The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) Reference Ingest Guide¶
Source Information¶
InfoRes ID: infores:gtopdb
Description: The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb; https://www.guidetopharmacology.org) is an open-access, expert-curated, online database that provides succinct overviews and key references for pharmacological targets and their recommended experimental ligands. It includes over 3039 protein targets and 12,163 ligand molecules, including approved drugs, small molecules, peptides and antibodies. GtoPdb) was established and developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). It originated from the IUPHAR-DB, a former resource focused on receptors and channels that was first compiled in 2003 and from the BPS‘ Guide to Receptors and Channels’, a compendium of a wider range of targets than those originally covered in IUPHAR-DB
Citations: - Harding SD, Armstrong JF, Faccenda E, Southan C, Alexander SPH, Davenport AP, Spedding M, Davies JA. (2023) The IUPHAR/BPS Guide to PHARMACOLOGY in 2024. Nucl. Acids Res. 2024; 52(D1):D1438-D1449. doi:10.1093/nar/gkad944. [Full text]. PMID: 37897341.
Data Access Locations: - gtoPdb Downloads: https://www.guidetopharmacology.org/download.jsp (this page includes file sizes and simple data dictionaries for each download)
Data Provision Mechanisms: file_download
Data Formats: csv
Data Versioning and Releases: Based on the FAQ section: Content expansion and feature enhancements are announced on the front page. Releases are approximately quarterly, designated as increments (e.g. 2024.4 in December 2024, 2024.3 in October 2023 etc.). The current database content for version 2025.3 released 10 September 2025. https://www.guidetopharmacology.org/databaseContent.jsp
Ingest Information¶
Ingest Categories: primary_knowledge_provider
Utility: The International Union of Basic and Clinical Pharmacology (IUPHAR) / British Pharmacological Society (BPS) Guide to PHARMACOLOGY is an expert-curated resource of ligand-activity-target relationships, the majority of which come from high-quality pharmacological and medicinal chemistry literature.
Scope: GtoPdb includes over 3039 protein targets and 12,163 ligand molecules, including approved drugs, small molecules, peptides and antibodies.
Relevant Files¶
| File Name | Location | Description |
|---|---|---|
| interactions.csv | https://www.guidetopharmacology.org/DATA/interactions.csv | all interaction data for ligands and targets |
| targets_and_families.csv | https://www.guidetopharmacology.org/DATA/targets_and_families.csv | complete target and family list |
| ligands.csv | https://www.guidetopharmacology.org/DATA/ligands.csv | complete ligand list |
| peptides.csv | https://www.guidetopharmacology.org/DATA/peptides.csv | complete peptide ligand list: |
| GtP_to_HGNC_mapping.csv | https://www.guidetopharmacology.org/DATA/GtP_to_HGNC_mapping.csv | mapping Guide to PHARMACOLOGY target and peptide ligand IDs and URLs to HGNC gene IDs and symbols |
Included Content¶
| File Name | Included Records | Fields Used |
|---|---|---|
| interactions.csv | No filtering. Records for all species included. Note however that records in the data describe results of a single published experiment. In our ingest records with the same ligand, target, and type + action are merged into a single edge, and metadata from each merged record (publications) combined into a list and attached to the edge. | Ligand Id, Target Species, Type, Target Ensembl Gene ID |
| targets_and_families.csv | subject: ChemicalEntity, MolecularMixture, SmallMolecule; object: Gene; Predicate: directly_physically_interacts_with | Type, Family id, Family name, Target id, Target name, Subunit id, Subunit name, Target systematic name, Target abbreviated name, synonyms, HGNC id, HGNC symbol, HGNC name, Human genetic localisation, Human nucleotide RefSeq, Human protein RefSeq, Human SwissProt, Human Entrez Gene, Human Ensembl Gene, RGD id, RGD symbol, RGD name, Rat genetic localisation, Rat nucleotide RefSeq, Rat protein RefSeq, Rat SwissProt, Rat Entrez Gene, Rat Ensembl Gene, MGI id, MGI symbol MGI name Mouse genetic localisation Mouse nucleotide RefSeq Mouse protein RefSeq Mouse SwissProt Mouse Entrez Gene Mouse Ensembl Gene |
| ligands.csv | Ligand ID Name Species Type Approved Withdrawn Labelled Radioactive PubChem SID PubChem CID UniProt ID Ensembl ID ChEMBL ID Ligand Subunit IDs Ligand Subunit Name Ligand Subunit UniProt IDs Ligand Subunit Ensembl IDs IUPAC name INN Synonyms SMILES InChIKey InChI GtoImmuPdb GtoMPdb Antibacterial | |
| peptides.csv | subject: Small Molecule; object: Small Molecule; predicate: has_part; Only if Human in Species | Species, Ligand Id, Subunit Ids |
| GtP_to_HGNC_mapping.csv | Use GtP to HGNC mappings to convert Gene symbols to HGNC ids | HGNC Symbol, HGNC ID, IUPHAR Name, IUPHAR ID |
Filtered Content¶
| File Name | Filtered Records | Rationale |
|---|---|---|
| peptides.csv | remove records with species in: Mouse, Rat, Pig, Bovine, Sheep, Bovine, Dog, Rabbit, European common frog, Rhesus macaque | Only include records with Human in Species |
Future Content Considerations¶
edge_content: Consider ingest the file 'approved_drug_primary_target_interactions.csv' which contains approved drugs detailed interactions list
edge_content: Consider ingest peptides.csv with species other than Human
edge_property_content: Longer term, consider creating ExperimentalStudyResult objects to capture metadata for each experiment that supports an edge (e.g. affinity data, assay descriptions, and associated publications)
Target Information¶
Target InfoRes ID: infores:translator-gtopdb
Edge Types¶
| Subject Categories | Predicate | Object Categories | Knowledge Level | Agent Type | UI Explanation |
|---|---|---|---|---|---|
| biolink:ChemicalEntity, biolink:MolecularMixture, biolink:SmallMolecule | biolink:Gene | knowledge_assertion | manual_agent | decision between up/down regulated or increased/decreased based on combination of type and action columns in gtopdb | |
| biolink:ChemicalEntity, biolink:MolecularMixture, biolink:SmallMolecule | biolink:Gene | knowledge_assertion | manual_agent | this separate directly_physically_interacts edge is created when the endogenous column == True | |
| biolink:ChemicalEntity, biolink:SmallMolecule | biolink:Gene | knowledge_assertion | manual_agent | ||
| biolink:SmallMolecule | biolink:SmallMolecule | knowledge_assertion | manual_agent | ||
| biolink:SmallMolecule, biolink:MolecularMixture | biolink:Gene | knowledge_assertion | manual_agent |
Node Types¶
| Node Category | Source Identifier Types | Additional Notes |
|---|---|---|
| biolink:ChemicalEntity | PubChem SID | |
| biolink:MolecularMixture | PubChem SID | |
| biolink:SmallMolecule | PubChem SID | |
| biolink:Gene | Ensembl Gene ID, HGNC ID |
Future Modeling Considerations¶
node_content: Considering future new biolink node types: stimulus and fusion protein for more accurate mapping into Biolink model
Provenance Information¶
Contributors: - Qi Wei: code author, data modeling - Yue Zhang: data modeling - Guangrong Qin: data modeling, domain expertise - Sierra Moxon: code support - Matthew Brush: data modeling, domain expertise
Artifacts: - Ingest Survey: https://docs.google.com/spreadsheets/d/1c6M71yrPNGTvH-LeKR75nf5iFOfz0IOOJLpGMy62t4Y/edit?gid=583858205#gid=583858205 - Ingest Ticket: