antibiotics: Data Sets with 607 Antimicrobial Drugs

In msberends/AMR: Antimicrobial Resistance Data Analysis

Data Sets with 607 Antimicrobial Drugs

Description

Two data sets containing all antibiotics/antimycotics and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.

Usage

antibiotics

antivirals

Format

For the antibiotics data set: a tibble with 487 observations and 14 variables:

• ab
  Antibiotic ID as used in this package (such as AMC), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. This is a unique identifier.

• cid
  Compound ID as found in PubChem. This is a unique identifier.

• name
  Official name as used by WHONET/EARS-Net or the WHO. This is a unique identifier.

• group
  A short and concise group name, based on WHONET and WHOCC definitions

• atc
  ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like J01CR02

• atc_group1
  Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like "Macrolides, lincosamides and streptogramins"

• atc_group2
  Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like "Macrolides"

• abbr
  List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)

• synonyms
  Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID

• oral_ddd
  Defined Daily Dose (DDD), oral treatment, currently available for 179 drugs

• oral_units
  Units of oral_ddd

• iv_ddd
  Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 153 drugs

• iv_units
  Units of iv_ddd

• loinc
  All codes associated with the name of the antimicrobial drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use ab_loinc() to retrieve them quickly, see ab_property().

For the antivirals data set: a tibble with 120 observations and 11 variables:

• av
  Antiviral ID as used in this package (such as ACI), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. This is a unique identifier. Combinations are codes that contain a + to indicate this, such as ATA+COBI for atazanavir/cobicistat.

• name
  Official name as used by WHONET/EARS-Net or the WHO. This is a unique identifier.

• atc
  ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC

• cid
  Compound ID as found in PubChem. This is a unique identifier.

• atc_group
  Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC

• synonyms
  Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID

• oral_ddd
  Defined Daily Dose (DDD), oral treatment

• oral_units
  Units of oral_ddd

• iv_ddd
  Defined Daily Dose (DDD), parenteral treatment

• iv_units
  Units of iv_ddd

• loinc
  All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use av_loinc() to retrieve them quickly, see av_property().

An object of class tbl_df (inherits from tbl, data.frame) with 120 rows and 11 columns.

Details

Properties that are based on an ATC code are only available when an ATC is available. These properties are: atc_group1, atc_group2, oral_ddd, oral_units, iv_ddd and iv_units.

Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column cid) and consequently only available where a CID is available.

Direct download

Like all data sets in this package, these data sets are publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, and Stata. Please visit our website for the download links. The actual files are of course available on our GitHub repository.

WHOCC

This package contains all ~550 antibiotic, antimycotic and antiviral drugs and their Anatomical Therapeutic Chemical (ATC) codes, ATC groups and Defined Daily Dose (DDD) from the World Health Organization Collaborating Centre for Drug Statistics Methodology (WHOCC, https://atcddd.fhi.no) and the Pharmaceuticals Community Register of the European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm).

These have become the gold standard for international drug utilisation monitoring and research.

The WHOCC is located in Oslo at the Norwegian Institute of Public Health and funded by the Norwegian government. The European Commission is the executive of the European Union and promotes its general interest.

NOTE: The WHOCC copyright does not allow use for commercial purposes, unlike any other info from this package. See https://atcddd.fhi.no/copyright_disclaimer/.

Source

• World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): https://atcddd.fhi.no/atc_ddd_index/

• Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Accessed from https://loinc.org on October 19th, 2023.

• European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm

See Also

microorganisms, intrinsic_resistant

Examples

antibiotics
antivirals

msberends/AMR documentation built on March 5, 2025, 2:28 p.m.