicity column in NHMC includes: + +- Not Hispanic or Latino +- Hispanic or Latino +- Declined +- Unable to Answer + +### `edouttime` + +The date and time at which arrival of the patient in the emergency department was registered. + +### `edouttime` +The date and time at which the patient was discharged from the emergency department, either discharged from the hospital or transferred. + +### `hospital_expire_flag` + +This is a binary flag which indicates whether the patient died within the given hospitalization. `1` indicates death in the hospital as noted in the `dod` column as part of the patient table, and `0` indicates survival to hospital discharge. diff --git a/content/en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md b/content/en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md new file mode 100644 index 00000000..edd6e912 --- /dev/null +++ b/content/en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md @@ -0,0 +1,77 @@ +--- +title: "d_icd_diagnoses" +linktitle: "d_icd_diagnoses" +weight: 6 +date: 2023-09-18 +description: > + Dimension table for *diagnoses_icd*; provides a description of ICD-9/ICD-10 billed diagnoses. +--- + +The *d_icd_diagnoses* table defines International Classification of Diseases (ICD) Version 9 and 10 codes for **diagnoses**. These codes are assigned at the end of the patient's stay and are used by the hospital to bill for care provided. + +### Links to + +* *diagnoses_icd* ON `icd_code` and `icd_version` + +## Table columns + +Name | Postgres data type +---- | ---- +`icd_code` | CHAR(7) NOT NULL +`icd_version` | INTEGER NOT NULL +`long_title` | VARCHAR(255) + +## Detailed Description + +### `icd_code` + +`icd_code` is the International Coding Definitions (ICD) code. + +### `icd_version` +There are two versions for this coding system: version 9 (ICD-9) and version 10 (ICD-10). These can be differentiated using the `icd_version` column. [ICD-9](https://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes) and [ICD-10](https://www.cms.gov/Medicare/Coding/ICD10/2019-ICD-10-CM.html) diagnosis codes are acquired from Centers for Medicare & Medicaid Services (CMS). + +In general, ICD-10 codes are more detailed, though code mappings (or "cross-walks") exist which convert ICD-9 codes to ICD-10 codes. + +Both ICD-9 and ICD-10 codes are often presented with a decimal. This decimal is not required for interpretation of an ICD code; i.e. the `icd_code` of '0010' is equivalent to '001.0'. + +ICD-9 and ICD-10 codes have distinct formats: ICD-9 codes are 5 character long strings which are entirely numeric (with the exception of codes prefixed with "E" or "V" which are used for external causes of injury or supplemental classification). Importantly, ICD-9 codes are retained as strings in the database as the leading 0s in codes are meaningful. + +ICD-10 codes are 3-7 characters long and always prefixed by a letter followed by a set of numeric values. + +ICD-11 became the official [WHO standard](https://www.who.int/standards/classifications/classification-of-diseases) on January 1, 2022 but has not been adopted in the US. The US Center for Medicare and Medicaid services (CMS) and HIPAA require ICD-10 since October 1, 2015. + +### `long_title` + +The `long_title` provides a description of the ICD code. For example, the ICD-10 code U07.1 has `long_title` "COVID-19 (confirmed by laboratory testing)". + +In the tables below, we provide ICD-10 codes related to covid or long covid. + +ICD-10 COVID markers terminologies: + +| icd_code | long_title | +| -------- | -------------------------------------------------------- | +| U07.1 | COVID-19 (confirmed by laboratory testing) | +| U07.2 | COVID-19, virus not identified | +| U10.9 | Multisystem inflammatory syndrome associated with COVID-19 | +| J12.81 | Pneumonia due to SARS-associated coronavirus | + + +ICD-10 Long COVID markers terminologies: + +| icd_code | long_title | +| -------- | ---------------------------------------------- | +| U09.9 | Post COVID-19 condition, unspecified | + +ICD-10 Other COVID related terminologies: + +| icd_code | long_title | +|----------|-----------------------------------------------------------------------------------------------------------| +| U08.9 | Personal history of COVID-19, unspecified (not a marker) | +| B97.2 | Coronavirus as the cause of diseases classified elsewhere (not necessarily COVID-19) | +| B97.21 | SARS-associated coronavirus as the cause of diseases classified elsewhere | +| Z28.31 | Underimmunization for COVID-19 status (see detailed codes below) | +| Z28.310 | Unvaccinated for COVID-19 | +| Z28.311 | Partially vaccinated for COVID-19 | +| B97.29 | Other coronavirus as the cause of diseases classified elsewhere (SUPERSEDED; early coding guidelines) | +| Z20.822 | Contact with and (suspected) exposure to COVID-19 (unconfirmed) | +| Z86.16 | Personal history of COVID-19 | diff --git a/content/en/docs/mimic-nw/modules/hosp/d_labitems.md b/content/en/docs/mimic-nw/modules/hosp/d_labitems.md new file mode 100644 index 00000000..da972580 --- /dev/null +++ b/content/en/docs/mimic-nw/modules/hosp/d_labitems.md @@ -0,0 +1,57 @@ +--- +title: "d_labitems" +linktitle: "d_labitems" +weight: 4 +date: 2023-09-18 +description: > + Dimension table for *labevents* provides a description of all lab items. +--- + +## *d_labitems* + +*d_labitems* contains definitions for all `itemid` associated with lab measurements in the MIMIC database. All data in *labevents* link to the *d_labitems* table. Each unique (`fluid`, `category`, `label`) tuple in the hospital database was assigned an `itemid` in this table, and the use of this `itemid` facilitates efficient storage and querying of the data. + +Laboratory data contains information collected and recorded in the hospital laboratory database. This includes measurements made in wards within the hospital and clinics outside the hospital. Most concepts in this table have been mapped to LOINC codes, an openly available ontology which facilitates interoperability. + +For the data sourced from NHMC, Illinois law defines certain categories of information as Sensitive Protected Health Information (SPHI) which require special treatment. SPHI includes genetic counseling but does not include genetic testing. + +To facilitate further federation processes, the lab mappings to standard terminologies (LOINC) will be released. + +### Links to + +* *labevents* on `itemid` + +## Table columns + +Name | Postgres data type +---- | ---- +`itemid` | INTEGER +`label` | VARCHAR(50) +`fluid` | VARCHAR(50) +`category` | VARCHAR(50) + +## Detailed Description + +### `itemid` + +A unique identifier for a laboratory concept. `itemid` is unique to each row, and can be used to identify data in labevents associated with a specific concept. + +### `label` + +The `label` column describes the concept which is represented by the `itemid`. + +We provide a list of common COVID-19 tests and measurements in the database, as defined by LOINC terminology, below: + +- SARS-CoV-2 (COVID-19) [Presence] in Specimen by Organism specific culture +- SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay +- SARS-CoV-2 (COVID-19) N gene [Cycle Threshold #] in Specimen by NAA with probe detection +- SARS-CoV-2 (COVID-19) E gene [Cycle Threshold #] in Respiratory specimen by NAA with probe detection + + +### `fluid` + +`fluid` describes the substance on which the measurement was made. These include blood, cerebrospinal fluid, joint fluid, ascites, urine and other body fluid. + +### `category` + +`category` provides higher level information as to the type of measurement. These categories include hematology, chemistry, and blood gas. For example, a category of 'ABG' indicates that the measurement is an arterial blood gas. diff --git a/content/en/docs/mimic-nw/modules/hosp/diagnoses_icd.md b/content/en/docs/mimic-nw/modules/hosp/diagnoses_icd.md new file mode 100644 index 00000000..c4c680cc --- /dev/null +++ b/content/en/docs/mimic-nw/modules/hosp/diagnoses_icd.md @@ -0,0 +1,43 @@ +--- +title: "diagnoses_icd" +linktitle: "diagnoses_icd" +weight: 5 +date: 2023-09-18 +description: > + Billed ICD-9/ICD-10 diagnoses for hospitalizations. +--- + +The *diagnoses_icd* contains a record of all diagnoses a patient was billed for during their hospital stay using the ICD-9 and ICD-10 ontologies. +Diagnoses are billed on hospital discharge, and are determined by trained persons who read signed clinical notes. + +### Links to + +* *d_icd_diagnoses* ON `icd_code` and `icd_version` + +## Table columns + +Name | Postgres data type +---- | ---- +`subject_id` | INTEGER NOT NULL +`hadm_id` | INTEGER NOT NULL +`icd_code` | VARCHAR(7) +`icd_version` | INTEGER + +## Detailed Description + +### `subject_id` + +`subject_id` is unique identifier for each patient. `subject_id` is unique to each row and can be used to identify data associated with a specific patient. It is a cryptographic random number and each patient has a `subject_id` which is consistent across tables. + +### `hadm_id` + +Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the PATIENTS table using `subject_id`. + +### `icd_code` + +`icd_code` is the International Coding Definitions (ICD) code. + +### `icd_version` + +There are two versions for this coding system: version 9 (ICD-9) and version 10 (ICD-10). These can be differentiated using the `icd_version` column. + diff --git a/content/en/docs/mimic-nw/modules/hosp/emar.md b/content/en/docs/mimic-nw/modules/hosp/emar.md new file mode 100644 index 00000000..b566c293 --- /dev/null +++ b/content/en/docs/mimic-nw/modules/hosp/emar.md @@ -0,0 +1,72 @@ +--- +title: "emar" +linktitle: "emar" +weight: 8 +date: 2023-09-18 +description: > + The Electronic Medicine Administration Record (eMAR); barcode scanning of medications at the time of administration. +--- + +## *emar* + +The EMAR table is used to record administrations of a given medicine to an individual patient. +Records in this table are populated by bedside nursing staff scanning barcodes associated with the medicine and the patient. + +## Links to + +* *prescriptions* on `pharmacy_id` + +## Important considerations + +* In the clinical process, a doctor prescribes the medication, a pharmacist fills the prescription, and a nurse administers it through the electronic Medication Administration Record (eMAR). Therefore, it is important to note that not all 'eMAR pharmacy_id’ entries should necessarily appear in the prescription table. +* It's possible for discrepancies to occur in the transition from left to right in this process, where a wrong prescription might be detected and corrected by the pharmacist before the medication is filled. +* Similarly, many prescriptions don’t have a corresponding eMAR entry, usually because the prescription is intended for outpatient use following discharge. +* It is typical for one prescription to have multiple eMAR entries; for example, a medication order “BID for 7 days” would be expected to have 14 eMAR entries. + +## Table columns + +Name | Postgres data type +---- | ---- +`subject_id` | INTEGER NOT NULL +`hadm_id` | INTEGER +`emar_id` | VARCHAR(25) NOT NULL +`emar_seq` | INTEGER NOT NULL +`pharmacy_id` | INTEGER +`charttime` | TIMESTAMP NOT NULL +`medication` | TEXT +`event_txt` | VARCHAR(100) +`scheduletime` | TIMESTAMP +`storetime` | TIMESTAMP NOT NULL + +### `subject_id` + +`subject_id` is unique identifier for each patient. `subject_id` is unique to each row and can be used to identify data associated with a specific patient. It is a cryptographic random number and each patient has a `subject_id` which is consistent across tables. + +### `hadm_id` + +Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the PATIENTS table using `subject_id`. + +### `emar_id`, `emar_seq` + +Identifiers for the eMAR table. `emar_id` is a unique identifier for each order made in eMAR. `emar_seq` is a consecutive integer which numbers eMAR orders chronologically. `emar_id` is composed of `subject_id` and `emar_seq` in the following pattern: '`subject_id`-`emar_seq`'. + +### `charttime` + +The date and time at which the medication was administered. + +### `medication` + +The name of the medication which was administered. + +### `event_txt` + +Information about the administration. Most frequently `event_txt` is 'Administered', but other possible values are 'Applied', 'Confirmed', 'Delayed', 'Not Given', and so on. The binary flags to denote adminstered and non-administered prescriptions will be released. + + +### `scheduletime` + +If present, the time at which the administration was scheduled. + +### `storetime` + +The time at which the administration was documented in the eMAR table. diff --git a/content/en/docs/mimic-nw/modules/hosp/labevents.md b/content/en/docs/mimic-nw/modules/hosp/labevents.md new file mode 100644 index 00000000..e530d345 --- /dev/null +++ b/content/en/docs/mimic-nw/modules/hosp/labevents.md @@ -0,0 +1,94 @@ +--- +title: "labevents" +linktitle: "labevents" +weight: 3 +date: 2023-09-18 +description: > + Laboratory measurements obtained from patient-derived specimens. +--- + +The *labevents* table stores the results of all laboratory measurements made for a single patient. +These include hematology measurements, blood gases, chemistry panels, and less common tests such as genetic assays. This table also includes COVID-19 diagnostic tests and measurements. + +## Links to + +* *d_labitems* on `itemid` + +## Table columns + +Name | Postgres data type +---- | ---- +`labevent_id` | INTEGER NOT NULL +`subject_id` | INTEGER NOT NULL +`hadm_id` | INTEGER +`specimen_id` | INTEGER NOT NULL +`itemid` | INTEGER NOT NULL +`order_provider_id` | VARCHAR(10) +`charttime` | TIMESTAMP(0) +`storetime` | TIMESTAMP(0) +`value` | VARCHAR(200) +`valuenum` | DOUBLE PRECISION +`valueuom` | VARCHAR(20) +`ref_range_lower` | DOUBLE PRECISION +`ref_range_upper` | DOUBLE PRECISION +`flag` | VARCHAR(10) +`priority` | VARCHAR(7) +`comments` | TEXT + +### `labevent_id` + +An integer which is unique for every row in the table. + +### `subject_id` + +{{% include "/static/include/subject_id.md" %}} + +### `hadm_id` + +{{% include "/static/include/hadm_id.md" %}} + +### `specimen_id` + +Uniquely denoted the specimen from which the lab measurement was made. Most lab measurements are made on patient derived samples (specimens) such as blood, urine, and so on. +Often multiple measurements are made on the same sample. The `specimen_id` will group measurements made on the same sample, e.g. blood gas measurements made on the same sample of blood. + +### `itemid` + +An identifier which uniquely denotes laboratory concepts. + +### `order_provider_id` + +`order_provider_id` provides an anonymous identifier for the provider who ordered the laboratory measurement. +{{% include "/static/include/provider_id.md" %}} + +### `charttime` + +The time at which the laboratory measurement was charted. This is usually the time at which the specimen was acquired, and is usually significantly **earlier** than the time at which the measurement is available. + +### `storetime` + +The time at which the measurement was made available in the laboratory system. This is when the information would have been available to care providers. + +### `value`, `valuenum` + +The result of the laboratory measurement and, if it is numeric, the value cast as a numeric data type. + +### `valueuom` + +The unit of measurement for the laboratory concept. + +### `ref_range_lower`, `ref_range_upper` + +Upper and lower reference ranges indicating the normal range for the laboratory measurements. Values outside the reference ranges are considered abnormal. + +### `flag` + +A brief string mainly used to indicate if the laboratory measurement is abnormal. + +### `priority` + +The priority of the laboratory measurement: either routine or stat (urgent). + +### `comments` + +Deidentified free-text comments associated with the laboratory measurement. Usually these provide information about the sample, whether any notifications were made to care providers regarding the results, considerations for interpretation, or in some cases the comments contain the result of the laboratory itself. Comments which have been fully deidentified (i.e. no information content retained) are present as three underscores: `___`. A `NULL` comment indicates no comment was made for the row. diff --git a/content/en/docs/mimic-nw/modules/hosp/patients.md b/content/en/docs/mimic-nw/modules/hosp/patients.md new file mode 100644 index 00000000..3daa8aaf --- /dev/null +++ b/content/en/docs/mimic-nw/modules/hosp/patients.md @@ -0,0 +1,50 @@ +--- +title: "patients table" +linktitle: "patients" +date: 2023-09-18 +weight: 2 +description: > + Detailed information about a patient's age, gender and date of death. +--- +The *patients* table gives information regarding a patient's gender, age, and date of death. + +## Table columns + +Name | Postgres data type +---- | ---- +`subject_id` | INTEGER NOT NULL +`gender` | VARCHAR(1) NOT NULL +`anchor_age` | INTEGER NOT NULL +`anchor_year` | INTEGER NOT NULL +`anchor_year_group` | VARCHAR(255) NOT NULL +`dod` | TIMESTAMP(0) + +## Detailed Description + +### `subject_id` + +`subject_id` is unique identifier for each patient. `subject_id` is unique to each row and can be used to identify data associated with a specific patient. It is a cryptographic random number and each patient has a `subject_id` which is consistent across tables. + +### `gender` + +The patient's administrative `gender`, sourced from the NW EDW and stored in the patient table, is represented as follows: F (Female), M (Male). + +### `anchor_age` + +`anchor_age` is the age of the patient as of their admission date (earliest admission date if more than one). If a patient’s `anchor_age` is over 89 in the anchor_year then their anchor_age is set to 91. + +This ensures that the statistical anonymity of a patient is maintained and that the data shared complies with the [HIPPA](https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html) standards, specifically: + +"(C) All elements of dates (except year) for dates that are directly related to an individual, including birth date, admission date, discharge date, death date, and all ages over 89 and all elements of dates (including year) indicative of such age, except that such ages and elements may be aggregated into a single category of age 90 or older." + +### `anchor_year`, +`anchor_year` is the shifted year based on the patient's shifted earliest admission date. + +### `anchor_year_group` + +`anchor_year_group` is the sequence of three years including the the year in which a patient was admitted. For example, if a patient was admitted in 2020, 2021, or 2022, the `anchor_year_group` will be "2020-2022." + +### `dod` + +The patient's date of death `dod` is shifted. Note, the `dod` is censored one year after discharge. Hence, if the death date is unknown it will be NULL. If this date is missing, `dod` will be NULL. If the date is not missing, and if the date is within 365 days after the latest discharge date, this date will be used as DOD. If the date is not missing and is 365 or more days after the latest discharge date, then DOD will be NULL. +Note, the BIDMC database also includes out of hospital data from the state, as part of dod sourced externally from the [Massachusetts State Registry of Vital Records and Statistics](https://www.mass.gov/orgs/registry-of-vital-records-and-statistics), by using identifiers including name, social security number and date of birth. diff --git a/content/en/docs/mimic-nw/modules/hosp/prescriptions.md b/content/en/docs/mimic-nw/modules/hosp/prescriptions.md new file mode 100644 index 00000000..b2aa7686 --- /dev/null +++ b/content/en/docs/mimic-nw/modules/hosp/prescriptions.md @@ -0,0 +1,116 @@ +--- +title: "prescriptions" +linktitle: "prescriptions" +weight: 7 +date: 2023-09-18 +description: > + Prescribed medications. +--- + +The *prescriptions* table provides information about prescribed medications. Information includes the name of the drug, coded identifiers including the Generic Sequence Number (GSN) and National Drug Code (NDC), the product strength, the formulary dose, and the route of administration. + +To facilitate further federation processes, the drug mappings to standard terminologies (RxNorm) will be released. + +We provide a list of some common COVID-19 drugs in the database, as defined by RxNorm terminology, below: + +- SARS-COV-2 (COVID-19) vaccine, vector - Ad26 100000000000 UNT/ML Injectable Suspension +- remdesivir 100 MG Injection [Veklury] +- 20 ML remdesivir 5 MG/ML Injection [Veklury] +- SARS-CoV-2 (COVID-19) vaccine, mRNA-BNT162b2 0.1 MG/ML Injectable Suspension +- SARS-CoV-2 (COVID-19) vaccine, mRNA-1273 0.2 MG/ML Injectable Suspension + + +## Links to + +* *emar* on `pharmacy_id` + +## Table columns + +Name | Postgres data type +---- | ---- +`subject_id` | INTEGER NOT NULL +`hadm_id` | INTEGER NOT NULL +`pharmacy_id` | INTEGER NOT NULL +`starttime` | TIMESTAMP(3) +`stoptime` | TIMESTAMP(3) +`drug_type` | VARCHAR(20) NOT NULL +`drug` | VARCHAR(255) NOT NULL +`gsn` | VARCHAR(255) +`ndc` | VARCHAR(25) +`prod_strength` | VARCHAR(255) +`form_rx` | VARCHAR(25) +`dose_val_rx` | VARCHAR(100) +`dose_unit_rx` | VARCHAR(50) +`form_val_disp` | VARCHAR(50) +`form_unit_disp` | VARCHAR(50) +`doses_per_24_hrs` | REAL +`route` | VARCHAR(50) + + + + + +### `subject_id` + +`subject_id` is unique identifier for each patient. `subject_id` is unique to each row and can be used to identify data associated with a specific patient. It is a cryptographic random number and each patient has a `subject_id` which is consistent across tables. + +### `hadm_id` + +Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the PATIENTS table using `subject_id`. + +### `pharmacy_id` + +An identifier which links administrations in *emar* to prescription information in the *prescription* table. + +### `starttime`, `stoptime` + +The prescribed start and stop time for the medication. `stop_time` could refer to an order to stop a prescription, but in this case, it means the end date for the prescription. For example, in a prescription for one dose per day for 14 days, the `stop_time` would be 14 days after the `start_time`. + +### `drug_type` + +The component of the prescription which the drug occupies. Can be one of 'MAIN', 'BASE', or 'ADDITIVE'. + +### `drug` + +A free-text description of the medication administered. Often includes the dose and form. + +### `gsn` + +The Generic Sequence Number (GSN), a coded identifier used for medications. + +### `ndc` + +The National Drug Code (NDC), a coded identifier which uniquely identifiers medications. + +### `prod_strength` + +A free-text description of the composition of the prescribed medication (e.g. '12 mg / 0.8 mL Oral Syringe', '12.5mg Tablet', etc). + +### `form_rx` + +The container in which the formulary dose is delivered (e.g. 'TABLET', 'VIAL','Solution', 'Syringe', 'Piggyback', 'Capsule', 'Suspension', etc). + +### `dose_val_rx` + +The prescribed dose for the patient intended to be administered over the given time period. + +### `dose_unit_rx` + +The unit of measurement for the dose. + +### `form_val_disp` + +The amount of the medication which is contained in a single formulary dose. + +### `form_unit_disp` + +The unit of measurement used for the formulary dosage. Examples include “mg”, “Units”, “mL”, “mEq”, “tablet”, “mcg/min”, “mcg/kg/hr”, etc. + + +### `doses_per_24_hrs` + +The number of doses per 24 hours for which the medication is to be given. A daily dose would result in `doses_per_24_hrs`: 1, bidaily (BID) or twice a day would be 2, and so on. Within NHMC, if the medication order couldn’t be converted to doses_per_24_hrs (such as “Once”, “PRN”, “Continuous”, “Weekly”’, or “Q 90 days”) the value would be missing. + +### `route` + +The route of administration for the medication, such as “Oral”, “Intravenous”, “Injection”, “Subcutaneous”, “Inhalation”, “Topical”, etc. May be missing. diff --git a/content/en/docs/mimic-nw/modules/icu/_index.md b/content/en/docs/mimic-nw/modules/icu/_index.md new file mode 100644 index 00000000..e2ccf434 --- /dev/null +++ b/content/en/docs/mimic-nw/modules/icu/_index.md @@ -0,0 +1,10 @@ +--- +title: "ICU" +linkTitle: "ICU" +date: 2023-09-18 +weight: 30 +description: > + The ICU module contains information collected from the clinical information system used within the ICU. Information covered includes icu admissions, procedures, and vital signs charted information. +--- + +The ICU module contains data sourced from the clinical information system at the BIDMC: MetaVision (iMDSoft). MetaVision tables were denormalized to create a star schema where the icustays and d_items tables link to a set of data tables all suffixed with "events". Data documented in the icu module includes icu admissions (icu stays) procedures (procedureevents, d_items), and vital signs charted information (chartevents, d_items). All events tables contain a stay_id column allowing identification of the associated ICU patient in icustays, and an itemid column allowing identification of the concept documented in d_items. \ No newline at end of file diff --git a/content/en/docs/mimic-nw/modules/icu/chartevents.md b/content/en/docs/mimic-nw/modules/icu/chartevents.md new file mode 100644 index 00000000..94788bb7 --- /dev/null +++ b/content/en/docs/mimic-nw/modules/icu/chartevents.md @@ -0,0 +1,71 @@ +--- +title: "chartevents" +linktitle: "chartevents" +weight: 3 +date: 2023-09-18 +description: > + Charted items during the ICU stay include numeric vital signs within respiratory, routine, general, and hemodynamic categories +--- + +**Links to:** + +* patients on `subject_id` +* admissions on `hadm_id` +* icustays on `stay_id` +* d_items on `itemid` + + +# Table columns + +Name | Postgres Data type +---- | -------- +subject\_id | INTEGER +hadm\_id | INTEGER +stay\_id | INTEGER +caregiver_id | INTEGER +charttime | TIMESTAMP(0) +storetime | TIMESTAMP(0) +itemid | INTEGER +value | VARCHAR(200) +valuenum | DOUBLE PRECISION +valueuom | VARCHAR(20) +warning | SMALLINT + +### `subject_id`, `hadm_id` + +Identifiers which specify the patient: `subject_id` is unique to a patient, `hadm_id` is unique to a patient hospital stay. + +### `stay_id` + +`stay_id` is an integer identifier which uniquely identifies each ICU admission within a hospital admission. Each hospital admission `hadm_id` must have at least one ICU admission `stay_id` but may include more than one. A `stay_id` groups all ICU admissions within 24 hours of each other. + +### `caregiver_id` + +`caregiver_id` uniquely identifies a single caregiver who measured the vital sign. + +### `charttime` + +Date and time when the vital sign was measured, deidentified. + +### `storetime` + +`charttime` records the time at which an observation was made, and is usually the closest proxy to the time the data was actually measured. `storetime` records the time at which an observation was manually input or manually validated by a member of the clinical staff. + +### `itemid` + +Identifier for a single measurement type in the database. Each row associated with one `itemid` (e.g. 220045) corresponds to an instantiation of the same measurement (e.g. Heart Rate) for Routine Vital Signs `category`, and 'bpm' `unit_name`. + +### `value`, `valuenum` + +`value` contains the numeric value in string format measured for the vital sign concept identified by the `itemid`. + +`valuenum` contains the same data in a numeric format. + +### `valueuom` + +`valueuom` is the unit of measurement for the `value`, if appropriate. Either missing or “%”. + +### `warning` + +`warning` specifies if a warning for this observation was manually documented by the care provider. A value which is considered excessive for this measurement. Either an integer or missing. + diff --git a/content/en/docs/mimic-nw/modules/icu/d_items.md b/content/en/docs/mimic-nw/modules/icu/d_items.md new file mode 100644 index 00000000..f6f9e427 --- /dev/null +++ b/content/en/docs/mimic-nw/modules/icu/d_items.md @@ -0,0 +1,77 @@ +--- +title: "d_items" +linktitle: "d_items" +weight: 2 +date: 2023-09-18 +description: > + Dimension table describing itemid. Defines concepts recorded in the events table in the ICU module. +--- + +**Links to:** + +* *chartevents* on `itemid` +* *procedureevents* on `itemid` + +# Table columns + +Name | Postgres data type +---- | ---- +itemid | INTEGER +label | VARCHAR(200) +abbreviation | VARCHAR(100) +linksto | VARCHAR(50) +category | VARCHAR(100) +unitname | VARCHAR(100) +param\_type | VARCHAR(30) +lownormalvalue | FLOAT +highnormalvalue | FLOAT + +# Detailed Description + +The D_ITEMS table defines `itemid`, which represents measurements in the database. Measurements of the same type (e.g. heart rate) will have the same `itemid` (e.g. 220045). Values in the `itemid` column are unique to each row. All `itemid`s will have a value > 220000. + +To facilitate further federation processes, the chartevents mappings (including vital signs and procedures) to standard terminologies (LOINC) and procedurevents mappints to standard terminologies (SNOMED) will be released. + +We provide a list of common vital sign labels in the database, as defined by LOINC terminology, below: + +- Heart rate +- Respiratory rate +- Oxygen saturation in Arterial blood by Pulse oximetry + +We provide a list of common procedure labels in the database, as defined by SNOMED terminology, below: + +- Plain chest X-ray +- Invasive ventilation +- Noninvasive ventilation + +### `itemid` + +As an alternate primary key to the table, `itemid` is unique to each row. + +### `label` + +The `label` column describes the concept which is represented by the `itemid`. + +### `abbreviation` + +The `abbreviation` column, lists a common abbreviation for the label. + +### `linksto` + +`linksto` provides the table name which the data links to. For example, a value of 'chartevents' indicates that the `itemid` of the given row is contained in CHARTEVENTS. A single `itemid` is only used in one event table, that is, if an `itemid` is contained in CHARTEVENTS it will *not* be contained in any other event table (e.g. PROCEDUREEVENTS, etc). + +### `category` + +`category` provides some information of the type of data the `itemid` corresponds to. Examples include 'ABG', which indicates the measurement is sourced from an arterial blood gas, 'IV Medication', which indicates that the medication is administered through an intravenous line, and so on. + +### `unitname` + +`unitname` specifies the unit of measurement used for the `itemid`. This column is not always available, and this may be because the unit of measurement varies, a unit of measurement does not make sense for the given data type, or the unit of measurement is simply missing. Note that there is sometimes additional information on the unit of measurement in the associated event table, e.g. the `valueuom` column in CHARTEVENTS. + +### `param_type` + +`param_type` describes the type of data which is recorded: a date, a number or a text field. + +### `lownormalvalue`, `highnormalvalue` + +These columns store reference ranges for the measurement. Note that a reference range encompasses the *expected* value of a measurement: values outside of this may still be physiologically plausible, but are considered unusual. \ No newline at end of file diff --git a/content/en/docs/mimic-nw/modules/icu/icustays.md b/content/en/docs/mimic-nw/modules/icu/icustays.md new file mode 100644 index 00000000..0752e762 --- /dev/null +++ b/content/en/docs/mimic-nw/modules/icu/icustays.md @@ -0,0 +1,75 @@ +--- +title: "ICU stays" +linktitle: "icustays" +weight: 1 +date: 2023-09-18 +description: > + Tracking information for ICU stays including admission and discharge times. +--- + +Defines each ICU stay in the database using STAY\_ID. + +**Links to:** + +* patients on `subject_id` +* admissions on `hadm_id` + +# Table columns + +Name | Postgres data type +---- | ---- +subject\_id | INT +hadm\_id | INT +stay\_id | INT +first\_careunit | VARCHAR(20) +last\_careunit | VARCHAR(20) +intime | TIMESTAMP(0) +outtime | TIMESTAMP(0) +los | DOUBLE PRECISION + +# Detailed Description + +### `subject_id`, `hadm_id` + +Identifiers which specify the patient: `subject_id` is unique to a patient, `hadm_id` is unique to a patient hospital stay. + +### `stay_id` + +`stay_id` is an integer identifier which uniquely identifies each ICU admission within a hospital admission. Each hospital admission `hadm_id` must have at least one ICU admission `stay_id` but may include more than one. If the time between two ICU stays is less than 24 hours, the two stays will be merged into one. + +### `first_careunit`, `last_careunit` + +`first_careunit` and `last_careunit` contain, respectively, the first and last ICU type in which the patient was cared for. + +NHMC defintions for first_careunit and last_careunit: + +| first_careunit/last_careunit | Full abbreviation (Epic) | +|------------------------------------|----------------------------------| +| ORTHOPEDICS | Emergency Medicine service | +| CCU | General Medicine ICU service | +| NSICU | Neuro Step Down service | +| ICU OVERFLOW | Internal Medicine service | +| IMCU | Neuro ICU service | +| MTU | General Medicine service | +| MICU | Medicine service | +| PICU | | +| BOARDERS | Internal Medicine service | +| CICU | Surgery service | +| NICU | | +| NEUROSCIENCE INPATIENT | Neurosurgery service | +| SICU | Surgery ICU service | +| ICU | | +| INPATIENT | | +| CTICU | Cardiology ICU | +| CTU | CARDIAC TELEMETRY UNIT, General Medicine service | +| RADIOLOGY | | + +Note, the addition of ICU overflow in both BIDMC and NHMC as a `first_careunit` and/or `last_careunit`. In the context of COVID-19, an "ICU overflow" typically refers to a situation in which intensive care units (ICUs) in a hospital or healthcare facility have reached or exceeded their capacity due to a surge in COVID-19 patients requiring critical care. This overflow occurs when the number of patients needing intensive care for COVID-19 exceeds the available ICU beds. + +### `intime`, `outtime` + +`intime` provides the date and time the patient was transferred into the ICU. `outtime` provides the date and time the patient was transferred out of the ICU. + +### `los` + +`los` is the length of stay for the patient for the given ICU stay, which may include one or more ICU units. The length of stay is measured in fractional days. diff --git a/content/en/docs/mimic-nw/modules/icu/procedureevents.md b/content/en/docs/mimic-nw/modules/icu/procedureevents.md new file mode 100644 index 00000000..c197ec7d --- /dev/null +++ b/content/en/docs/mimic-nw/modules/icu/procedureevents.md @@ -0,0 +1,100 @@ +--- +title: "procedureevents" +linktitle: "procedureevents" +weight: 4 +date: 2023-09-18 +description: > + Procedures documented during the ICU stay (e.g. ventilation), though not necessarily conducted within the ICU (e.g. x-ray imaging). +--- + +**Links to:** + +* patients on `subject_id` +* admissions on `hadm_id` +* icustays on `stay_id` +* d_items on `itemid` + +# Important considerations + +* In the context of COVID-19, it's important to note that there haven't been any new findings or observations, except for instances where the use of a certain procedured e.g. ventilation has increased. + +# Table columns + + +Name | Data type +---- | -------- +subject\_id | INTEGER +hadm\_id | INTEGER +stay\_id | INTEGER +caregiver_id | INTEGER +starttime | TIMESTAMP +endtime | TIMESTAMP +storetime | TIMESTAMP +itemid | INTEGER +value | DOUBLE PRECISION +valueuom | VARCHAR(20) +location | VARCHAR(100) +locationcategory | VARCHAR(50) +orderid | INTEGER +linkorderid | INTEGER +ordercategoryname | VARCHAR(50) +ordercategorydescription | VARCHAR(30) +patientweight | DOUBLE PRECISION +isopenbag | SMALLINT +continueinnextdept | SMALLINT +statusdescription | VARCHAR(20) +originalamount | DOUBLE PRECISION +originalrate | DOUBLE PRECISION + +# Detailed Description + +### `subject_id`, `hadm_id`, `stay_id` + +Identifiers which specify the patient: `subject_id` is unique to a patient, `hadm_id` is unique to a patient hospital stay and `stay_id` is unique to a patient ICU stay. + +### `caregiver_id` + +{{% include "/static/include/caregiver_id.md" %}} + +### `starttime` + +Date and time when the procedure started. + +### `endtime` + +Date and time when the procedure ended. + +### `storetime` + +`storetime` specifies the time when the event was recorded in the system. + +### `itemid` + +Identifier for a single event type in the procedurevents table. Each row associated with one `itemid` (e.g. 225792) corresponds to a type of measurement (e.g. Invasive Ventilation) within '2-Ventilation' `category`. The *d_items* table may be joined on this field. For any itemid appearing in the *procedureevents* table, *d_items* `linksto` column will have the value 'procedureevents'. +Note, in the context of COVID-19, + +## `value` + +In the `procedureevents` table, this identifies the duration of the procedure (if applicable). For example, if querying for itemid 225794 (“Non-invasive Ventilation”), then the value column indicates the duration of ventilation therapy. + +### `valueuom` + +The unit of measurement for the value. Most frequently "None" (no value recorded); otherwise one of "day", "hour", or "min". A query for itemiid 225794 ("Non-invasive Ventilation") returning a `value` of 461 and `valueuom` of 'min' would correspond to non-invasive ventilation provided for 461 minutes; this value is expected to match the difference between the `starttime` and `endtime` fields for the record. A procedure with `valueuom` equal to "None" corresponds to a procedure which is instantaneous (e.g. intubation, patient transfer) or whose duration is not relevant (e.g. imaging procedures). For these records, there will be a difference of one second between `starttime` and `endtime` values. + +### `statusdescription` + +`statusdescription` states the ultimate status of the procedure referred to in the row. The statuses appearing on the `procedureevents` table are: + +* `Paused` - The current delivery has been paused. +* `FinishedRunning` - The delivery of the item has finished (most frequently, the bag containing the compound is empty). +* `Stopped` - The delivery of the item been terminated by the caregiver. + +Nearly all procedures recorded in *procedureevents* have a status of `FinishedRunning`. + +In NMHC, this column is usually missing. If not missing, one of the following is included: + +* `Final result` - The final result of the procedure is available. +* `In process` - The procedure is currently in progress. +* `Edited Result - FINAL` - The result has been edited and finalized. +* `Preliminary result` - A preliminary result is available. +* `Edited` - The entry has been edited. From d886750a5d3302620135bba657fe040bac444f96 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Fri, 22 Sep 2023 16:50:05 -0400 Subject: [PATCH 02/23] fix typo --- content/en/docs/mimic-nw/_index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/en/docs/mimic-nw/_index.md b/content/en/docs/mimic-nw/_index.md index 648b7b8e..810c2036 100644 --- a/content/en/docs/mimic-nw/_index.md +++ b/content/en/docs/mimic-nw/_index.md @@ -8,7 +8,7 @@ cascade: _target: path: "/**" --- -MIMIC-Fed is a large, freely avaliable federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NHMC) from 2020 to 2022. The federated database adopts a similar data structure as MIMIC-IV v2.2. +MIMIC-Fed is a large, freely available federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NHMC) from 2020 to 2022. The federated database adopts a similar data structure as MIMIC-IV v2.2. Notably, Northwestern Memorial Health Center (NHMC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). From c720f84d476411ed8862b1fff4ba192e3e54f63b Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Wed, 27 Sep 2023 14:42:26 -0400 Subject: [PATCH 03/23] minor edits --- content/en/docs/mimic-nw/_index.md | 8 ++++---- content/en/docs/mimic-nw/modules/hosp/_index.md | 6 ++++-- content/en/docs/mimic-nw/modules/hosp/admissions.md | 4 ++-- .../en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md | 8 ++++---- .../en/docs/mimic-nw/modules/hosp/diagnoses_icd.md | 2 +- content/en/docs/mimic-nw/modules/hosp/emar.md | 12 ++++++------ content/en/docs/mimic-nw/modules/hosp/patients.md | 6 +++--- .../en/docs/mimic-nw/modules/hosp/prescriptions.md | 8 ++++---- content/en/docs/mimic-nw/modules/icu/_index.md | 6 ++++-- content/en/docs/mimic-nw/modules/icu/chartevents.md | 4 ++-- content/en/docs/mimic-nw/modules/icu/d_items.md | 9 +++++---- content/en/docs/mimic-nw/modules/icu/icustays.md | 6 +++--- .../en/docs/mimic-nw/modules/icu/procedureevents.md | 12 ++++++------ 13 files changed, 48 insertions(+), 43 deletions(-) diff --git a/content/en/docs/mimic-nw/_index.md b/content/en/docs/mimic-nw/_index.md index 810c2036..ebcfa035 100644 --- a/content/en/docs/mimic-nw/_index.md +++ b/content/en/docs/mimic-nw/_index.md @@ -8,7 +8,7 @@ cascade: _target: path: "/**" --- -MIMIC-Fed is a large, freely available federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NHMC) from 2020 to 2022. The federated database adopts a similar data structure as MIMIC-IV v2.2. +MIMIC-Fed is a large, freely available federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NHMC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The federated database adopts a similar data structure as MIMIC-IV v2.2. Notably, Northwestern Memorial Health Center (NHMC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). @@ -18,7 +18,7 @@ The NM EDW also includes auxiliary tables not directly related to patient care, MIMIC-Fed is currently organized into two distinct modules to highlight the source of the data: -- [hosp](/docs/mimic-nw/modules/hosp/) - Hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. -- [icu](/docs/mimic-nw/modules/icu/) - ICU level data including icu stays, procedure events, chartevents (vital signs). +- [HOSP](/docs/mimic-nw/modules/hosp/) - Federated hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. +- [ICU](/docs/mimic-nw/modules/icu/) - Federated ICU level data including icu stays, procedure events, chartevents (vital signs). -The tables structures adopted to align with MIMIC's data structure for each module are detailed in the respective sections. \ No newline at end of file +The tables structures adopted to align with MIMIC's data structure for each module are detailed in the respective sections. Additionally, we have incorporated COVID-related concepts and standard terminologies (LOINC, RxNorm, SNOMED, ICD-9/10) and derived mappings (for drug administration) into the dataset. This integration not only facilitates current federation efforts, but also facilities interoperability, allowing for seamless data exchange and collaboration across healthcare systems. diff --git a/content/en/docs/mimic-nw/modules/hosp/_index.md b/content/en/docs/mimic-nw/modules/hosp/_index.md index f36bd30e..72b0129f 100644 --- a/content/en/docs/mimic-nw/modules/hosp/_index.md +++ b/content/en/docs/mimic-nw/modules/hosp/_index.md @@ -4,9 +4,11 @@ linkTitle: "Hosp" date: 2023-09-18 weight: 20 description: > - The Hosp module comprises data sourced from the comprehensive Electronic Health Record (EHR) systems of both BIDMC and NMHC hospitals. Information covered includes patient and admission information, laboratory measurements, billed diagnoses, prescriptions, and electronic medication administration records. + The Hosp module comprises data sourced from the comprehensive Electronic Health Record (EHR) systems of both BIDMC and NHMC hospitals. Information covered includes patient and admission information, laboratory measurements, billed diagnoses, medication orders, and electronic medication administration records. --- -The hosp module contains data derived from the hospital wide EHR. These measurements are predominantly recorded during the hospital stay, though some tables include data from outside the hospital as well (e.g. outpatient laboratory tests in labevents). Information includes patient and admission details (patients, admissions), laboratory measurements (labevents, d_labitems), hospital billing information (diagnoses_icd, d_icd_diagnoses), medication prescription (prescriptions), and electronic medication administration records (emar). +The HOSP module contains data derived from the hospital wide EHR of BIDMC and NHMC. These measurements are predominantly recorded during the hospital stay, though some tables include data from outside the hospital as well (e.g. outpatient laboratory tests in *labevents*). + +Information includes patient and admission details (*patients*, *admissions*), laboratory measurements (*labevents*, *d_labitems*), hospital billing information (*diagnoses_icd*, *d_icd_diagnoses*), medication orders (*prescriptions*), and electronic medication administration records (*emar*). diff --git a/content/en/docs/mimic-nw/modules/hosp/admissions.md b/content/en/docs/mimic-nw/modules/hosp/admissions.md index a36a107e..9b61789b 100644 --- a/content/en/docs/mimic-nw/modules/hosp/admissions.md +++ b/content/en/docs/mimic-nw/modules/hosp/admissions.md @@ -44,7 +44,7 @@ The *admissions* table defines all hospitalizations in the database. Hospitaliza ### `hadm_id` -Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the PATIENTS table using `subject_id`. +Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the *patients* table using `subject_id`. ### `admittime` @@ -142,4 +142,4 @@ The date and time at which the patient was discharged from the emergency departm ### `hospital_expire_flag` -This is a binary flag which indicates whether the patient died within the given hospitalization. `1` indicates death in the hospital as noted in the `dod` column as part of the patient table, and `0` indicates survival to hospital discharge. +This is a binary flag which indicates whether the patient died within the given hospitalization. `1` indicates death in the hospital as noted in the `dod` column as part of the *patient* table, and `0` indicates survival to hospital discharge. diff --git a/content/en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md b/content/en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md index edd6e912..29ee9f4a 100644 --- a/content/en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md +++ b/content/en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md @@ -42,11 +42,11 @@ ICD-11 became the official [WHO standard](https://www.who.int/standards/classifi ### `long_title` -The `long_title` provides a description of the ICD code. For example, the ICD-10 code U07.1 has `long_title` "COVID-19 (confirmed by laboratory testing)". +The `long_title` provides a description of the ICD code. For example, the ICD-10 code U07.1 has a `long_title` of 'COVID-19 (confirmed by laboratory testing)'. In the tables below, we provide ICD-10 codes related to covid or long covid. -ICD-10 COVID markers terminologies: +Terminologies related to COVID markers in the ICD-10: | icd_code | long_title | | -------- | -------------------------------------------------------- | @@ -56,13 +56,13 @@ ICD-10 COVID markers terminologies: | J12.81 | Pneumonia due to SARS-associated coronavirus | -ICD-10 Long COVID markers terminologies: +Terminologies for Long COVID markers in ICD-10: | icd_code | long_title | | -------- | ---------------------------------------------- | | U09.9 | Post COVID-19 condition, unspecified | -ICD-10 Other COVID related terminologies: +Terminologies related to other COVID aspects in ICD-10: | icd_code | long_title | |----------|-----------------------------------------------------------------------------------------------------------| diff --git a/content/en/docs/mimic-nw/modules/hosp/diagnoses_icd.md b/content/en/docs/mimic-nw/modules/hosp/diagnoses_icd.md index c4c680cc..066aeada 100644 --- a/content/en/docs/mimic-nw/modules/hosp/diagnoses_icd.md +++ b/content/en/docs/mimic-nw/modules/hosp/diagnoses_icd.md @@ -31,7 +31,7 @@ Name | Postgres data type ### `hadm_id` -Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the PATIENTS table using `subject_id`. +Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the *patients* table using `subject_id`. ### `icd_code` diff --git a/content/en/docs/mimic-nw/modules/hosp/emar.md b/content/en/docs/mimic-nw/modules/hosp/emar.md index b566c293..02a80792 100644 --- a/content/en/docs/mimic-nw/modules/hosp/emar.md +++ b/content/en/docs/mimic-nw/modules/hosp/emar.md @@ -9,7 +9,7 @@ description: > ## *emar* -The EMAR table is used to record administrations of a given medicine to an individual patient. +The *emar* table is used to record administrations of a given medicine to an individual patient. Records in this table are populated by bedside nursing staff scanning barcodes associated with the medicine and the patient. ## Links to @@ -18,10 +18,10 @@ Records in this table are populated by bedside nursing staff scanning barcodes a ## Important considerations -* In the clinical process, a doctor prescribes the medication, a pharmacist fills the prescription, and a nurse administers it through the electronic Medication Administration Record (eMAR). Therefore, it is important to note that not all 'eMAR pharmacy_id’ entries should necessarily appear in the prescription table. +* In the clinical process, a doctor prescribes the medication, a pharmacist fills the prescription, and a nurse administers it through the electronic Medication Administration Record (eMAR). Therefore, it is important to note that not all 'eMAR pharmacy_id’ entries should necessarily appear in the *prescription* table. * It's possible for discrepancies to occur in the transition from left to right in this process, where a wrong prescription might be detected and corrected by the pharmacist before the medication is filled. * Similarly, many prescriptions don’t have a corresponding eMAR entry, usually because the prescription is intended for outpatient use following discharge. -* It is typical for one prescription to have multiple eMAR entries; for example, a medication order “BID for 7 days” would be expected to have 14 eMAR entries. +* It is typical for one prescription to have multiple eMAR entries; for example, a medication order 'BID for 7 days' would be expected to have 14 eMAR entries. ## Table columns @@ -44,11 +44,11 @@ Name | Postgres data type ### `hadm_id` -Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the PATIENTS table using `subject_id`. +Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the *patients* table using `subject_id`. ### `emar_id`, `emar_seq` -Identifiers for the eMAR table. `emar_id` is a unique identifier for each order made in eMAR. `emar_seq` is a consecutive integer which numbers eMAR orders chronologically. `emar_id` is composed of `subject_id` and `emar_seq` in the following pattern: '`subject_id`-`emar_seq`'. +Identifiers for the *emar* table. `emar_id` is a unique identifier for each order made in eMAR. `emar_seq` is a consecutive integer which numbers eMAR orders chronologically. `emar_id` is composed of `subject_id` and `emar_seq` in the following pattern: '`subject_id`-`emar_seq`'. ### `charttime` @@ -69,4 +69,4 @@ If present, the time at which the administration was scheduled. ### `storetime` -The time at which the administration was documented in the eMAR table. +The time at which the administration was documented in the *emar* table. diff --git a/content/en/docs/mimic-nw/modules/hosp/patients.md b/content/en/docs/mimic-nw/modules/hosp/patients.md index 3daa8aaf..0b53056d 100644 --- a/content/en/docs/mimic-nw/modules/hosp/patients.md +++ b/content/en/docs/mimic-nw/modules/hosp/patients.md @@ -27,7 +27,7 @@ Name | Postgres data type ### `gender` -The patient's administrative `gender`, sourced from the NW EDW and stored in the patient table, is represented as follows: F (Female), M (Male). +The patient's administrative `gender`, sourced from the NW EDW and stored in the *patient* table, is represented as follows: F (Female), M (Male). ### `anchor_age` @@ -35,14 +35,14 @@ The patient's administrative `gender`, sourced from the NW EDW and stored in the This ensures that the statistical anonymity of a patient is maintained and that the data shared complies with the [HIPPA](https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html) standards, specifically: -"(C) All elements of dates (except year) for dates that are directly related to an individual, including birth date, admission date, discharge date, death date, and all ages over 89 and all elements of dates (including year) indicative of such age, except that such ages and elements may be aggregated into a single category of age 90 or older." +'(C) All elements of dates (except year) for dates that are directly related to an individual, including birth date, admission date, discharge date, death date, and all ages over 89 and all elements of dates (including year) indicative of such age, except that such ages and elements may be aggregated into a single category of age 90 or older.' ### `anchor_year`, `anchor_year` is the shifted year based on the patient's shifted earliest admission date. ### `anchor_year_group` -`anchor_year_group` is the sequence of three years including the the year in which a patient was admitted. For example, if a patient was admitted in 2020, 2021, or 2022, the `anchor_year_group` will be "2020-2022." +`anchor_year_group` is the sequence of three years including the the year in which a patient was admitted. For example, if a patient was admitted in 2020, 2021, or 2022, the `anchor_year_group` will be '2020-2022'. ### `dod` diff --git a/content/en/docs/mimic-nw/modules/hosp/prescriptions.md b/content/en/docs/mimic-nw/modules/hosp/prescriptions.md index b2aa7686..24dcfe70 100644 --- a/content/en/docs/mimic-nw/modules/hosp/prescriptions.md +++ b/content/en/docs/mimic-nw/modules/hosp/prescriptions.md @@ -56,7 +56,7 @@ Name | Postgres data type ### `hadm_id` -Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The ADMISSIONS table can be linked to the PATIENTS table using `subject_id`. +Each row of this table contains a unique `hadm_id`, which represents a single patient's admission to the hospital. It is possible for this table to have duplicate `subject_id`, indicating that a single patient had multiple admissions to the hospital. The *admissions* table can be linked to the *patients* table using `subject_id`. ### `pharmacy_id` @@ -104,13 +104,13 @@ The amount of the medication which is contained in a single formulary dose. ### `form_unit_disp` -The unit of measurement used for the formulary dosage. Examples include “mg”, “Units”, “mL”, “mEq”, “tablet”, “mcg/min”, “mcg/kg/hr”, etc. +The unit of measurement used for the formulary dosage. Examples include 'mg', 'Units', 'mL', 'mEq', 'tablet', 'mcg/min', 'mcg/kg/hr', etc. ### `doses_per_24_hrs` -The number of doses per 24 hours for which the medication is to be given. A daily dose would result in `doses_per_24_hrs`: 1, bidaily (BID) or twice a day would be 2, and so on. Within NHMC, if the medication order couldn’t be converted to doses_per_24_hrs (such as “Once”, “PRN”, “Continuous”, “Weekly”’, or “Q 90 days”) the value would be missing. +The number of doses per 24 hours for which the medication is to be given. A daily dose would result in `doses_per_24_hrs`: 1, bidaily (BID) or twice a day would be 2, and so on. Within NHMC, if the medication order couldn’t be converted to `doses_per_24_hrs` (such as 'Once', 'PRN', 'Continuous', 'Weekly', or 'Q 90 days') the value would be missing. ### `route` -The route of administration for the medication, such as “Oral”, “Intravenous”, “Injection”, “Subcutaneous”, “Inhalation”, “Topical”, etc. May be missing. +The route of administration for the medication, such as 'Oral', 'Intravenous', 'Injection', 'Subcutaneous', 'Inhalation', 'Topical', etc. May be missing. diff --git a/content/en/docs/mimic-nw/modules/icu/_index.md b/content/en/docs/mimic-nw/modules/icu/_index.md index e2ccf434..9271f309 100644 --- a/content/en/docs/mimic-nw/modules/icu/_index.md +++ b/content/en/docs/mimic-nw/modules/icu/_index.md @@ -4,7 +4,9 @@ linkTitle: "ICU" date: 2023-09-18 weight: 30 description: > - The ICU module contains information collected from the clinical information system used within the ICU. Information covered includes icu admissions, procedures, and vital signs charted information. + The ICU module contains information collected from the clinical information system of both BIDMC and NHMC used within the ICU. Information covered includes icu admissions, procedures, and charted vital sign data. --- -The ICU module contains data sourced from the clinical information system at the BIDMC: MetaVision (iMDSoft). MetaVision tables were denormalized to create a star schema where the icustays and d_items tables link to a set of data tables all suffixed with "events". Data documented in the icu module includes icu admissions (icu stays) procedures (procedureevents, d_items), and vital signs charted information (chartevents, d_items). All events tables contain a stay_id column allowing identification of the associated ICU patient in icustays, and an itemid column allowing identification of the concept documented in d_items. \ No newline at end of file +The ICU module contains data sourced from the clinical information system at the BIDMC (MetaVision (iMDSoft)) and NHMC. MetaVision tables in BIDMC were denormalized to create a star schema where the icustays and d_items tables link to a set of data tables all suffixed with *events*. + +Data documented in the ICU module includes icu admissions (*icu stays*), procedures (*procedureevents*, *d_items*), and charted vital sign data (*chartevents*, *d_items*). All events tables contain a `stay_id` column allowing identification of the associated ICU patient in *icustays*, and an `itemid` column allowing identification of the concept documented in *d_items*. \ No newline at end of file diff --git a/content/en/docs/mimic-nw/modules/icu/chartevents.md b/content/en/docs/mimic-nw/modules/icu/chartevents.md index 94788bb7..780087a3 100644 --- a/content/en/docs/mimic-nw/modules/icu/chartevents.md +++ b/content/en/docs/mimic-nw/modules/icu/chartevents.md @@ -53,7 +53,7 @@ Date and time when the vital sign was measured, deidentified. ### `itemid` -Identifier for a single measurement type in the database. Each row associated with one `itemid` (e.g. 220045) corresponds to an instantiation of the same measurement (e.g. Heart Rate) for Routine Vital Signs `category`, and 'bpm' `unit_name`. +Identifier for a single measurement type in the database. Each row associated with one `itemid` (e.g. 220045) corresponds to an instantiation of the same measurement (e.g. Heart Rate) within the `category` of 'Routine Vital Signs', and `unit_name` of 'bpm'. ### `value`, `valuenum` @@ -63,7 +63,7 @@ Identifier for a single measurement type in the database. Each row associated wi ### `valueuom` -`valueuom` is the unit of measurement for the `value`, if appropriate. Either missing or “%”. +`valueuom` is the unit of measurement for the `value`, if appropriate. Either missing or '%'. ### `warning` diff --git a/content/en/docs/mimic-nw/modules/icu/d_items.md b/content/en/docs/mimic-nw/modules/icu/d_items.md index f6f9e427..dfb878c9 100644 --- a/content/en/docs/mimic-nw/modules/icu/d_items.md +++ b/content/en/docs/mimic-nw/modules/icu/d_items.md @@ -28,9 +28,10 @@ highnormalvalue | FLOAT # Detailed Description -The D_ITEMS table defines `itemid`, which represents measurements in the database. Measurements of the same type (e.g. heart rate) will have the same `itemid` (e.g. 220045). Values in the `itemid` column are unique to each row. All `itemid`s will have a value > 220000. +The *d_items* table defines `itemid`, which represents measurements in the database. Measurements of the same type (e.g. heart rate) will have the same `itemid` (e.g. 220045). Values in the `itemid` column are unique to each row. All `itemid`s will have a value > 220000. + +To faciliate future federation processes, we will release mappings within charted events (including vital signs) to standard terminologies (LOINC) and mappings for procedure events to standard terminologies (SNOMED). -To facilitate further federation processes, the chartevents mappings (including vital signs and procedures) to standard terminologies (LOINC) and procedurevents mappints to standard terminologies (SNOMED) will be released. We provide a list of common vital sign labels in the database, as defined by LOINC terminology, below: @@ -58,7 +59,7 @@ The `abbreviation` column, lists a common abbreviation for the label. ### `linksto` -`linksto` provides the table name which the data links to. For example, a value of 'chartevents' indicates that the `itemid` of the given row is contained in CHARTEVENTS. A single `itemid` is only used in one event table, that is, if an `itemid` is contained in CHARTEVENTS it will *not* be contained in any other event table (e.g. PROCEDUREEVENTS, etc). +`linksto` provides the table name which the data links to. For example, a value of 'chartevents' indicates that the `itemid` of the given row is contained in CHARTEVENTS. A single `itemid` is only used in one event table, that is, if an `itemid` is contained in CHARTEVENTS it will *not* be contained in any other event table (e.g. *procedureevents*, etc). ### `category` @@ -66,7 +67,7 @@ The `abbreviation` column, lists a common abbreviation for the label. ### `unitname` -`unitname` specifies the unit of measurement used for the `itemid`. This column is not always available, and this may be because the unit of measurement varies, a unit of measurement does not make sense for the given data type, or the unit of measurement is simply missing. Note that there is sometimes additional information on the unit of measurement in the associated event table, e.g. the `valueuom` column in CHARTEVENTS. +`unitname` specifies the unit of measurement used for the `itemid`. This column is not always available, and this may be because the unit of measurement varies, a unit of measurement does not make sense for the given data type, or the unit of measurement is simply missing. Note that there is sometimes additional information on the unit of measurement in the associated event table, e.g. the `valueuom` column in *chartevents*. ### `param_type` diff --git a/content/en/docs/mimic-nw/modules/icu/icustays.md b/content/en/docs/mimic-nw/modules/icu/icustays.md index 0752e762..f415a09b 100644 --- a/content/en/docs/mimic-nw/modules/icu/icustays.md +++ b/content/en/docs/mimic-nw/modules/icu/icustays.md @@ -7,7 +7,7 @@ description: > Tracking information for ICU stays including admission and discharge times. --- -Defines each ICU stay in the database using STAY\_ID. +Defines each ICU stay in the database using `stay_id`. **Links to:** @@ -41,7 +41,7 @@ Identifiers which specify the patient: `subject_id` is unique to a patient, `had `first_careunit` and `last_careunit` contain, respectively, the first and last ICU type in which the patient was cared for. -NHMC defintions for first_careunit and last_careunit: +NHMC definitions for `first_careunit` and `last_careunit`: | first_careunit/last_careunit | Full abbreviation (Epic) | |------------------------------------|----------------------------------| @@ -64,7 +64,7 @@ NHMC defintions for first_careunit and last_careunit: | CTU | CARDIAC TELEMETRY UNIT, General Medicine service | | RADIOLOGY | | -Note, the addition of ICU overflow in both BIDMC and NHMC as a `first_careunit` and/or `last_careunit`. In the context of COVID-19, an "ICU overflow" typically refers to a situation in which intensive care units (ICUs) in a hospital or healthcare facility have reached or exceeded their capacity due to a surge in COVID-19 patients requiring critical care. This overflow occurs when the number of patients needing intensive care for COVID-19 exceeds the available ICU beds. +Note, the addition of ICU overflow in both BIDMC and NHMC as a `first_careunit` and/or `last_careunit`. In the context of COVID-19, an 'ICU overflow' typically refers to a situation in which intensive care units (ICUs) in a hospital or healthcare facility have reached or exceeded their capacity due to a surge in COVID-19 patients requiring critical care. This overflow occurs when the number of patients needing intensive care for COVID-19 exceeds the available ICU beds. ### `intime`, `outtime` diff --git a/content/en/docs/mimic-nw/modules/icu/procedureevents.md b/content/en/docs/mimic-nw/modules/icu/procedureevents.md index c197ec7d..a075bd41 100644 --- a/content/en/docs/mimic-nw/modules/icu/procedureevents.md +++ b/content/en/docs/mimic-nw/modules/icu/procedureevents.md @@ -16,7 +16,7 @@ description: > # Important considerations -* In the context of COVID-19, it's important to note that there haven't been any new findings or observations, except for instances where the use of a certain procedured e.g. ventilation has increased. +* In the context of COVID-19, we have observed a higher frequency of certain procedures, such as invasive ventilation. # Table columns @@ -70,20 +70,20 @@ Date and time when the procedure ended. ### `itemid` -Identifier for a single event type in the procedurevents table. Each row associated with one `itemid` (e.g. 225792) corresponds to a type of measurement (e.g. Invasive Ventilation) within '2-Ventilation' `category`. The *d_items* table may be joined on this field. For any itemid appearing in the *procedureevents* table, *d_items* `linksto` column will have the value 'procedureevents'. -Note, in the context of COVID-19, +Identifier for a single event type in the *procedurevents* table. Each row associated with one `itemid` (e.g. 225792) corresponds to a type of measurement (e.g. Invasive Ventilation) and `category` (e.g. 2-Ventilation). The *d_items* table may be joined on this field. For any itemid appearing in the *procedureevents* table, *d_items* `linksto` column will have the value 'procedureevents'. + ## `value` -In the `procedureevents` table, this identifies the duration of the procedure (if applicable). For example, if querying for itemid 225794 (“Non-invasive Ventilation”), then the value column indicates the duration of ventilation therapy. +In the *procedureevents* table, this identifies the duration of the procedure (if applicable). For example, if querying for `itemid` 225794 (Non-invasive Ventilation), then the value column indicates the duration of ventilation therapy. ### `valueuom` -The unit of measurement for the value. Most frequently "None" (no value recorded); otherwise one of "day", "hour", or "min". A query for itemiid 225794 ("Non-invasive Ventilation") returning a `value` of 461 and `valueuom` of 'min' would correspond to non-invasive ventilation provided for 461 minutes; this value is expected to match the difference between the `starttime` and `endtime` fields for the record. A procedure with `valueuom` equal to "None" corresponds to a procedure which is instantaneous (e.g. intubation, patient transfer) or whose duration is not relevant (e.g. imaging procedures). For these records, there will be a difference of one second between `starttime` and `endtime` values. +The unit of measurement for the value. Most frequently 'None' (no value recorded); otherwise one of 'day', 'hour', or 'min'. A query for itemiid 225794 (Non-invasive Ventilation) returning a `value` of 461 and `valueuom` of 'min' would correspond to non-invasive ventilation provided for 461 minutes; this value is expected to match the difference between the `starttime` and `endtime` fields for the record. A procedure with `valueuom` equal to 'None' corresponds to a procedure which is instantaneous (e.g. intubation, patient transfer) or whose duration is not relevant (e.g. imaging procedures). For these records, there will be a difference of one second between `starttime` and `endtime` values. ### `statusdescription` -`statusdescription` states the ultimate status of the procedure referred to in the row. The statuses appearing on the `procedureevents` table are: +`statusdescription` states the ultimate status of the procedure referred to in the row. The statuses appearing on the *procedureevents* table are: * `Paused` - The current delivery has been paused. * `FinishedRunning` - The delivery of the item has finished (most frequently, the bag containing the compound is empty). From d3104c2ff6209ffdb27a765a330b7c29dc7fd1fd Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Wed, 27 Sep 2023 14:49:47 -0400 Subject: [PATCH 04/23] fix abbreviations --- content/en/docs/mimic-nw/_index.md | 4 ++-- content/en/docs/mimic-nw/modules/hosp/_index.md | 4 ++-- content/en/docs/mimic-nw/modules/hosp/admissions.md | 8 ++++---- content/en/docs/mimic-nw/modules/hosp/d_labitems.md | 2 +- content/en/docs/mimic-nw/modules/hosp/prescriptions.md | 2 +- content/en/docs/mimic-nw/modules/icu/_index.md | 4 ++-- content/en/docs/mimic-nw/modules/icu/icustays.md | 4 ++-- 7 files changed, 14 insertions(+), 14 deletions(-) diff --git a/content/en/docs/mimic-nw/_index.md b/content/en/docs/mimic-nw/_index.md index ebcfa035..ef962eca 100644 --- a/content/en/docs/mimic-nw/_index.md +++ b/content/en/docs/mimic-nw/_index.md @@ -8,9 +8,9 @@ cascade: _target: path: "/**" --- -MIMIC-Fed is a large, freely available federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NHMC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The federated database adopts a similar data structure as MIMIC-IV v2.2. +MIMIC-Fed is a large, freely available federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NMHC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The federated database adopts a similar data structure as MIMIC-IV v2.2. -Notably, Northwestern Memorial Health Center (NHMC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). +Notably, Northwestern Memorial Health Center (NMHC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). The NM EDW tables are categorized into two primary categories, Fact and Dimension, following data warehousing conventions. As implemented in the NM EDW, Fact tables primarily contain events (such as encounters, admissions, diagnosis events, procedure orders, and medication orders), while Dimension tables describe persistent attributes of entities (patients, procedure names, the medication formulary). diff --git a/content/en/docs/mimic-nw/modules/hosp/_index.md b/content/en/docs/mimic-nw/modules/hosp/_index.md index 72b0129f..f6cc9c9c 100644 --- a/content/en/docs/mimic-nw/modules/hosp/_index.md +++ b/content/en/docs/mimic-nw/modules/hosp/_index.md @@ -4,10 +4,10 @@ linkTitle: "Hosp" date: 2023-09-18 weight: 20 description: > - The Hosp module comprises data sourced from the comprehensive Electronic Health Record (EHR) systems of both BIDMC and NHMC hospitals. Information covered includes patient and admission information, laboratory measurements, billed diagnoses, medication orders, and electronic medication administration records. + The Hosp module comprises data sourced from the comprehensive Electronic Health Record (EHR) systems of both BIDMC and NMHC hospitals. Information covered includes patient and admission information, laboratory measurements, billed diagnoses, medication orders, and electronic medication administration records. --- -The HOSP module contains data derived from the hospital wide EHR of BIDMC and NHMC. These measurements are predominantly recorded during the hospital stay, though some tables include data from outside the hospital as well (e.g. outpatient laboratory tests in *labevents*). +The HOSP module contains data derived from the hospital wide EHR of BIDMC and NMHC. These measurements are predominantly recorded during the hospital stay, though some tables include data from outside the hospital as well (e.g. outpatient laboratory tests in *labevents*). Information includes patient and admission details (*patients*, *admissions*), laboratory measurements (*labevents*, *d_labitems*), hospital billing information (*diagnoses_icd*, *d_icd_diagnoses*), medication orders (*prescriptions*), and electronic medication administration records (*emar*). diff --git a/content/en/docs/mimic-nw/modules/hosp/admissions.md b/content/en/docs/mimic-nw/modules/hosp/admissions.md index 9b61789b..954a35d8 100644 --- a/content/en/docs/mimic-nw/modules/hosp/admissions.md +++ b/content/en/docs/mimic-nw/modules/hosp/admissions.md @@ -71,7 +71,7 @@ Each row of this table contains a unique `hadm_id`, which represents a single pa Similarly, `discharge_location` is the disposition of the patient after they are discharged from the hospital. There are 33 discharge locations from NW EDW. Some of the 33 discharge locations are suppressed under 'Other Facility' for privacy. -NHMC discharge locations: +NMHC discharge locations: | Discharge Location | Full Abbreviation (for clarity) | | ------------------------------------------------------- | --------------------------------- | @@ -111,9 +111,9 @@ NHMC discharge locations: ### `insurance`, `language`, `marital_status`, `race`, `ethnicity` -The `insurance`, `language`, `marital_status`, and `race` and `ethnicity` columns provide information about patient demographics for the given hospitalization. Note, in BIDMC there is only one column for `race`, however we have added `ethnicity` column to federate NHMC's data. +The `insurance`, `language`, `marital_status`, and `race` and `ethnicity` columns provide information about patient demographics for the given hospitalization. Note, in BIDMC there is only one column for `race`, however we have added `ethnicity` column to federate NMHC's data. -The race column in NHMC includes: +The race column in NMHC includes: - American Indian or Alaska Native - Other @@ -126,7 +126,7 @@ The race column in NHMC includes: - Declined - Black or African American -The ethnicity column in NHMC includes: +The ethnicity column in NMHC includes: - Not Hispanic or Latino - Hispanic or Latino diff --git a/content/en/docs/mimic-nw/modules/hosp/d_labitems.md b/content/en/docs/mimic-nw/modules/hosp/d_labitems.md index da972580..67d27568 100644 --- a/content/en/docs/mimic-nw/modules/hosp/d_labitems.md +++ b/content/en/docs/mimic-nw/modules/hosp/d_labitems.md @@ -13,7 +13,7 @@ description: > Laboratory data contains information collected and recorded in the hospital laboratory database. This includes measurements made in wards within the hospital and clinics outside the hospital. Most concepts in this table have been mapped to LOINC codes, an openly available ontology which facilitates interoperability. -For the data sourced from NHMC, Illinois law defines certain categories of information as Sensitive Protected Health Information (SPHI) which require special treatment. SPHI includes genetic counseling but does not include genetic testing. +For the data sourced from NMHC, Illinois law defines certain categories of information as Sensitive Protected Health Information (SPHI) which require special treatment. SPHI includes genetic counseling but does not include genetic testing. To facilitate further federation processes, the lab mappings to standard terminologies (LOINC) will be released. diff --git a/content/en/docs/mimic-nw/modules/hosp/prescriptions.md b/content/en/docs/mimic-nw/modules/hosp/prescriptions.md index 24dcfe70..4b73dbcd 100644 --- a/content/en/docs/mimic-nw/modules/hosp/prescriptions.md +++ b/content/en/docs/mimic-nw/modules/hosp/prescriptions.md @@ -109,7 +109,7 @@ The unit of measurement used for the formulary dosage. Examples include 'mg', 'U ### `doses_per_24_hrs` -The number of doses per 24 hours for which the medication is to be given. A daily dose would result in `doses_per_24_hrs`: 1, bidaily (BID) or twice a day would be 2, and so on. Within NHMC, if the medication order couldn’t be converted to `doses_per_24_hrs` (such as 'Once', 'PRN', 'Continuous', 'Weekly', or 'Q 90 days') the value would be missing. +The number of doses per 24 hours for which the medication is to be given. A daily dose would result in `doses_per_24_hrs`: 1, bidaily (BID) or twice a day would be 2, and so on. Within NMHC, if the medication order couldn’t be converted to `doses_per_24_hrs` (such as 'Once', 'PRN', 'Continuous', 'Weekly', or 'Q 90 days') the value would be missing. ### `route` diff --git a/content/en/docs/mimic-nw/modules/icu/_index.md b/content/en/docs/mimic-nw/modules/icu/_index.md index 9271f309..e8d543cb 100644 --- a/content/en/docs/mimic-nw/modules/icu/_index.md +++ b/content/en/docs/mimic-nw/modules/icu/_index.md @@ -4,9 +4,9 @@ linkTitle: "ICU" date: 2023-09-18 weight: 30 description: > - The ICU module contains information collected from the clinical information system of both BIDMC and NHMC used within the ICU. Information covered includes icu admissions, procedures, and charted vital sign data. + The ICU module contains information collected from the clinical information system of both BIDMC and NMHC used within the ICU. Information covered includes icu admissions, procedures, and charted vital sign data. --- -The ICU module contains data sourced from the clinical information system at the BIDMC (MetaVision (iMDSoft)) and NHMC. MetaVision tables in BIDMC were denormalized to create a star schema where the icustays and d_items tables link to a set of data tables all suffixed with *events*. +The ICU module contains data sourced from the clinical information system at the BIDMC (MetaVision (iMDSoft)) and NMHC. MetaVision tables in BIDMC were denormalized to create a star schema where the icustays and d_items tables link to a set of data tables all suffixed with *events*. Data documented in the ICU module includes icu admissions (*icu stays*), procedures (*procedureevents*, *d_items*), and charted vital sign data (*chartevents*, *d_items*). All events tables contain a `stay_id` column allowing identification of the associated ICU patient in *icustays*, and an `itemid` column allowing identification of the concept documented in *d_items*. \ No newline at end of file diff --git a/content/en/docs/mimic-nw/modules/icu/icustays.md b/content/en/docs/mimic-nw/modules/icu/icustays.md index f415a09b..36f8ec01 100644 --- a/content/en/docs/mimic-nw/modules/icu/icustays.md +++ b/content/en/docs/mimic-nw/modules/icu/icustays.md @@ -41,7 +41,7 @@ Identifiers which specify the patient: `subject_id` is unique to a patient, `had `first_careunit` and `last_careunit` contain, respectively, the first and last ICU type in which the patient was cared for. -NHMC definitions for `first_careunit` and `last_careunit`: +NMHC definitions for `first_careunit` and `last_careunit`: | first_careunit/last_careunit | Full abbreviation (Epic) | |------------------------------------|----------------------------------| @@ -64,7 +64,7 @@ NHMC definitions for `first_careunit` and `last_careunit`: | CTU | CARDIAC TELEMETRY UNIT, General Medicine service | | RADIOLOGY | | -Note, the addition of ICU overflow in both BIDMC and NHMC as a `first_careunit` and/or `last_careunit`. In the context of COVID-19, an 'ICU overflow' typically refers to a situation in which intensive care units (ICUs) in a hospital or healthcare facility have reached or exceeded their capacity due to a surge in COVID-19 patients requiring critical care. This overflow occurs when the number of patients needing intensive care for COVID-19 exceeds the available ICU beds. +Note, the addition of ICU overflow in both BIDMC and NMHC as a `first_careunit` and/or `last_careunit`. In the context of COVID-19, an 'ICU overflow' typically refers to a situation in which intensive care units (ICUs) in a hospital or healthcare facility have reached or exceeded their capacity due to a surge in COVID-19 patients requiring critical care. This overflow occurs when the number of patients needing intensive care for COVID-19 exceeds the available ICU beds. ### `intime`, `outtime` From f3e35fc0a004001b3cc2e5c0fe648d9f9f656518 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Wed, 27 Sep 2023 18:05:30 -0400 Subject: [PATCH 05/23] removes freely available --- content/en/docs/mimic-nw/_index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/en/docs/mimic-nw/_index.md b/content/en/docs/mimic-nw/_index.md index ef962eca..71dcc42f 100644 --- a/content/en/docs/mimic-nw/_index.md +++ b/content/en/docs/mimic-nw/_index.md @@ -8,7 +8,7 @@ cascade: _target: path: "/**" --- -MIMIC-Fed is a large, freely available federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NMHC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The federated database adopts a similar data structure as MIMIC-IV v2.2. +MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NMHC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The federated database adopts a similar data structure as MIMIC-IV v2.2. Notably, Northwestern Memorial Health Center (NMHC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). From 1a96d3413469c8213dd16c22b57948f15c5d4219 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Wed, 27 Sep 2023 18:08:14 -0400 Subject: [PATCH 06/23] adds MIMIC-Fed is not yet released and its structure is subject to change. --- content/en/docs/mimic-nw/_index.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/content/en/docs/mimic-nw/_index.md b/content/en/docs/mimic-nw/_index.md index 71dcc42f..000e4a76 100644 --- a/content/en/docs/mimic-nw/_index.md +++ b/content/en/docs/mimic-nw/_index.md @@ -21,4 +21,8 @@ MIMIC-Fed is currently organized into two distinct modules to highlight the sour - [HOSP](/docs/mimic-nw/modules/hosp/) - Federated hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. - [ICU](/docs/mimic-nw/modules/icu/) - Federated ICU level data including icu stays, procedure events, chartevents (vital signs). +{{% pageinfo %}} +MIMIC-Fed is not yet released and its structure is subject to change. +{{% /pageinfo %}} + The tables structures adopted to align with MIMIC's data structure for each module are detailed in the respective sections. Additionally, we have incorporated COVID-related concepts and standard terminologies (LOINC, RxNorm, SNOMED, ICD-9/10) and derived mappings (for drug administration) into the dataset. This integration not only facilitates current federation efforts, but also facilities interoperability, allowing for seamless data exchange and collaboration across healthcare systems. From 0b8287ffa6f589ee799b52d90dbb48e3cdaf7618 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Wed, 27 Sep 2023 18:20:48 -0400 Subject: [PATCH 07/23] restructures mimicfed --- content/en/docs/{mimic-nw => IV/federated}/_index.md | 7 +++++-- .../en/docs/{mimic-nw => IV/federated}/modules/_index.md | 0 .../docs/{mimic-nw => IV/federated}/modules/hosp/_index.md | 0 .../{mimic-nw => IV/federated}/modules/hosp/admissions.md | 0 .../federated}/modules/hosp/d_icd_diagnoses.md | 0 .../{mimic-nw => IV/federated}/modules/hosp/d_labitems.md | 0 .../federated}/modules/hosp/diagnoses_icd.md | 0 .../docs/{mimic-nw => IV/federated}/modules/hosp/emar.md | 0 .../{mimic-nw => IV/federated}/modules/hosp/labevents.md | 0 .../{mimic-nw => IV/federated}/modules/hosp/patients.md | 0 .../federated}/modules/hosp/prescriptions.md | 0 .../docs/{mimic-nw => IV/federated}/modules/icu/_index.md | 0 .../{mimic-nw => IV/federated}/modules/icu/chartevents.md | 0 .../docs/{mimic-nw => IV/federated}/modules/icu/d_items.md | 0 .../{mimic-nw => IV/federated}/modules/icu/icustays.md | 0 .../federated}/modules/icu/procedureevents.md | 0 16 files changed, 5 insertions(+), 2 deletions(-) rename content/en/docs/{mimic-nw => IV/federated}/_index.md (90%) rename content/en/docs/{mimic-nw => IV/federated}/modules/_index.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/hosp/_index.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/hosp/admissions.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/hosp/d_icd_diagnoses.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/hosp/d_labitems.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/hosp/diagnoses_icd.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/hosp/emar.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/hosp/labevents.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/hosp/patients.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/hosp/prescriptions.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/icu/_index.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/icu/chartevents.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/icu/d_items.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/icu/icustays.md (100%) rename content/en/docs/{mimic-nw => IV/federated}/modules/icu/procedureevents.md (100%) diff --git a/content/en/docs/mimic-nw/_index.md b/content/en/docs/IV/federated/_index.md similarity index 90% rename from content/en/docs/mimic-nw/_index.md rename to content/en/docs/IV/federated/_index.md index 000e4a76..109b0a0d 100644 --- a/content/en/docs/mimic-nw/_index.md +++ b/content/en/docs/IV/federated/_index.md @@ -1,12 +1,15 @@ --- -title: MIMIC-Fed documentation -linktitle: MIMIC-Fed +title: MIMIC-Fed +linktitle: Federated (Beta) weight: 50 cascade: - type: "docs" _target: path: "/**" + +description: > + MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NMHC) from 2020 to 2022. --- MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NMHC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The federated database adopts a similar data structure as MIMIC-IV v2.2. diff --git a/content/en/docs/mimic-nw/modules/_index.md b/content/en/docs/IV/federated/modules/_index.md similarity index 100% rename from content/en/docs/mimic-nw/modules/_index.md rename to content/en/docs/IV/federated/modules/_index.md diff --git a/content/en/docs/mimic-nw/modules/hosp/_index.md b/content/en/docs/IV/federated/modules/hosp/_index.md similarity index 100% rename from content/en/docs/mimic-nw/modules/hosp/_index.md rename to content/en/docs/IV/federated/modules/hosp/_index.md diff --git a/content/en/docs/mimic-nw/modules/hosp/admissions.md b/content/en/docs/IV/federated/modules/hosp/admissions.md similarity index 100% rename from content/en/docs/mimic-nw/modules/hosp/admissions.md rename to content/en/docs/IV/federated/modules/hosp/admissions.md diff --git a/content/en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md b/content/en/docs/IV/federated/modules/hosp/d_icd_diagnoses.md similarity index 100% rename from content/en/docs/mimic-nw/modules/hosp/d_icd_diagnoses.md rename to content/en/docs/IV/federated/modules/hosp/d_icd_diagnoses.md diff --git a/content/en/docs/mimic-nw/modules/hosp/d_labitems.md b/content/en/docs/IV/federated/modules/hosp/d_labitems.md similarity index 100% rename from content/en/docs/mimic-nw/modules/hosp/d_labitems.md rename to content/en/docs/IV/federated/modules/hosp/d_labitems.md diff --git a/content/en/docs/mimic-nw/modules/hosp/diagnoses_icd.md b/content/en/docs/IV/federated/modules/hosp/diagnoses_icd.md similarity index 100% rename from content/en/docs/mimic-nw/modules/hosp/diagnoses_icd.md rename to content/en/docs/IV/federated/modules/hosp/diagnoses_icd.md diff --git a/content/en/docs/mimic-nw/modules/hosp/emar.md b/content/en/docs/IV/federated/modules/hosp/emar.md similarity index 100% rename from content/en/docs/mimic-nw/modules/hosp/emar.md rename to content/en/docs/IV/federated/modules/hosp/emar.md diff --git a/content/en/docs/mimic-nw/modules/hosp/labevents.md b/content/en/docs/IV/federated/modules/hosp/labevents.md similarity index 100% rename from content/en/docs/mimic-nw/modules/hosp/labevents.md rename to content/en/docs/IV/federated/modules/hosp/labevents.md diff --git a/content/en/docs/mimic-nw/modules/hosp/patients.md b/content/en/docs/IV/federated/modules/hosp/patients.md similarity index 100% rename from content/en/docs/mimic-nw/modules/hosp/patients.md rename to content/en/docs/IV/federated/modules/hosp/patients.md diff --git a/content/en/docs/mimic-nw/modules/hosp/prescriptions.md b/content/en/docs/IV/federated/modules/hosp/prescriptions.md similarity index 100% rename from content/en/docs/mimic-nw/modules/hosp/prescriptions.md rename to content/en/docs/IV/federated/modules/hosp/prescriptions.md diff --git a/content/en/docs/mimic-nw/modules/icu/_index.md b/content/en/docs/IV/federated/modules/icu/_index.md similarity index 100% rename from content/en/docs/mimic-nw/modules/icu/_index.md rename to content/en/docs/IV/federated/modules/icu/_index.md diff --git a/content/en/docs/mimic-nw/modules/icu/chartevents.md b/content/en/docs/IV/federated/modules/icu/chartevents.md similarity index 100% rename from content/en/docs/mimic-nw/modules/icu/chartevents.md rename to content/en/docs/IV/federated/modules/icu/chartevents.md diff --git a/content/en/docs/mimic-nw/modules/icu/d_items.md b/content/en/docs/IV/federated/modules/icu/d_items.md similarity index 100% rename from content/en/docs/mimic-nw/modules/icu/d_items.md rename to content/en/docs/IV/federated/modules/icu/d_items.md diff --git a/content/en/docs/mimic-nw/modules/icu/icustays.md b/content/en/docs/IV/federated/modules/icu/icustays.md similarity index 100% rename from content/en/docs/mimic-nw/modules/icu/icustays.md rename to content/en/docs/IV/federated/modules/icu/icustays.md diff --git a/content/en/docs/mimic-nw/modules/icu/procedureevents.md b/content/en/docs/IV/federated/modules/icu/procedureevents.md similarity index 100% rename from content/en/docs/mimic-nw/modules/icu/procedureevents.md rename to content/en/docs/IV/federated/modules/icu/procedureevents.md From f2580ef6a5488f76e145e4c35b0c9c5ab7f9d335 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Thu, 28 Sep 2023 00:33:37 -0400 Subject: [PATCH 08/23] adds mimic feature block for consistency. --- content/en/_index.html | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/content/en/_index.html b/content/en/_index.html index dbdc722f..92d07ec8 100644 --- a/content/en/_index.html +++ b/content/en/_index.html @@ -52,6 +52,10 @@ The Note module contains deidentified free-text clinical notes for hospitalized patients. {{% /blocks/feature %}} +{{% blocks/feature icon="fa-lightbulb" title="MIMIC-IV-Fed" url="/docs/iv/federated/" %}} +MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NMHC) from 2020 to 2022. +{{% /blocks/feature %}} + {{% blocks/feature icon="fa-scroll" title="MIMIC-III" url="/docs/iii/" %}} MIMIC-III is an older version of MIMIC. It contains an older group of patients (ending in 2012), and a subset of the ICU and hospital information available in MIMIC-IV. We highly recommend researchers starting new studies to use the above modules in MIMIC-IV. From 1d5e663a5c095e144ed5566affaca09e4bd6856e Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Wed, 4 Oct 2023 14:28:52 -0400 Subject: [PATCH 09/23] update NMHC Branded Name w/ HealthCare. --- content/en/docs/IV/federated/_index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/content/en/docs/IV/federated/_index.md b/content/en/docs/IV/federated/_index.md index 109b0a0d..0714e9b3 100644 --- a/content/en/docs/IV/federated/_index.md +++ b/content/en/docs/IV/federated/_index.md @@ -9,11 +9,11 @@ cascade: path: "/**" description: > - MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NMHC) from 2020 to 2022. + MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) from 2020 to 2022. --- -MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NMHC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The federated database adopts a similar data structure as MIMIC-IV v2.2. +MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The federated database adopts a similar data structure as MIMIC-IV v2.2. -Notably, Northwestern Memorial Health Center (NMHC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). +Notably, Northwestern Memorial HealthCare (NMHC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). The NM EDW tables are categorized into two primary categories, Fact and Dimension, following data warehousing conventions. As implemented in the NM EDW, Fact tables primarily contain events (such as encounters, admissions, diagnosis events, procedure orders, and medication orders), while Dimension tables describe persistent attributes of entities (patients, procedure names, the medication formulary). From a94bf9e260a77eb6f83db8bf8e7d86b57d6827d3 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Wed, 4 Oct 2023 14:53:01 -0400 Subject: [PATCH 10/23] restructures harmonized multicenter db to the main docs page. --- content/en/docs/{IV => }/federated/_index.md | 0 content/en/docs/{IV => }/federated/modules/_index.md | 0 content/en/docs/{IV => }/federated/modules/hosp/_index.md | 0 content/en/docs/{IV => }/federated/modules/hosp/admissions.md | 0 .../en/docs/{IV => }/federated/modules/hosp/d_icd_diagnoses.md | 0 content/en/docs/{IV => }/federated/modules/hosp/d_labitems.md | 0 content/en/docs/{IV => }/federated/modules/hosp/diagnoses_icd.md | 0 content/en/docs/{IV => }/federated/modules/hosp/emar.md | 0 content/en/docs/{IV => }/federated/modules/hosp/labevents.md | 0 content/en/docs/{IV => }/federated/modules/hosp/patients.md | 0 content/en/docs/{IV => }/federated/modules/hosp/prescriptions.md | 0 content/en/docs/{IV => }/federated/modules/icu/_index.md | 0 content/en/docs/{IV => 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-0400 Subject: [PATCH 11/23] minor edits and removes mentions of federated --- content/en/_index.html | 4 +-- content/en/docs/federated/_index.md | 31 ------------------- content/en/docs/multi-center/_index.md | 31 +++++++++++++++++++ .../modules/_index.md | 2 +- .../modules/hosp/_index.md | 2 +- .../modules/hosp/admissions.md | 2 +- .../modules/hosp/d_icd_diagnoses.md | 0 .../modules/hosp/d_labitems.md | 2 +- .../modules/hosp/diagnoses_icd.md | 0 .../modules/hosp/emar.md | 0 .../modules/hosp/labevents.md | 0 .../modules/hosp/patients.md | 0 .../modules/hosp/prescriptions.md | 2 +- .../modules/icu/_index.md | 0 .../modules/icu/chartevents.md | 0 .../modules/icu/d_items.md | 2 +- .../modules/icu/icustays.md | 0 .../modules/icu/procedureevents.md | 0 18 files changed, 39 insertions(+), 39 deletions(-) delete mode 100644 content/en/docs/federated/_index.md create mode 100644 content/en/docs/multi-center/_index.md rename content/en/docs/{federated => multi-center}/modules/_index.md (67%) rename content/en/docs/{federated => multi-center}/modules/hosp/_index.md (93%) rename content/en/docs/{federated => multi-center}/modules/hosp/admissions.md (99%) rename content/en/docs/{federated => multi-center}/modules/hosp/d_icd_diagnoses.md (100%) rename content/en/docs/{federated => multi-center}/modules/hosp/d_labitems.md (95%) rename content/en/docs/{federated => multi-center}/modules/hosp/diagnoses_icd.md (100%) rename content/en/docs/{federated => multi-center}/modules/hosp/emar.md (100%) rename content/en/docs/{federated => multi-center}/modules/hosp/labevents.md (100%) rename content/en/docs/{federated => multi-center}/modules/hosp/patients.md (100%) rename content/en/docs/{federated => multi-center}/modules/hosp/prescriptions.md (97%) rename content/en/docs/{federated => multi-center}/modules/icu/_index.md (100%) rename content/en/docs/{federated => multi-center}/modules/icu/chartevents.md (100%) rename content/en/docs/{federated => multi-center}/modules/icu/d_items.md (93%) rename content/en/docs/{federated => multi-center}/modules/icu/icustays.md (100%) rename content/en/docs/{federated => multi-center}/modules/icu/procedureevents.md (100%) diff --git a/content/en/_index.html b/content/en/_index.html index 92d07ec8..4111ddc3 100644 --- a/content/en/_index.html +++ b/content/en/_index.html @@ -52,8 +52,8 @@ The Note module contains deidentified free-text clinical notes for hospitalized patients. {{% /blocks/feature %}} -{{% blocks/feature icon="fa-lightbulb" title="MIMIC-IV-Fed" url="/docs/iv/federated/" %}} -MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial Health Center (NMHC) from 2020 to 2022. +{{% blocks/feature icon="fa-lightbulb" title="MIMIC-Northwestern" url="/docs/multi-center/" %}} +MIMIC-Northwestern is a large harmonized multi-center COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) from 2020 to 2022. {{% /blocks/feature %}} {{% blocks/feature icon="fa-scroll" title="MIMIC-III" url="/docs/iii/" %}} diff --git a/content/en/docs/federated/_index.md b/content/en/docs/federated/_index.md deleted file mode 100644 index 0714e9b3..00000000 --- a/content/en/docs/federated/_index.md +++ /dev/null @@ -1,31 +0,0 @@ ---- -title: MIMIC-Fed -linktitle: Federated (Beta) -weight: 50 - -cascade: -- type: "docs" - _target: - path: "/**" - -description: > - MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) from 2020 to 2022. ---- -MIMIC-Fed is a large federated COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The federated database adopts a similar data structure as MIMIC-IV v2.2. - -Notably, Northwestern Memorial HealthCare (NMHC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). - -The NM EDW tables are categorized into two primary categories, Fact and Dimension, following data warehousing conventions. As implemented in the NM EDW, Fact tables primarily contain events (such as encounters, admissions, diagnosis events, procedure orders, and medication orders), while Dimension tables describe persistent attributes of entities (patients, procedure names, the medication formulary). - -The NM EDW also includes auxiliary tables not directly related to patient care, such as a list of International Classification of Disease codes (ICD-9 and ICD-10). In response to the COVID-19/SARS-COV-2 pandemic, a COVID-19 data mart was created within the EDW to provide convenient access to information on COVID-19 patients, lab results, medications and treatments. - -MIMIC-Fed is currently organized into two distinct modules to highlight the source of the data: - -- [HOSP](/docs/mimic-nw/modules/hosp/) - Federated hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. -- [ICU](/docs/mimic-nw/modules/icu/) - Federated ICU level data including icu stays, procedure events, chartevents (vital signs). - -{{% pageinfo %}} -MIMIC-Fed is not yet released and its structure is subject to change. -{{% /pageinfo %}} - -The tables structures adopted to align with MIMIC's data structure for each module are detailed in the respective sections. Additionally, we have incorporated COVID-related concepts and standard terminologies (LOINC, RxNorm, SNOMED, ICD-9/10) and derived mappings (for drug administration) into the dataset. This integration not only facilitates current federation efforts, but also facilities interoperability, allowing for seamless data exchange and collaboration across healthcare systems. diff --git a/content/en/docs/multi-center/_index.md b/content/en/docs/multi-center/_index.md new file mode 100644 index 00000000..3cb59d70 --- /dev/null +++ b/content/en/docs/multi-center/_index.md @@ -0,0 +1,31 @@ +--- +title: "MIMIC-Northwestern: A Harmonized Multi-center COVID-rich ICU Database documentation" +linktitle: Multi-center +weight: 40 + +cascade: +- type: "docs" + _target: + path: "/**" + +# description: > +# We introduce a large harmonized multi-center COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) from 2020 to 2022. +--- +We introduce MIMIC-Northwestern, a large harmonized multi-center COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The database adopts a similar data structure as MIMIC-IV v2.2. + +Notably, Northwestern Memorial HealthCare (NMHC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). + +The NM EDW tables are categorized into two primary categories, Fact and Dimension, following data warehousing conventions. As implemented in the NM EDW, Fact tables primarily contain events (such as encounters, admissions, diagnosis events, procedure orders, and medication orders), while Dimension tables describe persistent attributes of entities (patients, procedure names, the medication formulary). + +The NM EDW also includes auxiliary tables not directly related to patient care, such as a list of International Classification of Disease codes (ICD-9 and ICD-10). In response to the COVID-19/SARS-COV-2 pandemic, a COVID-19 data mart was created within the EDW to provide convenient access to information on COVID-19 patients, lab results, medications and treatments. + +The multi-center database is currently organized into two distinct modules to highlight the source of the data: + +- [Hosp](/docs/federated/modules/hosp/) - Hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. +- [ICU](/docs/federated/modules/icu/) - ICU level data including icu stays, procedure events, chartevents (vital signs). + +{{% pageinfo %}} +The multi-center database is not yet released and its structure is subject to change. +{{% /pageinfo %}} + +The tables structures adopted to align with MIMIC's data structure for each module are detailed in the respective sections. Additionally, we have incorporated COVID-related concepts and standard terminologies (LOINC, RxNorm, SNOMED, ICD-9/10) and derived mappings (for drug administration) into the dataset. This integration not only facilitates current multi-center initiatives, but also facilities interoperability, allowing for seamless data exchange and collaboration across healthcare systems. diff --git a/content/en/docs/federated/modules/_index.md b/content/en/docs/multi-center/modules/_index.md similarity index 67% rename from content/en/docs/federated/modules/_index.md rename to content/en/docs/multi-center/modules/_index.md index 0f374cbf..9463729d 100644 --- a/content/en/docs/federated/modules/_index.md +++ b/content/en/docs/multi-center/modules/_index.md @@ -4,7 +4,7 @@ linkTitle: "Modules" weight: 3 date: 2023-09-18 description: > - Description of the data contained in each of the MIMIC-Fed modules. + Description of the data contained in each of the multi-center modules. --- Data within the modules will be made available on PhysioNet. diff --git a/content/en/docs/federated/modules/hosp/_index.md b/content/en/docs/multi-center/modules/hosp/_index.md similarity index 93% rename from content/en/docs/federated/modules/hosp/_index.md rename to content/en/docs/multi-center/modules/hosp/_index.md index f6cc9c9c..4f6f3de9 100644 --- a/content/en/docs/federated/modules/hosp/_index.md +++ b/content/en/docs/multi-center/modules/hosp/_index.md @@ -7,7 +7,7 @@ description: > The Hosp module comprises data sourced from the comprehensive Electronic Health Record (EHR) systems of both BIDMC and NMHC hospitals. Information covered includes patient and admission information, laboratory measurements, billed diagnoses, medication orders, and electronic medication administration records. --- -The HOSP module contains data derived from the hospital wide EHR of BIDMC and NMHC. These measurements are predominantly recorded during the hospital stay, though some tables include data from outside the hospital as well (e.g. outpatient laboratory tests in *labevents*). +The Hosp module contains data derived from the hospital wide EHR of BIDMC and NMHC. These measurements are predominantly recorded during the hospital stay, though some tables include data from outside the hospital as well (e.g. outpatient laboratory tests in *labevents*). Information includes patient and admission details (*patients*, *admissions*), laboratory measurements (*labevents*, *d_labitems*), hospital billing information (*diagnoses_icd*, *d_icd_diagnoses*), medication orders (*prescriptions*), and electronic medication administration records (*emar*). diff --git a/content/en/docs/federated/modules/hosp/admissions.md b/content/en/docs/multi-center/modules/hosp/admissions.md similarity index 99% rename from content/en/docs/federated/modules/hosp/admissions.md rename to content/en/docs/multi-center/modules/hosp/admissions.md index 954a35d8..f22c5344 100644 --- a/content/en/docs/federated/modules/hosp/admissions.md +++ b/content/en/docs/multi-center/modules/hosp/admissions.md @@ -111,7 +111,7 @@ NMHC discharge locations: ### `insurance`, `language`, `marital_status`, `race`, `ethnicity` -The `insurance`, `language`, `marital_status`, and `race` and `ethnicity` columns provide information about patient demographics for the given hospitalization. Note, in BIDMC there is only one column for `race`, however we have added `ethnicity` column to federate NMHC's data. +The `insurance`, `language`, `marital_status`, and `race` and `ethnicity` columns provide information about patient demographics for the given hospitalization. Note, in BIDMC there is only one column for `race`, however we have added `ethnicity` column to incorporate NMHC's data. The race column in NMHC includes: diff --git a/content/en/docs/federated/modules/hosp/d_icd_diagnoses.md b/content/en/docs/multi-center/modules/hosp/d_icd_diagnoses.md similarity index 100% rename from content/en/docs/federated/modules/hosp/d_icd_diagnoses.md rename to content/en/docs/multi-center/modules/hosp/d_icd_diagnoses.md diff --git a/content/en/docs/federated/modules/hosp/d_labitems.md b/content/en/docs/multi-center/modules/hosp/d_labitems.md similarity index 95% rename from content/en/docs/federated/modules/hosp/d_labitems.md rename to content/en/docs/multi-center/modules/hosp/d_labitems.md index 67d27568..4beb2741 100644 --- a/content/en/docs/federated/modules/hosp/d_labitems.md +++ b/content/en/docs/multi-center/modules/hosp/d_labitems.md @@ -15,7 +15,7 @@ Laboratory data contains information collected and recorded in the hospital labo For the data sourced from NMHC, Illinois law defines certain categories of information as Sensitive Protected Health Information (SPHI) which require special treatment. SPHI includes genetic counseling but does not include genetic testing. -To facilitate further federation processes, the lab mappings to standard terminologies (LOINC) will be released. +To facilitate further multi-center initiatives, the lab mappings to standard terminologies (LOINC) will be released. ### Links to diff --git a/content/en/docs/federated/modules/hosp/diagnoses_icd.md b/content/en/docs/multi-center/modules/hosp/diagnoses_icd.md similarity index 100% rename from content/en/docs/federated/modules/hosp/diagnoses_icd.md rename to content/en/docs/multi-center/modules/hosp/diagnoses_icd.md diff --git a/content/en/docs/federated/modules/hosp/emar.md b/content/en/docs/multi-center/modules/hosp/emar.md similarity index 100% rename from content/en/docs/federated/modules/hosp/emar.md rename to content/en/docs/multi-center/modules/hosp/emar.md diff --git a/content/en/docs/federated/modules/hosp/labevents.md b/content/en/docs/multi-center/modules/hosp/labevents.md similarity index 100% rename from content/en/docs/federated/modules/hosp/labevents.md rename to content/en/docs/multi-center/modules/hosp/labevents.md diff --git a/content/en/docs/federated/modules/hosp/patients.md b/content/en/docs/multi-center/modules/hosp/patients.md similarity index 100% rename from content/en/docs/federated/modules/hosp/patients.md rename to content/en/docs/multi-center/modules/hosp/patients.md diff --git a/content/en/docs/federated/modules/hosp/prescriptions.md b/content/en/docs/multi-center/modules/hosp/prescriptions.md similarity index 97% rename from content/en/docs/federated/modules/hosp/prescriptions.md rename to content/en/docs/multi-center/modules/hosp/prescriptions.md index 4b73dbcd..c27fae06 100644 --- a/content/en/docs/federated/modules/hosp/prescriptions.md +++ b/content/en/docs/multi-center/modules/hosp/prescriptions.md @@ -9,7 +9,7 @@ description: > The *prescriptions* table provides information about prescribed medications. Information includes the name of the drug, coded identifiers including the Generic Sequence Number (GSN) and National Drug Code (NDC), the product strength, the formulary dose, and the route of administration. -To facilitate further federation processes, the drug mappings to standard terminologies (RxNorm) will be released. +To facilitate further multi-center initiatives, the drug mappings to standard terminologies (RxNorm) will be released. We provide a list of some common COVID-19 drugs in the database, as defined by RxNorm terminology, below: diff --git a/content/en/docs/federated/modules/icu/_index.md b/content/en/docs/multi-center/modules/icu/_index.md similarity index 100% rename from content/en/docs/federated/modules/icu/_index.md rename to content/en/docs/multi-center/modules/icu/_index.md diff --git a/content/en/docs/federated/modules/icu/chartevents.md b/content/en/docs/multi-center/modules/icu/chartevents.md similarity index 100% rename from content/en/docs/federated/modules/icu/chartevents.md rename to content/en/docs/multi-center/modules/icu/chartevents.md diff --git a/content/en/docs/federated/modules/icu/d_items.md b/content/en/docs/multi-center/modules/icu/d_items.md similarity index 93% rename from content/en/docs/federated/modules/icu/d_items.md rename to content/en/docs/multi-center/modules/icu/d_items.md index dfb878c9..258c3625 100644 --- a/content/en/docs/federated/modules/icu/d_items.md +++ b/content/en/docs/multi-center/modules/icu/d_items.md @@ -30,7 +30,7 @@ highnormalvalue | FLOAT The *d_items* table defines `itemid`, which represents measurements in the database. Measurements of the same type (e.g. heart rate) will have the same `itemid` (e.g. 220045). Values in the `itemid` column are unique to each row. All `itemid`s will have a value > 220000. -To faciliate future federation processes, we will release mappings within charted events (including vital signs) to standard terminologies (LOINC) and mappings for procedure events to standard terminologies (SNOMED). +To faciliate future multi-center initiatives, we will release mappings within charted events (including vital signs) to standard terminologies (LOINC) and mappings for procedure events to standard terminologies (SNOMED). We provide a list of common vital sign labels in the database, as defined by LOINC terminology, below: diff --git a/content/en/docs/federated/modules/icu/icustays.md b/content/en/docs/multi-center/modules/icu/icustays.md similarity index 100% rename from content/en/docs/federated/modules/icu/icustays.md rename to content/en/docs/multi-center/modules/icu/icustays.md diff --git a/content/en/docs/federated/modules/icu/procedureevents.md b/content/en/docs/multi-center/modules/icu/procedureevents.md similarity index 100% rename from content/en/docs/federated/modules/icu/procedureevents.md rename to content/en/docs/multi-center/modules/icu/procedureevents.md From 4a74db511754de2640126f3511393d5aff37d5d0 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Wed, 4 Oct 2023 16:48:49 -0400 Subject: [PATCH 12/23] edits formatting. --- content/en/_index.html | 2 +- content/en/docs/multi-center/_index.md | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/content/en/_index.html b/content/en/_index.html index 4111ddc3..e9145e7b 100644 --- a/content/en/_index.html +++ b/content/en/_index.html @@ -53,7 +53,7 @@ {{% /blocks/feature %}} {{% blocks/feature icon="fa-lightbulb" title="MIMIC-Northwestern" url="/docs/multi-center/" %}} -MIMIC-Northwestern is a large harmonized multi-center COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) from 2020 to 2022. +A large harmonized multi-center COVID-rich ICU database from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) spanning 2020 to 2022. {{% /blocks/feature %}} {{% blocks/feature icon="fa-scroll" title="MIMIC-III" url="/docs/iii/" %}} diff --git a/content/en/docs/multi-center/_index.md b/content/en/docs/multi-center/_index.md index 3cb59d70..d2bbfbae 100644 --- a/content/en/docs/multi-center/_index.md +++ b/content/en/docs/multi-center/_index.md @@ -1,17 +1,17 @@ --- -title: "MIMIC-Northwestern: A Harmonized Multi-center COVID-rich ICU Database documentation" +title: "MIMIC-Northwestern documentation" linktitle: Multi-center -weight: 40 +weight: 45 cascade: - type: "docs" _target: path: "/**" -# description: > -# We introduce a large harmonized multi-center COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) from 2020 to 2022. +description: > + MIMIC-Northwestern: A Harmonized Multi-center COVID-rich ICU Database --- -We introduce MIMIC-Northwestern, a large harmonized multi-center COVID-rich ICU database comprising deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) from 2020 to 2022, capturing the evolving distribution shifts in data over this critical time period. The database adopts a similar data structure as MIMIC-IV v2.2. +We introduce MIMIC-Northwestern, a large harmonized multi-center COVID-rich ICU database. It comprises deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) spanning 2020 to 2022, capturing the data distribution shifts during this critical period. The database adopts a similar data structure as MIMIC-IV v2.2. Notably, Northwestern Memorial HealthCare (NMHC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). From 9739e7e25484baa90e96fc90b9bf56ed3861ab55 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Wed, 4 Oct 2023 16:54:40 -0400 Subject: [PATCH 13/23] updates links and text. --- content/en/docs/multi-center/_index.md | 8 ++++---- content/en/docs/multi-center/modules/_index.md | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/content/en/docs/multi-center/_index.md b/content/en/docs/multi-center/_index.md index d2bbfbae..a218ea20 100644 --- a/content/en/docs/multi-center/_index.md +++ b/content/en/docs/multi-center/_index.md @@ -19,13 +19,13 @@ The NM EDW tables are categorized into two primary categories, Fact and Dimensio The NM EDW also includes auxiliary tables not directly related to patient care, such as a list of International Classification of Disease codes (ICD-9 and ICD-10). In response to the COVID-19/SARS-COV-2 pandemic, a COVID-19 data mart was created within the EDW to provide convenient access to information on COVID-19 patients, lab results, medications and treatments. -The multi-center database is currently organized into two distinct modules to highlight the source of the data: +The MIMIC-Northwestern database is currently organized into two distinct modules to highlight the source of the data: -- [Hosp](/docs/federated/modules/hosp/) - Hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. -- [ICU](/docs/federated/modules/icu/) - ICU level data including icu stays, procedure events, chartevents (vital signs). +- [Hosp](/docs/multi-center/modules/hosp/) - Hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. +- [ICU](/docs/multi-center/modules/icu/) - ICU level data including icu stays, procedure events, chartevents (vital signs). {{% pageinfo %}} -The multi-center database is not yet released and its structure is subject to change. +The MIMIC-Northwestern database is not yet released and its structure is subject to change. {{% /pageinfo %}} The tables structures adopted to align with MIMIC's data structure for each module are detailed in the respective sections. Additionally, we have incorporated COVID-related concepts and standard terminologies (LOINC, RxNorm, SNOMED, ICD-9/10) and derived mappings (for drug administration) into the dataset. This integration not only facilitates current multi-center initiatives, but also facilities interoperability, allowing for seamless data exchange and collaboration across healthcare systems. diff --git a/content/en/docs/multi-center/modules/_index.md b/content/en/docs/multi-center/modules/_index.md index 9463729d..603c918a 100644 --- a/content/en/docs/multi-center/modules/_index.md +++ b/content/en/docs/multi-center/modules/_index.md @@ -4,7 +4,7 @@ linkTitle: "Modules" weight: 3 date: 2023-09-18 description: > - Description of the data contained in each of the multi-center modules. + Description of the data contained in each of the MIMIC-Northwestern modules. --- Data within the modules will be made available on PhysioNet. From 1a8190469af8368eb3a2856d79d9731bfecc33b8 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Tue, 10 Oct 2023 12:09:05 -0400 Subject: [PATCH 14/23] replaces endouttime with edregttime --- content/en/docs/multi-center/modules/hosp/admissions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/en/docs/multi-center/modules/hosp/admissions.md b/content/en/docs/multi-center/modules/hosp/admissions.md index f22c5344..5356dcc8 100644 --- a/content/en/docs/multi-center/modules/hosp/admissions.md +++ b/content/en/docs/multi-center/modules/hosp/admissions.md @@ -137,7 +137,7 @@ The ethnicity column in NMHC includes: The date and time at which arrival of the patient in the emergency department was registered. -### `edouttime` +### `edregtime` The date and time at which the patient was discharged from the emergency department, either discharged from the hospital or transferred. ### `hospital_expire_flag` From e6fa4d1ad34bfbb6e0daae5bd8aee001b304701b Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Tue, 10 Oct 2023 12:09:20 -0400 Subject: [PATCH 15/23] removes order_provider_id --- content/en/docs/multi-center/modules/hosp/labevents.md | 6 ------ 1 file changed, 6 deletions(-) diff --git a/content/en/docs/multi-center/modules/hosp/labevents.md b/content/en/docs/multi-center/modules/hosp/labevents.md index e530d345..3a20853a 100644 --- a/content/en/docs/multi-center/modules/hosp/labevents.md +++ b/content/en/docs/multi-center/modules/hosp/labevents.md @@ -23,7 +23,6 @@ Name | Postgres data type `hadm_id` | INTEGER `specimen_id` | INTEGER NOT NULL `itemid` | INTEGER NOT NULL -`order_provider_id` | VARCHAR(10) `charttime` | TIMESTAMP(0) `storetime` | TIMESTAMP(0) `value` | VARCHAR(200) @@ -56,11 +55,6 @@ Often multiple measurements are made on the same sample. The `specimen_id` will An identifier which uniquely denotes laboratory concepts. -### `order_provider_id` - -`order_provider_id` provides an anonymous identifier for the provider who ordered the laboratory measurement. -{{% include "/static/include/provider_id.md" %}} - ### `charttime` The time at which the laboratory measurement was charted. This is usually the time at which the specimen was acquired, and is usually significantly **earlier** than the time at which the measurement is available. From 9cc1e4197e7e205b72be4053aa10670b90ed2639 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Tue, 10 Oct 2023 12:22:53 -0400 Subject: [PATCH 16/23] adds more explicit description for hospital expire flag. --- content/en/docs/multi-center/modules/hosp/admissions.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/en/docs/multi-center/modules/hosp/admissions.md b/content/en/docs/multi-center/modules/hosp/admissions.md index 5356dcc8..9c67fe0a 100644 --- a/content/en/docs/multi-center/modules/hosp/admissions.md +++ b/content/en/docs/multi-center/modules/hosp/admissions.md @@ -142,4 +142,4 @@ The date and time at which the patient was discharged from the emergency departm ### `hospital_expire_flag` -This is a binary flag which indicates whether the patient died within the given hospitalization. `1` indicates death in the hospital as noted in the `dod` column as part of the *patient* table, and `0` indicates survival to hospital discharge. +This is a binary flag which indicates whether the patient died within the associated hospital admission. `1` indicates death in the hospital as noted in the `dod` column as part of the *patient* table, and `0` indicates survival to hospital discharge. This binary flag therefore specifically indicates death in the hospital as opposed to death at any time. From d54af004c02046d27018fb329fc991c1150f6f45 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Tue, 10 Oct 2023 12:23:43 -0400 Subject: [PATCH 17/23] clarifies ICD10 use compared to ICD9 for 2020-2022 period. --- content/en/docs/multi-center/modules/hosp/d_icd_diagnoses.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/content/en/docs/multi-center/modules/hosp/d_icd_diagnoses.md b/content/en/docs/multi-center/modules/hosp/d_icd_diagnoses.md index 29ee9f4a..49a5d77e 100644 --- a/content/en/docs/multi-center/modules/hosp/d_icd_diagnoses.md +++ b/content/en/docs/multi-center/modules/hosp/d_icd_diagnoses.md @@ -9,6 +9,11 @@ description: > The *d_icd_diagnoses* table defines International Classification of Diseases (ICD) Version 9 and 10 codes for **diagnoses**. These codes are assigned at the end of the patient's stay and are used by the hospital to bill for care provided. +## Important considerations +The ICD-9 code is included in the documentation for informational purposes only. +The database include ICD-10 codes as the transition to ICD-10 is a mandate that was effective October 1,2015 according to the [CMS](https://www.cms.gov/medicare/coding-billing/icd-10-codes#:~:text=ICD%2D10%20Implementation%20Date%3A%20October%201%2C%202015&text=The%20ICD%2D10%20transition%20is,who%20bill%20Medicare%20or%20Medicaid.). + + ### Links to * *diagnoses_icd* ON `icd_code` and `icd_version` From a34c0e931e5f8b6da26a54533a817a0c012b3918 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Tue, 10 Oct 2023 12:26:33 -0400 Subject: [PATCH 18/23] removes caregiver-id. --- content/en/docs/multi-center/modules/icu/chartevents.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/content/en/docs/multi-center/modules/icu/chartevents.md b/content/en/docs/multi-center/modules/icu/chartevents.md index 780087a3..b04e601f 100644 --- a/content/en/docs/multi-center/modules/icu/chartevents.md +++ b/content/en/docs/multi-center/modules/icu/chartevents.md @@ -22,7 +22,6 @@ Name | Postgres Data type subject\_id | INTEGER hadm\_id | INTEGER stay\_id | INTEGER -caregiver_id | INTEGER charttime | TIMESTAMP(0) storetime | TIMESTAMP(0) itemid | INTEGER @@ -39,10 +38,6 @@ Identifiers which specify the patient: `subject_id` is unique to a patient, `had `stay_id` is an integer identifier which uniquely identifies each ICU admission within a hospital admission. Each hospital admission `hadm_id` must have at least one ICU admission `stay_id` but may include more than one. A `stay_id` groups all ICU admissions within 24 hours of each other. -### `caregiver_id` - -`caregiver_id` uniquely identifies a single caregiver who measured the vital sign. - ### `charttime` Date and time when the vital sign was measured, deidentified. From edb72f0ef0d1108c8114155c320d4e587c790bcf Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Tue, 10 Oct 2023 12:29:51 -0400 Subject: [PATCH 19/23] adds references to mimic code repo for mappings. --- content/en/docs/multi-center/modules/icu/d_items.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/en/docs/multi-center/modules/icu/d_items.md b/content/en/docs/multi-center/modules/icu/d_items.md index 258c3625..30722663 100644 --- a/content/en/docs/multi-center/modules/icu/d_items.md +++ b/content/en/docs/multi-center/modules/icu/d_items.md @@ -30,7 +30,7 @@ highnormalvalue | FLOAT The *d_items* table defines `itemid`, which represents measurements in the database. Measurements of the same type (e.g. heart rate) will have the same `itemid` (e.g. 220045). Values in the `itemid` column are unique to each row. All `itemid`s will have a value > 220000. -To faciliate future multi-center initiatives, we will release mappings within charted events (including vital signs) to standard terminologies (LOINC) and mappings for procedure events to standard terminologies (SNOMED). +To faciliate future multi-center initiatives, the mappings within charted events (including vital signs) to standard terminologies (LOINC) and mappings for procedure events to standard terminologies (SNOMED) is in the [MIMIC Code Repository](https://github.com/MIT-LCP/mimic-code/tree/main/mimic-iv/concepts/concept_map). We provide a list of common vital sign labels in the database, as defined by LOINC terminology, below: From 2f8806ed61e55dbc17282b6d21f9f820783eca70 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Tue, 10 Oct 2023 12:41:40 -0400 Subject: [PATCH 20/23] fixes typos in start/stoptime & adds itemid and loinc for examples. --- .../en/docs/multi-center/modules/hosp/d_labitems.md | 11 +++++------ .../docs/multi-center/modules/hosp/prescriptions.md | 5 +---- 2 files changed, 6 insertions(+), 10 deletions(-) diff --git a/content/en/docs/multi-center/modules/hosp/d_labitems.md b/content/en/docs/multi-center/modules/hosp/d_labitems.md index 4beb2741..95f2b013 100644 --- a/content/en/docs/multi-center/modules/hosp/d_labitems.md +++ b/content/en/docs/multi-center/modules/hosp/d_labitems.md @@ -40,13 +40,12 @@ A unique identifier for a laboratory concept. `itemid` is unique to each row, an The `label` column describes the concept which is represented by the `itemid`. -We provide a list of common COVID-19 tests and measurements in the database, as defined by LOINC terminology, below: - -- SARS-CoV-2 (COVID-19) [Presence] in Specimen by Organism specific culture -- SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay -- SARS-CoV-2 (COVID-19) N gene [Cycle Threshold #] in Specimen by NAA with probe detection -- SARS-CoV-2 (COVID-19) E gene [Cycle Threshold #] in Respiratory specimen by NAA with probe detection +We provide a list of some common COVID-19 tests and measurements in the database, as defined by LOINC terminology: +| itemid | loinc | loinc_label | +|--------|---------|-------------------------------------------------------------------------------------------------------| +| 51853 | 94763-0 | SARS-CoV-2 (COVID-19) [Presence] in Specimen by Organism specific culture | +| 51890 | 94558-4 | SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay | ### `fluid` diff --git a/content/en/docs/multi-center/modules/hosp/prescriptions.md b/content/en/docs/multi-center/modules/hosp/prescriptions.md index c27fae06..e1d8edcd 100644 --- a/content/en/docs/multi-center/modules/hosp/prescriptions.md +++ b/content/en/docs/multi-center/modules/hosp/prescriptions.md @@ -46,9 +46,6 @@ Name | Postgres data type `doses_per_24_hrs` | REAL `route` | VARCHAR(50) - - - ### `subject_id` @@ -64,7 +61,7 @@ An identifier which links administrations in *emar* to prescription information ### `starttime`, `stoptime` -The prescribed start and stop time for the medication. `stop_time` could refer to an order to stop a prescription, but in this case, it means the end date for the prescription. For example, in a prescription for one dose per day for 14 days, the `stop_time` would be 14 days after the `start_time`. +The prescribed start and stop time for the medication. `stoptime` could refer to an order to stop a prescription, but in this case, it means the end date for the prescription. For example, in a prescription for one dose per day for 14 days, the `stop_time` would be 14 days after the `starttime`. ### `drug_type` From 5f05e6f1c40235379ebe7268dd2f1127b55dc1d5 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Tue, 10 Oct 2023 12:45:46 -0400 Subject: [PATCH 21/23] adds a clarifying statement about dod in northwestern db. --- content/en/docs/multi-center/modules/hosp/patients.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/en/docs/multi-center/modules/hosp/patients.md b/content/en/docs/multi-center/modules/hosp/patients.md index 0b53056d..7a100fd4 100644 --- a/content/en/docs/multi-center/modules/hosp/patients.md +++ b/content/en/docs/multi-center/modules/hosp/patients.md @@ -47,4 +47,4 @@ This ensures that the statistical anonymity of a patient is maintained and that ### `dod` The patient's date of death `dod` is shifted. Note, the `dod` is censored one year after discharge. Hence, if the death date is unknown it will be NULL. If this date is missing, `dod` will be NULL. If the date is not missing, and if the date is within 365 days after the latest discharge date, this date will be used as DOD. If the date is not missing and is 365 or more days after the latest discharge date, then DOD will be NULL. -Note, the BIDMC database also includes out of hospital data from the state, as part of dod sourced externally from the [Massachusetts State Registry of Vital Records and Statistics](https://www.mass.gov/orgs/registry-of-vital-records-and-statistics), by using identifiers including name, social security number and date of birth. +Note, the BIDMC database also includes out of hospital data from the state, as part of dod sourced externally from the [Massachusetts State Registry of Vital Records and Statistics](https://www.mass.gov/orgs/registry-of-vital-records-and-statistics), by using identifiers including name, social security number and date of birth. However, in the Northwestern database, `dod` represents date of death as recorded in the NMHC medical record system. From 908c7c358f0c336f9deac210ee6d21c675cfa41f Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Tue, 10 Oct 2023 12:51:50 -0400 Subject: [PATCH 22/23] updates mutlicenter to mimic-northwestern --- content/en/_index.html | 2 +- .../en/docs/{multi-center => mimic-northwestern}/_index.md | 4 ++-- .../{multi-center => mimic-northwestern}/modules/_index.md | 0 .../modules/hosp/_index.md | 0 .../modules/hosp/admissions.md | 0 .../modules/hosp/d_icd_diagnoses.md | 0 .../modules/hosp/d_labitems.md | 0 .../modules/hosp/diagnoses_icd.md | 0 .../{multi-center => mimic-northwestern}/modules/hosp/emar.md | 0 .../modules/hosp/labevents.md | 0 .../modules/hosp/patients.md | 0 .../modules/hosp/prescriptions.md | 0 .../modules/icu/_index.md | 0 .../modules/icu/chartevents.md | 0 .../modules/icu/d_items.md | 0 .../modules/icu/icustays.md | 0 .../modules/icu/procedureevents.md | 0 17 files changed, 3 insertions(+), 3 deletions(-) rename content/en/docs/{multi-center => mimic-northwestern}/_index.md (87%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/_index.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/hosp/_index.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/hosp/admissions.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/hosp/d_icd_diagnoses.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/hosp/d_labitems.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/hosp/diagnoses_icd.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/hosp/emar.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/hosp/labevents.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/hosp/patients.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/hosp/prescriptions.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/icu/_index.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/icu/chartevents.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/icu/d_items.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/icu/icustays.md (100%) rename content/en/docs/{multi-center => mimic-northwestern}/modules/icu/procedureevents.md (100%) diff --git a/content/en/_index.html b/content/en/_index.html index e9145e7b..bd88cbf7 100644 --- a/content/en/_index.html +++ b/content/en/_index.html @@ -52,7 +52,7 @@ The Note module contains deidentified free-text clinical notes for hospitalized patients. {{% /blocks/feature %}} -{{% blocks/feature icon="fa-lightbulb" title="MIMIC-Northwestern" url="/docs/multi-center/" %}} +{{% blocks/feature icon="fa-lightbulb" title="MIMIC-Northwestern" url="/docs/mimic-northwestern/" %}} A large harmonized multi-center COVID-rich ICU database from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) spanning 2020 to 2022. {{% /blocks/feature %}} diff --git a/content/en/docs/multi-center/_index.md b/content/en/docs/mimic-northwestern/_index.md similarity index 87% rename from content/en/docs/multi-center/_index.md rename to content/en/docs/mimic-northwestern/_index.md index a218ea20..e715e370 100644 --- a/content/en/docs/multi-center/_index.md +++ b/content/en/docs/mimic-northwestern/_index.md @@ -21,8 +21,8 @@ The NM EDW also includes auxiliary tables not directly related to patient care, The MIMIC-Northwestern database is currently organized into two distinct modules to highlight the source of the data: -- [Hosp](/docs/multi-center/modules/hosp/) - Hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. -- [ICU](/docs/multi-center/modules/icu/) - ICU level data including icu stays, procedure events, chartevents (vital signs). +- [Hosp](/docs/mimic-northwestern/modules/hosp/) - Hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. +- [ICU](/docs/mimic-northwestern/modules/icu/) - ICU level data including icu stays, procedure events, chartevents (vital signs). {{% pageinfo %}} The MIMIC-Northwestern database is not yet released and its structure is subject to change. diff --git a/content/en/docs/multi-center/modules/_index.md b/content/en/docs/mimic-northwestern/modules/_index.md similarity index 100% rename from content/en/docs/multi-center/modules/_index.md rename to content/en/docs/mimic-northwestern/modules/_index.md diff --git a/content/en/docs/multi-center/modules/hosp/_index.md b/content/en/docs/mimic-northwestern/modules/hosp/_index.md similarity index 100% rename from content/en/docs/multi-center/modules/hosp/_index.md rename to content/en/docs/mimic-northwestern/modules/hosp/_index.md diff --git a/content/en/docs/multi-center/modules/hosp/admissions.md b/content/en/docs/mimic-northwestern/modules/hosp/admissions.md similarity index 100% rename from content/en/docs/multi-center/modules/hosp/admissions.md rename to content/en/docs/mimic-northwestern/modules/hosp/admissions.md diff --git a/content/en/docs/multi-center/modules/hosp/d_icd_diagnoses.md b/content/en/docs/mimic-northwestern/modules/hosp/d_icd_diagnoses.md similarity index 100% rename from content/en/docs/multi-center/modules/hosp/d_icd_diagnoses.md rename to content/en/docs/mimic-northwestern/modules/hosp/d_icd_diagnoses.md diff --git a/content/en/docs/multi-center/modules/hosp/d_labitems.md b/content/en/docs/mimic-northwestern/modules/hosp/d_labitems.md similarity index 100% rename from content/en/docs/multi-center/modules/hosp/d_labitems.md rename to content/en/docs/mimic-northwestern/modules/hosp/d_labitems.md diff --git a/content/en/docs/multi-center/modules/hosp/diagnoses_icd.md 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diff --git a/content/en/docs/multi-center/modules/icu/d_items.md b/content/en/docs/mimic-northwestern/modules/icu/d_items.md similarity index 100% rename from content/en/docs/multi-center/modules/icu/d_items.md rename to content/en/docs/mimic-northwestern/modules/icu/d_items.md diff --git a/content/en/docs/multi-center/modules/icu/icustays.md b/content/en/docs/mimic-northwestern/modules/icu/icustays.md similarity index 100% rename from content/en/docs/multi-center/modules/icu/icustays.md rename to content/en/docs/mimic-northwestern/modules/icu/icustays.md diff --git a/content/en/docs/multi-center/modules/icu/procedureevents.md b/content/en/docs/mimic-northwestern/modules/icu/procedureevents.md similarity index 100% rename from content/en/docs/multi-center/modules/icu/procedureevents.md rename to content/en/docs/mimic-northwestern/modules/icu/procedureevents.md From 0f0db10a7f47b9b8426e612dcba009b64911fb02 Mon Sep 17 00:00:00 2001 From: Dana Moukheiber Date: Mon, 10 Jun 2024 11:26:33 -0400 Subject: [PATCH 23/23] updates MIMIC-NW docs. --- content/en/docs/mimic-northwestern/_index.md | 13 +++++++------ .../en/docs/mimic-northwestern/modules/_index.md | 4 ++-- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/content/en/docs/mimic-northwestern/_index.md b/content/en/docs/mimic-northwestern/_index.md index e715e370..d08e009a 100644 --- a/content/en/docs/mimic-northwestern/_index.md +++ b/content/en/docs/mimic-northwestern/_index.md @@ -1,6 +1,6 @@ --- -title: "MIMIC-Northwestern documentation" -linktitle: Multi-center +title: "MIMIC-NW documentation" +linktitle: MIMIC-NW weight: 45 cascade: @@ -9,9 +9,10 @@ cascade: path: "/**" description: > - MIMIC-Northwestern: A Harmonized Multi-center COVID-rich ICU Database + MIMIC-NW: Harmonizing Northwestern's ICU Data with MIMIC's Data Structure. + --- -We introduce MIMIC-Northwestern, a large harmonized multi-center COVID-rich ICU database. It comprises deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) spanning 2020 to 2022, capturing the data distribution shifts during this critical period. The database adopts a similar data structure as MIMIC-IV v2.2. +We introduce MIMIC-NW, a large harmonized multi-center COVID-rich ICU database. It comprises deidentified health-related data from Beth Israel Deaconess Medical Center (BIDMC) and Northwestern Memorial HealthCare (NMHC) spanning 2020 to 2022, capturing the data distribution shifts during this critical period. The database adopts a similar data structure as MIMIC-IV v2.2. Notably, Northwestern Memorial HealthCare (NMHC) uses the Epic electronic medical records (EMR) system. To make the EMR data available for research and quality assurance, the NM EMR systems transfer selected data into a relational Enterprise Data Warehouse (NM EDW). @@ -19,13 +20,13 @@ The NM EDW tables are categorized into two primary categories, Fact and Dimensio The NM EDW also includes auxiliary tables not directly related to patient care, such as a list of International Classification of Disease codes (ICD-9 and ICD-10). In response to the COVID-19/SARS-COV-2 pandemic, a COVID-19 data mart was created within the EDW to provide convenient access to information on COVID-19 patients, lab results, medications and treatments. -The MIMIC-Northwestern database is currently organized into two distinct modules to highlight the source of the data: +The MIMIC-NW database is currently organized into two distinct modules to highlight the source of the data: - [Hosp](/docs/mimic-northwestern/modules/hosp/) - Hospital level data including patients, admissions, labs, ICD diagnoses for billing purposes, prescriptions, and electronic medication administration records. - [ICU](/docs/mimic-northwestern/modules/icu/) - ICU level data including icu stays, procedure events, chartevents (vital signs). {{% pageinfo %}} -The MIMIC-Northwestern database is not yet released and its structure is subject to change. +The MIMIC-NW database is not yet publicly released and its structure is subject to change. {{% /pageinfo %}} The tables structures adopted to align with MIMIC's data structure for each module are detailed in the respective sections. Additionally, we have incorporated COVID-related concepts and standard terminologies (LOINC, RxNorm, SNOMED, ICD-9/10) and derived mappings (for drug administration) into the dataset. This integration not only facilitates current multi-center initiatives, but also facilities interoperability, allowing for seamless data exchange and collaboration across healthcare systems. diff --git a/content/en/docs/mimic-northwestern/modules/_index.md b/content/en/docs/mimic-northwestern/modules/_index.md index 603c918a..08365494 100644 --- a/content/en/docs/mimic-northwestern/modules/_index.md +++ b/content/en/docs/mimic-northwestern/modules/_index.md @@ -4,7 +4,7 @@ linkTitle: "Modules" weight: 3 date: 2023-09-18 description: > - Description of the data contained in each of the MIMIC-Northwestern modules. + Description of the data contained in each of the MIMIC-NW modules. --- -Data within the modules will be made available on PhysioNet. +Data within the modules will be made available on [PhysioNet](https://physionet.org).