ROMOP

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R package to easily interface with OMOP-formatted EHR data.

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ROMOP Readme
================
Benjamin S. Glicksberg
9/14/2018

## ROMOP

ROMOP is a flexible R package to interface with the [Observational
Health Data Sciences and Informatics (OHDSI)](https://www.ohdsi.org/)
[OMOP Common Data Model](https://www.ohdsi.org/data-standardization/).
Briefly, OMOP is a standardized relational database schema for
Electronic Health Record (EHR) or Electronic Medical Record (EMR) data
(i.e., patient data collected during clinical visits to a health
system). The main benefit of a standardized schema is that it allows for
interoperability between institutions, even if the underlying EHR
vendors are disparate.

For a detailed description of the OMOP common data model, please visit
this [helpful wiki](https://github.com/OHDSI/CommonDataModel/wiki).

In its backend, OMOP relies on standardized data ontologies and
metathesaureses, such as the [Unified Medical Language System
(UMLS)](https://www.nlm.nih.gov/research/umls/), and as such, the
queries within ROMOP heavily rely on these vocabularies.
[Athena](http://athena.ohdsi.org/) is a great tool to better understand
the concepts in these ontologies and identify ideal search terms of
interest.

![Features of
ROMOP](www/figure1a_v3.png)

Manuscript information:  
Glicksberg BS, Oskotsky B, Giangreco N, Thangaraj PM, Rudrapatna V, Datta D, Frazier R, Lee N, Larsen R, Tatonetti NP, Butte AJ. ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data. JAMIA open. 2019 Apr;2(1):10-4.

## Sandbox Server

The Centers for Medicare and Medicaid Services (CMS) have released a
synthetic clinical dataset
[DE-SynPUF](https://www.cms.gov/Research-Statistics-Data-and-Systems/Downloadable-Public-Use-Files/SynPUFs/DE_Syn_PUF.html))
in the public domain with the aim of being reflective of the patient
population but containing no protected health information. The OHDSI
group has underwent the task of converting these data into the [OMOP CDM
format](https://github.com/OHDSI/ETL-CMS). Users are certainly able to
set up this configuration on their own system following the instructions
on the GitHub page. We obtained all data files from the [OHDSI FTP
server](ftp://ftp.ohdsi.org/synpuf) (accessed June 17th, 2018) and
created the CDM (DDL and indexes) according to their [official
instructions](https://github.com/OHDSI/CommonDataModel/tree/master/PostgreSQL),
but modified for MySQL. For space considerations, we only uploaded one
million rows of each of the data files. The sandbox server is a Rshiny
server running as an Elastic Compute Cloud (EC2) instance on Amazon Web
Services (AWS) querying a MySQL database server (AWS Aurora MySQL).

## Requirements

#### Clinical Data

ROMOP requires EHR data to be in OMOP format and on a server accessible
to by the user. In it’s current form, ROMOP can connect to databases in
*MySQL* using the RMySQL driver or many other formats, including
*Oracle*, *PostgreSQL*, *Microsoft SQL Server*, *Amazon Redshift*,
*Google BigQuery*, and *Microsoft Parallel Data Warehouse*, through
utilization of the DatabaseConnector and SqlRender packages developed by
the OHDSI group (see below).

Users without access to EHR data might consider using synthetic public
data following the instructions provided by the OHDSI group
[here](https://github.com/OHDSI/ETL-CMS).

#### Programming Language

ROMOP is built in the R environment and developed on version 3.4.4
(2018-03-15).

ROMOP requires the following R packages:

- [DBI](https://cran.r-project.org/web/packages/DBI/index.html)
    (developed on version
    1.0.0)
  - [data.table](https://cran.r-project.org/web/packages/data.table/data.table.pdf)
    (developed on version 1.10.4-3).
  - [dplyr](https://dplyr.tidyverse.org/) (developed on version 0.7.4).

Driver-specific:

- [RMySQL](https://cran.r-project.org/web/packages/RMySQL/index.html)
    (developed on version
    0.10.14).
  - [DatabaseConnector](https://cran.r-project.org/web/packages/DatabaseConnector/index.html)
    (developed on version
    2.2.0)
  - [DatabaseConnectorJars](https://cran.r-project.org/web/packages/DatabaseConnectorJars/index.html)
    (developed on version
    1.0.0)
  - [SqlRender](https://cran.r-project.org/web/packages/SqlRender/index.html)
    (developed on version 1.5.2)

## Installation

### Download

ROMOP can be installed easily from github using the
[devtools](https://cran.r-project.org/web/packages/devtools/index.html)
package:

library(devtools)
    install_github("BenGlicksberg/ROMOP")

Alternatively, the package can be downloaded directly from the [github
page](https://github.com/BenGlicksberg/ROMOP) and installed by the
following steps:

1.  Unzip ROMOP-master.zip
2.  R CMD INSTALL ROMOP-master

Please see the [Setup](#setup) section to properly configure the package
to work.

### Setup

#### Credentials

In accordance with best practices for storing sensitive information,
credentials are not saved in plain text but in the .Renviron file. A
formatted .Renviron file is provided with the package with the following
fields to fill in:

``` 
driver = ""
host = ""
username = ""
password = ""
dbname = ""
port = "3306" 
```

- driver (case insensitive): “mysql” for MySQL or (according to [OHDSI
    DatabaseConnector
    package](https://github.com/OHDSI/DatabaseConnector)) “postgresql”
    for PostgreSQL, “oracle” for Oracle, “sql server” for Microsoft SQL
    Server, “redshift” for Amazon Redshift, “pdw” for Microsoft Parallel
    Data Warehouse, or “bigquery” for Google BigQuery.  
  - host (or server depending on database format)  
  - dbname: OMOP EHR database name (or schema depending on database
    format)

Note that this .Renviron file has to be in the same directory where R is
launched. If already using an .Renviron file, add this information to
it.

#### Checks

With credentials correctly configured, the package can be loaded. ROMOP
will now check for 3 conditions to be met:

1.  Check that the credentials exist and can be retrieved from .Renviron
    file:  
    *requires driver, host, username, password, dbname, and port exist*

2.  Check that connection to OMOP EHR server and database can be made:  
    *uses the above credentails*

3.  Check to ensure all required OMOP tables exist and contain (any)
    data:  
    *the required tables
    are:*

"concept","concept_ancestor","concept_relationship","condition_occurrence","death",
    "device_exposure","drug_exposure","measurement","observation","person","procedure_occurrence","visit_occurrence"

- if any of the above tables are missing, a warning message will be
    produced and the package will not be able to load properly.
  - if any of the above tables exist, but do not contain any data, a
    warning message will be produced but the package will still be able
    to function.

#### On start

Successfully pasing all checks will allow the user to begin using ROMOP.

1.  Set an output directory to use with the
    [changeOutDirectory](#changeoutdirectory) function (note: the
    default output directory will be declared on package load).  
2.  Create/load the Data ontology (required to decode data types) using
    the [makeDataOntology](#makedataontology). For the first time
    running this package, the concept ontology will have to first be
    built, but if the store\_ontology option is selected, the ontology
    will be saved as an .rds file for subsequent loading.

## Functions

### Utility

#### getDemographics

*Description*:  Retrieves and formats patient demographic data from the
**person** and **death** tables. Option to restrict to patientlist of
interest.

*Usage*:  ptDemo \<- getDemographics(patient\_list=NULL,declare=TRUE)

*Arguments*:

patient\_list         *comma-separated string of patient ids*  
         a provdied patientlist will restrict search to ids. NULL will
return demographic data for all available patients

declare         *TRUE/FALSE*  
         if TRUE, outputs status and updates to the screen

*Value*:

Returns a data.table with demographic data: person\_id,
birth\_datetime, age, Gender, Race, Ethnicity, death\_date, Status
(Alive/Deceased)

*Details*:

- patient\_list should be in the following format: “patient\_id\_1,
    patient\_id\_2, …”

#### getEncounters

*Description*:  Retrieves and formats patient encounter data from the
**visit\_occurrence** table. Requires patientlist input.

*Usage*:  ptEncs \<- getEncounters(patient\_list,declare=TRUE)

*Arguments*:

patient\_list         *comma-separated string of patient ids*  
         searches for all encounter data for the patientlist inout.

declare         *TRUE/FALSE*  
         if TRUE, outputs status and updates to the screen

*Value*:

Returns a data.table with encounter data: person\_id,
visit\_occurrence\_id, visit\_start\_datetime, visit\_end\_datetime,
visit\_source\_value, visit\_concept, visit\_source\_concept,
admitting\_concept, discharge\_concept

*Details*:

- patient\_list should be in the following format: “patient\_id\_1,
    patient\_id\_2, …”

#### getClinicalData

*Description*:  Retrieves all relevant clinical data for individuals in
a patientlist. Wrapper for domain-specific getData functions (which can
also be used separately).

*Usage*:  ptClinicalData \<- getClinicalData(patient\_list,
declare=TRUE)

*Arguments*:

declare         *TRUE/FALSE*  
         if TRUE, outputs status and updates to the screen

*Value*:  
  Returns a list of data.tables stratified by domain type (e.g.,
ptClinicalData$Condition, ptClinicalData$Observation, etc…)

*Details*:

- patient\_list should be in the following format: “patient\_id\_1,
    patient\_id\_2, …”  
  - getClinicalData calls domain-specific getData functions for the
    following domains: Observation, Condition, Procedure, Medication
    (Drug), Measurement, and Device. Each function can also be run
    individually (e.g, getConditions; getMedications).  
  - In addition to datetimes, visit\_occurrence\_ids,
    <domain>\_concept\_ids and <domain>\_source\_concept\_ids, other
    domain-specific concepts and values are retrieved and mapped:
      - Observation: observation\_type\_concept, value\_as\_number,
        value\_as\_string, value\_as\_concept, unit\_source\_value  
      - Condition: condition\_type\_concept, condition\_status  
      - Procedure: procedure\_type\_concept, quantity,  
      - Medication: drug\_type\_concept, stop\_reason, refills,
        quantity, days\_supply, sig, route\_concept,
        effective\_drug\_dose, dose\_unit\_concept,
        route\_source\_value, frequency, frequency\_unit,
        rx\_quantity\_unit\_source\_value  
      - Measurement: measurement\_type\_concept, value\_as\_number,
        value\_as\_concept, unit\_concept
      - Device: device\_type\_concept

#### findPatients

*Description*:  Main function to identify patients based on clinical
data inclusion (and exclusion, if desired) criteria. Flexible to allow
for multiple data types, vocabularies, and concepts.

*Usage*:   patientlist \<- findPatients(strategy\_in=“mapped”,
vocabulary\_in, codes\_in, function\_in = “or”, strategy\_out = NULL,
vocabulary\_out = NULL, codes\_out = NULL, function\_out = NULL,
declare=FALSE, save=FALSE, out\_name=NULL)

*Arguments*:

strategy\_in         *mapped* or *direct*  
         dictates the strategy for how inclusion criteria are treated
(see Details).

vocabulary\_in         *vocabularies for inclusion criteria*  
         comma-separated string of relevant vocabularies for inclusion
criteria (see Details).

codes\_in         *specific concept codes for inclusion criteria*  
         semi-colon separated string of code concepts for inclusion
criteria, corresponding to the order for vocabulary\_in. Multiple codes
can be used per vocabulary and should be comma-separated (see Details).

function\_in         *and* or *or*  
         dictates how multiple inclusion should be treated. *and*
necessitates that all inclusion criteria are met (i.e., intersection),
while *or* allows for any critera to be met (i.e., union) (see Details).

strategy\_out         *mapped* or *direct* or NULL (default)  
         dictates the strategy for how exclusion are treated. NULL
indicates no exclusion criteria.

vocabulary\_out         *vocabularies for exclusion criteria* or NULL
(default)  
         comma-separated string of relevant vocabularies for exclusion
criteria. NULL indicates no exclusion criteria.

codes\_out         *specific concept codes for exclusion criteria* or
NULL (default)  
         semi-colon separated string of code concepts for inclusion
criteria, corresponding to the order for vocabulary\_out. Multiple codes
can be used per vocabulary and should be comma-separated. NULL indicates
no exclusion criteria.

function\_out         *and* or *or* or NULL  
         dictates how multiple exclusion should be treated. *and*
necessitates that all exclusion criteria are met (i.e., intersection),
while *or* allows for any critera to be met (i.e., union). NULL
indicates no exclusion criteria.

declare         *TRUE/FALSE*  
         if TRUE, outputs status and updates to the screen.

save         *TRUE/FALSE*  
         if TRUE, various query output saved to outDirectory (see
Details).

out\_name         *name assigned to search query* or NULL  
         if save == TRUE, saves query using provided name. If the
provided name already exists as a directory (or is NULL), the directory
defaults to datetime name (see Details).

*Value*:  
  Returns a list of patients that meet inclusion criteria (and not
exclusion criteria if entered).

*Details*:

- *direct* strategy queries the concepts directly by \_source\_concept
    in clinical tables. *mapped* maps to common ontology (via
    **concept\_synonym**) and identifies relevant descendants (via
    **concept\_ancestor**) to search for in \_concept fields.
  - the [exploreConcepts](#exploreconcepts) function can be used to find
    ideal concepts to search for.  
  - vocabulary\_ input for multiple inputs should use relevant
    vocabularies (see [showDataTypes](#showdatatypes) ) as a
    comma-separated string, e.g., “ATC, ICD10CM, SNOMED”.
  - codes\_ input correspond to the order as the vocabulary\_ input and
    should be semi-comma separated string in the same order as above.
    Multiple terms per vocabulary type should be comma-separated. e.g.,
    “A01A; K50, K51; 235599003” correspond to “A01A” for ATC, “K50”
    and “K51” for ICD10CM, and “235599003” for SNOMED.  
  - function\_ corresponds to how criteria should be treated. *and*
    necessitates patients meet all criteria while *or* allows for
    patients to meet any of the criteria.
  - Please note that if no standard common concepts are found per search
    domain, a warning message will appear and the search will not be
    able to be performed (see [Helpful Hints](#helpful-hints) for more
    details.)
  - if save == TRUE, the following information is saved in a directory
    per query:
      - query: all arguments for the search.
      - \_criteria\_mapped: all original criteria for inclusion (and
        exclusion if applicable) that are mapped to dataOntology.
      - criteria\_mapped\_concepts: all mapped concepts used for
        inclusion (and exclusion if applicable) that are used to search
        in clinical data tables. Additionally, the pt\_count column
        displays the number of unique patients that have a record with
        the corresponding concept.  
      - outcome: results of the search (most relevant when exclusion
        criteria are applied).  
      - patient\_list: list of patients that meet inclusion (and not
        exclusion, if applicable) criteria.

### Misc.

#### changeOutDirectory

*Description*:   Sets the current outDirectory which will store the Data
Ontology and all function output. Option to create directory if does not
exist.

*Usage*:  changeOutDirectory(outdir=“path/to/directory”, create=FALSE)

*Arguments*:  
  outdir         directory path

create         *TRUE/FALSE*  
         will create the directory if it does not exist

*Value*:  
   Nothing returned; simply sets (and creates if set to) output
directory

*Details*:

- If directory does not exist and create=FALSE, a warning message will
    appear and the output directory will not be changed.

#### makeDataOntology

*Description*:  Creates general Data Ontology used by all data tables
from the **concept** table. Option to save/load.

*Usage*:  dataOntology \<-
makeDataOntology(declare=TRUE,store\_ontology=FALSE)

*Arguments*:  
  declare         *TRUE/FALSE*  
         if TRUE, outputs status and updates to the screen

store\_ontology         *TRUE/FALSE*  
         if TRUE, will save/load the ontology instead of active querying

*Value*:  
  Returns a data.table with concept data.

*Details*:

- Generating the Data Ontology takes ~31.2 secs and is ~491.6 Mb.  
  - If declare == TRUE, the following information will be returned:

Retrieving concept data...
    Concept data loaded; data found for: 
    ## unique domains.
    ## unique vocabularies.
    ### unique concept classes.

- If store\_ontology == TRUE, attempts to load from memory (in the
    outDirectory) and saves if does not exist (~53 Mb). Loading takes ~8
    secs.

#### summarizeDemographics

*Description*:  Summarizes patient demographic data from the
[getDemographics](#getdemographics) function.

*Usage*:  summarizeDemographics(ptDemo)

*Arguments*:

ptDemo         *patient demographics table*  
         ptDemo is the patient demographics object from the
getDemographics function output

*Value*:

N/A; outputs message with descriptive summary statistics for the
relevant patient demographic data.

#### showDataTypes

*Description*:  Details relevant vocabularies per domain. Requires
dataOntology to have been created (via
[makeDataOntology](#makedataontology)).

*Usage*:  showDataTypes()

*Arguments*:

N/A

*Value*:

Returns a table of vocabularies contained within clinical domains:
Condition, Observation, Measurement, Device, Procedure, Drug.

#### exploreConcepts

*Description*:  For given vocabulary and concept, returns the mapped
standard concept(s) as well as decendent concept(s)

*Usage*:  conceptsInfo \<- exploreConcepts(vocabulary, codes)

*Arguments*:

vocabulary         *vocabulary*  
         comma-separated string of relevant vocabularies for inclusion
criteria (see Details).

codes         *concept codes*  
         semi-colon separated string of code concepts for inclusion
criteria, corresponding to the order for vocabulary. Multiple codes can
be used per vocabulary and should be comma-separated (see Details).

*Value*:

Returns a table of concepts contained under (i.e., below in the
heirarchy) the query concept.

*Details*:

- vocabulary input for multiple inputs should use relevant
    vocabularies (see [showDataTypes](#showdatatypes) ) as a
    comma-separated string, e.g., “ATC, ICD10CM”.
  - codes input correspond to the order as the vocabulary input and
    should be semi-comma separated string in the same order as above.
    Multiple terms per vocabulary type should be comma-separated. e.g.,
    “A01A; K50, K51” correspond to “A01A” for ATC and “K50” and “K51”
    for ICD10CM.

## Examples

Both simple and advanced [findPatients](#findpatients) queries will be
outlined. See the [Output](#output) section for description of output if
save == TRUE. For the process timing provided, all queries were run on
an Amazon Elastic Compute Cloud (EC2) instance.

### Simple

1.  Disease category (ICD10CM): find all “Type 2 Diabetes Mellitus”
    patients (E11)

Here we will set a single inclusion criterion. The inclusion vocbulary
is set to *ICD10CM* and the inclusion code is *E11* corresponding to the
vocabulary. Because the inclusion strategy is set as “mapped”, ROMOP
will map the ICD10CM code to a common ontology (SNOMED) term and find
all descendants to search for (see [Code Breakdown](#code-breakdown) for
details on how this
works).

*query*

``` 
patient_list = findPatients(strategy_in="mapped", vocabulary_in = "ICD10CM", codes_in = "E11")  
```

*time*: 15.3 secs

2.  Specific disease (ICD9CM): find all patients with “Diabetes with
    ketoacidosis, type I \[juvenile type\], not stated as uncontrolled”
    **only** (250.11)

Here we will search for patients that have the specific *ICD9CM* code
*250.11* **only**, i.e., not map to common ontology (see [Code
Breakdown](#code-breakdown) for the importance of this
distiction).

*query*

``` 
patient_list = findPatients(strategy_in="direct", vocabulary_in = "ICD9CM", codes_in = "250.11")  
```

*time*: 1.1 min

3.  Multiple diseases (ICD10CM): find all patients with “Essential
    (primary) hypertension” (I10) **and** “Angina pectoris with
    documented spasm” (I20.1)

Here we will search for patients that have the multiple ICD10CM codes.
While we put a single inclusion vocabulary, we will put two inclusion
codes separated by a comma. Also we set the inclusion function to “and”
which requires **both** criteria to be
met.

*query*

``` 
patient_list = findPatients(strategy_in="mapped", vocabulary_in = "ICD10CM", codes_in = "I10, I20.1", function_in = "and")  
```

*time*: 23.8 secs

4.  Drug class (ATC): find all patients prescribed with any “Serotonin
    receptor antagonists” (A03AE)

Here we will search for patients by drug ATC code. As the inclusion
strategy is set to “mapped”, all drugs that fall into this category will
automatically be identified and searched for (see [Code
Breakdown](#code-breakdown) for details on how this
works).

*query*

``` 
patient_list = findPatients(strategy_in="mapped", vocabulary_in = "ATC", codes_in = "A03AE")  
```

*time*: 1.1 secs

5.  Disease category (ICD10CM) but not Drug (MeSH): find all patients
    with “Other anxiety disorders” (F31), but *not* prescribed with
    “Clonazepam” (D002998)

Here we will search for patients by ICD10CM code as before. We also
identify all patients prescribed with the MeSH term for “Clonazepam”,
which will be removed from the original
list.

*query*

``` 
patient_list = findPatients(strategy_in="mapped", vocabulary_in = "ICD10CM", codes_in = "F41", strategy_out="mapped", vocabulary_out = "MeSH", codes_out = "D002998", function_out = "and")  
```

*time*: 16.5 secs

### Advanced

1.  Multiple disease categories (ICD10CM) and lab test (LOINC) but not
    multiple disease categories (ICD10CM) nor drug class (RxNorm): find
    all patients with “Crohn’s disease” (F31) and “Malignant neoplasm of
    prostate” (C61) with “CBC W Auto Differential panel - Blood”
    (57021-8), but *not* “Gastroenteritis and colitis due to radiation”
    (K52.0) nor “Allergic and dietetic gastroenteritis and colitis”
    (K52.2) nor prescribed with any “Aminosalicylate” (113374)

Here we will search for patients by ICD10CM code as before. We also
identify all patients prescribed with the MeSH term for “Clonazepam”,
which will be removed from the original list.

*query*

``` 
vocabulary_in = "ICD10CM, LOINC"
codes_in = "K50;C61, 57021-8" 
vocabulary_out = "ICD10CM, RxNorm"
codes_out = "K52.0; K52.2,  113374"

patient_list = findPatients(strategy_in="mapped", vocabulary_in = vocabulary_in, codes_in = codes_in, function_in = "and", strategy_out="mapped", vocabulary_out = vocabulary_out, codes_out = codes_out, function_out = "or")  
```

*time*: 5.9 mins

## Output

All output is saved in the output directory (use
[changeOutDirectory](#changeoutdirectory) to set). Additionally, the
data ontology file will be loaded from here and saved if set to using
the makeDataOntology\](\#makedataontology) function.

If save==TRUE is selected for [findPatients](#findPatients) queries,
various information will be saved in a created query-specific directory
within the outDirectory:  
\+ query: all arguments for the search. + \_criteria\_mapped: all
original criteria for inclusion (and exclusion if applicable) that are
mapped to dataOntology. + criteria\_mapped\_concepts: all mapped
concepts used for inclusion (and exclusion if applicable) that are used
to search in clinical data tables. Additionally, the pt\_count column
displays the number of unique patients that have a record with the
corresponding concept.  
\+ outcome: results of the search (most relevant when exclusion criteria
are applied).  
\+ patient\_list: list of patients that meet inclusion (and not
exclusion, if applicable) criteria.

We will detail the respective output files that are derived from Simple
[Examples](#examples) \#5:

### query.txt

cat query.txt

inclusion strategy: mapped
    inclusion vocabularies: ICD10CM
    inclusion codes: F41
    inclusion function: or
    exclusion strategy: mapped
    exclusion vocabularies: MeSH
    exclusion codes: D002998
    exclusion function: and

### inclusion\_criteria\_mapped.txt

``` 
 cat inclusion_criteria_mapped.txt
```

codes   vocabularies    concept_id  concept_name    domain_id   vocabulary_id   concept_class_id
    F41 ICD10CM 1568230 Other anxiety disorders Condition   ICD10CM 3-char nonbill code

### inclusion\_criteria\_mapped\_concepts.txt

``` 
 head inclusion_criteria_mapped_concepts.txt
```

descendant_concept_id   ancestor_concept_id concept_name    domain_id   vocabulary_id   concept_class_id    concept_code    pt_count
    381537  442077  Organic anxiety disorder    Condition   SNOMED  Clinical Finding    17496003    NA
    432600  442077  Stress reaction causing mixed disturbance of emotion and conduct    Condition   SNOMED  Clinical Finding    192044009   NA
    433178  442077  Anxiety disorder of childhood OR adolescence    Condition   SNOMED  Clinical Finding    109006  NA
    434613  442077  Generalized anxiety disorder    Condition   SNOMED  Clinical Finding    21897009    NA
    434628  442077  Separation anxiety  Condition   SNOMED  Clinical Finding    126943008   NA
    436074  442077  Panic disorder  Condition   SNOMED  Clinical Finding    371631005   NA
    436390  442077  Psychogenic rumination  Condition   SNOMED  Clinical Finding    192014006   NA
    436676  442077  Posttraumatic stress disorder   Condition   SNOMED  Clinical Finding    47505003    NA
    437537  442077  Shyness disorder of childhood   Condition   SNOMED  Clinical Finding    83253003    NA

### exclusion\_criteria\_mapped.txt

``` 
 cat exclusion_criteria_mapped.txt
```

codes   vocabularies    concept_id  concept_name    domain_id   vocabulary_id   concept_class_id
    D002998 MeSH    45612901    Clonazepam  Drug    MeSH    Main Heading

### exclusion\_criteria\_mapped\_concepts.txt

``` 
 head exclusion_criteria_mapped_concepts.txt
```

descendant_concept_id   ancestor_concept_id concept_name    domain_id   vocabulary_id   concept_class_id    concept_code    pt_count
    798874  798874  Clonazepam  Drug    RxNorm  Ingredient  2598    NA
    798875  798874  Clonazepam 0.5 MG Oral Tablet   Drug    RxNorm  Clinical Drug   197527  NA
    798876  798874  Clonazepam 1 MG Oral Tablet Drug    RxNorm  Clinical Drug   197528  NA
    798877  798874  Clonazepam 2 MG Oral Tablet Drug    RxNorm  Clinical Drug   197529  NA
    798893  798874  Clonazepam 0.125 MG Oral Tablet [Klonopin]  Drug    RxNorm  Branded Drug    211761  NA
    798894  798874  Clonazepam 0.25 MG Oral Tablet [Klonopin]   Drug    RxNorm  Branded Drug    211762  NA
    798896  798874  Clonazepam 1 MG/ML Injectable Solution  Drug    RxNorm  Clinical Drug   249943  NA
    798897  798874  Clonazepam 0.5 MG   Drug    RxNorm  Clinical Drug Comp  315699  NA
    798899  798874  Clonazepam 2 MG Drug    RxNorm  Clinical Drug Comp  317336  NA

### outcome.txt

``` 
 cat outcome.txt
```

# patients found from the inclusion criteria ONLY.
    # patients found from the exclusion criteria ONLY.
    # overlapping patients excluded from the original inclusion input based on the exclusion criteria.
    # patients found that meet the inclusion and exclusion criteria.

### patient\_list.txt

``` 
 head patient_list.txt 
```

patient_list
    1
    2
    3

## Code Breakdown

![Workflow of ROMOP
functionality](www/figure1b_v3.png)

ROMOP first requires the creation a data dictionary (using
[makeDataOntology](#makedataontology) function) of the ontology (from
*concept* table) that is referenced and utilized to map to all concepts
for all functions. Using this ontology, all searches and extractions are
optimized to only query tables in which the data could be found.

### Data Retrieval

The majority of data in clinical tables are stored as concepts. When
data is extracted, ROMOP first maps the relevant concepts (e.g.,
device\_type\_concept\_id) to the data dictionary and then returns the
mapped concepts to the user.

### Searching

In the OMOP data structure, there is a distinction between how concepts
are recorded and what can be directly searched for. For instance, if the
user is interested in the medication idelalisib, it is not possible to
directly identify records by searching for the general concept (e.g.,
RxNorm code 1544460) as the data are recorded by the bottom-most (i.e.,
most specific) concepts of the hierarchy (e.g., idelalisib 150 MG
Delayed Release Oral Tablet). The hierarchical structure of these
concepts in the OMOP CDM back-end, however, facilitates more powerful
searches. In most extracted EHR systems, the user has to define all
medications to search, for instance through a pre-populated list or by
wildcard string matching (e.g., all drug names LIKE “%statin%”). This
strategy is ultimately not ideal as it is not extensible to other
systems (e.g., one system might prescribe a version or formulation of a
drug that is in not in another) and requires extensive manual
quality-control (e.g., removing “nystatin” drugs from the string
matching results). For the [findPatients](#findpatients) function, if
the “mapped” option is selected, searching for a broad code like ATC
level 3 code A05A (bile therapies), or even a specific term code like
RxNorm code 1544460 for idelalisib, will automatically identify and
query for all bottom-level (e.g., idelalisib 150 MG Delayed Release Oral
Tablet) codes contained underneath that seed concept. This works by
ROMOP first mapping the initial search criteria to a standard concept
(SNOMED or RxNorm) and finding all descendants underneath it. Another
benefit to this “mapped” option is that terms are not reliant on how the
data were originally entered. For instance, if a health system switches
from ICD-9CM to ICD-10CM coding, there might be discrepancies in
prevalence of codes over time. Mapping to a common concept, however,
often alleviates this issue as codes from both vocabularies are
typically linked to a common code in the standard vocabulary. Of course
the user can search for the concepts they entered only using the
“direct” option (i.e., search for ICD-9CM code 230.0 only).

## Helpful Hints

- We recommend using the *mapped* argument for the
    [findPatients](#findpatients) function because the concepts will not
    depend on by which format the data was entered (i.e., the
    *source\_concept*). This is important as diffierent institutions may
    utilize different underlying terminologies, as well as switch
    primary data entry vocabularies over time (i.e., the switch from
    ICD-9 to ICD-10). For example, if the user is interested in
    “Trigeminal neuralgia”, using the ICD-10 code “G50.1” with the
    *direct* argument, all prior entries that utilized the corresponding
    ICD-9 code (“350.1”) most likely will not be found as many data
    warehouses do not “back-map” codes. Using the *mapped* argument will
    bypass this issue as the standard concept will be used which should
    capture both options.
  - Standard vocabularies: while the OMOP common data model utilizes
    many ontologies, **SNOMED** and **RxNorm** are used primarily for
    common concepts in the clincal data tables. As such, while any
    vocabulary can be used for [findPatients](#findpatients), the
    *mapped* function will only be able to find data contained within
    the following common concepts per domain:

##   domain_type                concepts
    ## 1 Measurement       LOINC,SNOMED,CPT4
    ## 2   Condition                  SNOMED
    ## 3        Drug         RxNorm,CPT4,NDC
    ## 4 Observation SNOMED,CPT4,LOINC,HCPCS
    ## 5      Device            SNOMED,HCPCS
    ## 6   Procedure       SNOMED,CPT4,HCPCS

Consequently, if inclusion/exclusion criteria can be be mapped to the
data ontology, but no synonym/descendants are contained within the above
common concepts, no search will be performed (as no patients would be
returned). This most directly affects searching for *Drug* concepts, in
which we reccommend not using standard common concepts (e.g., RxNorm,
ATC) for search criteria.

- To ensure complete capture of data concepts of interest, we
    recommend identifying multiple vocabulary/codes to use using the
    [Athena](http://athena.ohdsi.org/search-terms/terms) resource. For
    instance, if interested in finding all individuals taking a
    Benzodiazepine, consider using both the relevant ATC classes (e.g.,
    N03AE) as well as the relevant Substance (SNOMED) codes (e.g.,
    16047007). The [exploreConcepts](#exploreconcepts) function can be
    used to identify and prioiritize which codes are optimal to use.

## License

MIT License

Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the
“Software”), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:

The above copyright notice and this permission notice shall be included
in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

## Contact

For questions, comments, errors, bug reports, or issues, please contact:
<benjamin.glicksberg@ucsf.edu>  
For general correspondance, please contact: <atul.butte@ucsf.edu>

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