SIDER Reference Ingest Guide¶
Source Information¶
InfoRes ID: infores:sider
Description: SIDER contains information on marketed drugs and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The current version of the database contains data on 1,430 drugs and 5,868 adverse drug reactions.
Citations: - Kuhn M, Letunic I, Jensen LJ, Bork P. The SIDER database of drugs and side effects. Nucleic Acids Research. 2016;44(D1):D1075-9. DOI: 10.1093/nar/gkv1075
Data Access Locations: - http://sideeffects.embl.de/download/
Data Provision Mechanisms: file_download
Data Formats: tsv
Data Versioning and Releases: SIDER version 4.1 released in 2015. Updates are irregular and infrequent. Database maintenance is limited.
Additional Notes: It may not include the most recent drug approvals or complete adverse event profiles.
Ingest Information¶
Ingest Categories: primary_knowledge_provider
Utility: Provides drug-adverse drug reaction associations for pharmacovigilance, drug safety analysis, and adverse drug reaction prediction studies.
Scope: Covers marketed drugs and their documented adverse drug reactions as found in public documents and package inserts.
Relevant Files¶
| File Name | Location | Description |
|---|---|---|
| meddra_all_label_se.tsv.gz | http://sideeffects.embl.de/media/download/meddra_all_label_se.tsv.gz | Side effects specifically found on drug labels |
| drug_names.tsv | http://sideeffects.embl.de/media/download/drug_names.tsv | Drug identifiers and common names mapping STITCH IDs to drug names |
| meddra.tsv | http://sideeffects.embl.de/media/download/meddra.tsv | MedDRA terms and hierarchy information |
Included Content¶
| File Name | Included Records | Fields Used |
|---|---|---|
| meddra_all_label_se.tsv.gz | All records (~63,473 label-specific side effect associations) | STITCH_compound_id_flat, UMLS_concept_id_label, MedDRA_concept_type, UMLS_concept_id_MedDRA, side_effect_name |
Filtered Content¶
| File Name | Filtered Records | Rationale |
|---|---|---|
| meddra_all_label_se.tsv.gz | include only MedDRA_concept_type = PT (preferred term) | from http://sideeffects.embl.de/media/download/README: There is at least one PT for every LLT, but sometimes the PT is the same as the LLT. LLTs are sometimes too detailed, and therefore you might want to filter for PT." |
Target Information¶
Target InfoRes ID: infores:translator-sider-kgx
Edge Types¶
| Subject Categories | Predicate | Object Categories | Knowledge Level | Agent Type | UI Explanation |
|---|---|---|---|---|---|
| biolink:ChemicalEntity | biolink:has_side_effect | biolink:DiseaseOrPhenotypicFeature | knowledge_assertion | manual_agent | SIDER data report side effect information that is extracted from product labels, regulatory documents, and official package inserts - by an automated NLP-based pipeline tuned to parse text, recognize side-effect relationships between drug and condition concepts, and map them to vocabularies such as MedDRA. The SIDER record used here reports that [OBJECT] can have the side effect [SUBJECT]. This is represented in Translator using the [has_side_efect] relationship. |
Node Types¶
| Node Category | Source Identifier Types | Additional Notes |
|---|---|---|
| biolink:ChemicalEntity | PUBCHEM.COMPOUND | |
| biolink:DiseaseOrPhenotypicFeature | UMLS |
Future Modeling Considerations¶
edge_content: Some background exploration suggested that SIDER provides qualitative frequency info about side effects (e.g. terms like 'very common', 'uncommon'). This seems like useful info we should consider pulling in.
Provenance Information¶
Contributors: - Vlado Dancik - code author, domain expertise - Kevin Schaper - code support - Evan Morris - code support - Sierra Moxon - data modeling, code support - Matthew Brush - data modeling, domain expertise