sider — SIDER drug side effects and indications (2015)

Description

Bipartite networks of marketed drugs and their side effects (adverse drug reactions) and indications, from the Side Effect Resource SIDER, version 4.1 (released on October 21, 2015), by the Bork group at EMBL. SIDER is compiled from public documents of drug labels (package inserts), mostly from the FDA, the EMA and other sources: the side effects and indications mentioned in the labels were extracted by text mining, mapped to medical concepts of the UMLS (Unified Medical Language System) and to terms of the MedDRA dictionary of adverse event terms, and the labels were mapped to the drugs' compound identifiers of STITCH (derived from PubChem compound identifiers) through the drug names they mention. Each network has two kinds of nodes: drugs (1,430 to 1,437 compounds, identified by their "flat" STITCH ids, i.e. ignoring stereochemistry) and medical concepts (side effects or indications), identified by their UMLS concept ids.

For each concept found on a label, SIDER gives its MedDRA term as the "lowest level term" (LLT) and, additionally, each "preferred term" (PT) that it maps to (the PT may be the same concept as the LLT); in a few cases the concept is neither (e.g. a system organ class), and then the concept found on the label is used as the node. Each row of the SIDER files is an edge, from the drug to the MedDRA concept, so that a drug is usually joined to the same concept by several edges (as LLT and as PT, for several concepts found on its labels, for several stereoisomers, from several labels, or with several frequencies), and the networks are multigraphs. The networks are:

side_effects: the side effects of each drug, collected from all its labels (meddra_all_se).
side_effect_frequencies: the frequencies of side effects given on the labels, for the subset of side effects for which the labels give them, e.g. from clinical trials (meddra_freq); a side effect can have several frequencies, e.g. from different trials, for different levels of severity, or with placebo administration.
indications: the indications of each drug, collected from all its labels (meddra_all_indications).
label_side_effects and label_indications: the same as side_effects and indications, but with an edge for each label on which the side effect or the indication was found (meddra_all_label_se and meddra_all_label_indications).

SIDER contains errors due to the automatic text mining (a list of known errors is maintained on GitHub, mkuhn/sider, and is not applied here). Earlier versions of SIDER (1, 2 and 4.0) are no longer available for download. The SIDER side effects of the drugs approved in 2016 are also part of the entry hetionet.

The networks have the following properties:

(Node) is_drug: whether the node is a drug (otherwise it is a medical concept).
(Node) name: the name of the drug (generated automatically by SIDER; empty for the few drugs of the indication files that are missing from its list of names) or of the concept (its MedDRA term).
(Node) id: the flat STITCH compound id of the drug (e.g. CID100000085) or the UMLS concept id (e.g. C0000737).
(Node) pubchem_cid: the PubChem compound id of the drug (-1 for concepts).
(Node) atc: the ATC codes of the drug.
(Node) meddra_ids: the MedDRA codes of the concept (from the MedDRA file of SIDER).
(Edge) meddra_type: the kind of MedDRA term of the concept: LLT (lowest level term), PT (preferred term), or empty if it is neither.
(Edge) label_concept: the UMLS concept id as found on the label (which the MedDRA term maps to).
(Edge) stereo_id (side_effects, side_effect_frequencies and label_side_effects): the STITCH compound id with stereochemistry of the drug on the label.
(Edge) placebo (side_effect_frequencies): whether the frequency is for placebo administration.
(Edge) frequency (side_effect_frequencies): the frequency as given on the label (e.g. 21%, rare, postmarketing).
(Edge) frequency_lower, frequency_upper (side_effect_frequencies): lower and upper bounds of the frequency, as fractions.
(Edge) method (indications and label_indications): the method of detection (NLP_indication, NLP_precondition or text_mention).
(Edge) label_concept_name (indications and label_indications): the name of the concept as found on the label.
(Edge) label (label_side_effects and label_indications): the label (source document) on which it was found (e.g. EMA/WC500020092.html).

Tags

Biological Drug interactions Unweighted Multigraph Metadata

Added

2026-10-27

Citation

M. Kuhn, I. Letunic, L. J. Jensen, P. Bork, "The SIDER database of drugs and side effects." Nucleic Acids Research 44, D1075-D1079 (2016) 10.1093/nar/gkv1075 Sci-Hub
M. Kuhn, M. Campillos, I. Letunic, L. J. Jensen, P. Bork, "A side effect resource to capture phenotypic effects of drugs." Molecular Systems Biology 6, 343 (2010) 10.1038/msb.2009.98 Sci-Hub

Upstream URL OK

https://sideeffects.embl.de/download/

Upstream license

Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0); drug names and ATC codes CC0, https://creativecommons.org/licenses/by-sa/4.0/

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
side_effects	7,553	309,849	82.05	198.09	225.99	3.92	-0.20	7	1.00	Undirected	Bipartite	is_drug name id pubchem_cid atc meddra_ids	meddra_type label_concept stereo_id	677 KiB	1.8 MiB	1.7 MiB	1.7 MiB
side_effect_frequencies	4,932	291,632	118.26	391.88	134.47	8.97	-0.11	7	1.00	Undirected	Bipartite	is_drug name id pubchem_cid atc meddra_ids	meddra_type label_concept stereo_id placebo frequency frequency_lower frequency_upper	889 KiB	2.2 MiB	2.1 MiB	1.7 MiB
indications	4,491	30,835	13.73	25.23	32.30	14.53	-0.11	12	1.00	Undirected	Bipartite	is_drug name id pubchem_cid atc meddra_ids	meddra_type label_concept method label_concept_name	275 KiB	391 KiB	385 KiB	447 KiB
label_side_effects	7,553	4,753,141	1258.61	5402.39	225.99	3.92	-0.19	7	1.00	Undirected	Bipartite	is_drug name id pubchem_cid atc meddra_ids	meddra_type label_concept stereo_id label	2.0 MiB	22.8 MiB	20.7 MiB	23.0 MiB
label_indications	4,487	447,150	199.31	717.42	32.27	28.56	-0.18	12	1.00	Undirected	Bipartite	is_drug name id pubchem_cid atc meddra_ids	meddra_type label_concept stereo_id method label_concept_name label	1.1 MiB	3.4 MiB	3.2 MiB	3.1 MiB

Ridiculograms^*

side_effect_frequencies drawing — side_effect_frequencies

label_side_effects drawing — label_side_effects

label_indications drawing — label_indications

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.