Data sets with ~550 antimicrobials
antibiotics.RdTwo data sets containing all antibiotics/antimycotics and antivirals. Use as.ab or one of the ab_property 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.
antibiotics antivirals
Format
For the antibiotics data set: a data.frame with 452 observations and 13 variables:
abAntibiotic ID as used in this package (like
AMC), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where availableatcATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like
J01CR02cidCompound ID as found in PubChem
nameOfficial name as used by WHONET/EARS-Net or the WHO
groupA short and concise group name, based on WHONET and WHOCC definitions
atc_group1Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like
"Macrolides, lincosamides and streptogramins"atc_group2Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like
"Macrolides"abbrList of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)
synonymsSynonyms (often trade names) of a drug, as found in PubChem based on their compound ID
oral_dddDefined Daily Dose (DDD), oral treatment
oral_unitsUnits of
oral_dddiv_dddDefined Daily Dose (DDD), parenteral treatment
iv_unitsUnits of
iv_ddd
For the antivirals data set: a data.frame with 102 observations and 9 variables:
atcATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC
cidCompound ID as found in PubChem
nameOfficial name as used by WHONET/EARS-Net or the WHO
atc_groupOfficial pharmacological subgroup (3rd level ATC code) as defined by the WHOCC
synonymsSynonyms (often trade names) of a drug, as found in PubChem based on their compound ID
oral_dddDefined Daily Dose (DDD), oral treatment
oral_unitsUnits of
oral_dddiv_dddDefined Daily Dose (DDD), parenteral treatment
iv_unitsUnits of
iv_ddd
Source
World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (WHOCC): https://www.whocc.no/atc_ddd_index/
WHONET 2019 software: http://www.whonet.org/software.html
European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: http://ec.europa.eu/health/documents/community-register/html/atc.htm
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) are derived from the Compound ID (cid) and consequently only available where a CID is available.
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://www.whocc.no) and the Pharmaceuticals Community Register of the European Commission (http://ec.europa.eu/health/documents/community-register/html/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://www.whocc.no/copyright_disclaimer/.
Read more on our website!
On our website https://msberends.gitlab.io/AMR you can find a tutorial about how to conduct AMR analysis, the complete documentation of all functions (which reads a lot easier than here in R) and an example analysis using WHONET data.