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 3,039 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 covering 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. 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 2024). The ingest derives the source version by scraping the download page (https://www.guidetopharmacology.org/download.jsp), which reports text of the form "Downloads are from the 2025.4 version." Release history is documented at https://www.guidetopharmacology.org/databaseContent.jsp
Ingest Information¶
Ingest Categories: primary_knowledge_provider
Utility: The IUPHAR/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. These curated chemical-to-target interactions are an important type of edge for Translator query and reasoning use cases, including drug mechanism-of-action and chemical-target regulation predictions.
Scope: This ingest covers curated ligand-target interaction records from GtoPdb's interactions.csv file, producing chemical-to-protein edges. No species or record-level filtering is applied. Records with the same ligand, target, and Type + Action are aggregated into a single edge, with publications from the merged records combined into a list. Only the interactions.csv and ligands.csv files are used in this phase.
Relevant Files¶
| File Name | Location | Description |
|---|---|---|
| interactions.csv | https://www.guidetopharmacology.org/DATA/interactions.csv | All interaction data for ligands and targets. |
| ligands.csv | https://www.guidetopharmacology.org/DATA/ligands.csv | Complete ligand list; used to map GtoPdb Ligand IDs to PubChem CIDs for subject node identifiers. |
Included Content¶
| File Name | Included Records | Fields Used |
|---|---|---|
| interactions.csv | No filtering. Records for all species are included. Note that records in the source 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) is combined into a list and attached to the edge. Records lacking a Target UniProt ID or Ligand ID, and records whose Ligand ID has no PubChem CID mapping in ligands.csv, are dropped because they cannot be turned into a well-identified edge. | Ligand, Target, Ligand ID, Target UniProt ID, Type, Action, PubMed ID, Endogenous |
| ligands.csv | Used only for identifier mapping (Ligand ID to PubChem CID); no edges are created directly from this file. | Ligand ID, PubChem CID |
Future Content Considerations¶
edge_content: Leverage the value of the ENDOGENOUS column to inform when to use the regulates predicate and upregulates/downregulates direction qualifier values.
edge_content: Consider ingesting the file 'approved_drug_primary_target_interactions.csv', which contains a detailed interactions list for approved drugs.
edge_content: Consider ingesting peptides.csv, including records 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¶
Edge Types¶
| Subject Categories | Predicate | Object Categories | Knowledge Level | Agent Type | UI Explanation |
|---|---|---|---|---|---|
| biolink:ChemicalEntity, biolink:MolecularMixture, biolink:SmallMolecule | biolink:Protein | knowledge_assertion | manual_agent | Source GtoPdb data provides expert-curated assertions about how a ligand affects the activity of a protein target, based on pharmacological and medicinal chemistry literature. The record used to create this Translator edge reports a ligand-target interaction whose GtoPdb Type + Action values indicate an effect on target activity, with a direction (increased or decreased). This is represented using the Biolink 'affects'/'causes' predicate with an object_aspect_qualifier of 'activity', an object_direction_qualifier capturing the direction of the effect, and a causal_mechanism_qualifier capturing the mechanism (e.g. agonism, antagonism, inhibition, allosteric modulation). This edge type is emitted when GtoPdb's ENDOGENOUS flag is FALSE (i.e. the ligand is not an endogenous regulator of the target). | |
| biolink:ChemicalEntity, biolink:MolecularMixture, biolink:SmallMolecule | biolink:Protein | knowledge_assertion | manual_agent | Source GtoPdb data provides expert-curated assertions about how an endogenous ligand regulates the activity of a protein target. This edge type is emitted when GtoPdb's ENDOGENOUS flag is TRUE, indicating the ligand is an endogenous regulator of the target. It is otherwise identical in structure to the 'affects' edge type above: the interaction's Type + Action values are represented using the Biolink 'regulates'/'causes' predicate with an object_aspect_qualifier of 'activity', an object_direction_qualifier of upregulated or downregulated, and a causal_mechanism_qualifier capturing the mechanism. | |
| biolink:ChemicalEntity, biolink:MolecularMixture, biolink:SmallMolecule | biolink:Protein | knowledge_assertion | manual_agent | Source GtoPdb data provides expert-curated assertions about ligand-target interactions. This edge reports that a ligand physically binds to a protein target, without asserting a direction of effect. It is created (in addition to the corresponding 'affects'/'regulates' edge) when the GtoPdb Type + Action values imply that a direct physical interaction is occurring (e.g. agonist, antagonist, binding, inhibitor mechanisms). This relationship is represented using the symmetric Biolink 'directly_physically_interacts_with' predicate, and carries no aspect, direction, or mechanism qualifier. | |
| biolink:ChemicalEntity, biolink:MolecularMixture, biolink:SmallMolecule | biolink:Protein | knowledge_assertion | manual_agent | Source GtoPdb data provides an expert-curated ligand-target interaction for which the source records a Type of 'None' and an Action of 'None' - i.e. an interaction is documented but no mechanism, direction, or effect on activity is specified. Because no more specific relationship can be inferred, this is represented using the generic Biolink 'related_to' predicate. This is a fallback edge type of last resort, and the source publications are retained on the edge. |
Node Types¶
| Node Category | Source Identifier Types | Additional Notes |
|---|---|---|
| biolink:ChemicalEntity | PUBCHEM.COMPOUND | Ligand nodes are identified in the target graph by PubChem CID (PUBCHEM.COMPOUND prefix). The ingest reads the GtoPdb Ligand ID from interactions.csv and maps it to a PubChem CID via the ligands.csv file; ligands with no PubChem CID mapping are dropped. The ingest assigns biolink:ChemicalEntity to all ligand nodes; downstream normalization may reassign more specific categories such as biolink:SmallMolecule or biolink:MolecularMixture. |
| biolink:MolecularMixture | PUBCHEM.COMPOUND | |
| biolink:SmallMolecule | PUBCHEM.COMPOUND | |
| biolink:Protein | UniProtKB | Target nodes are identified by UniProt accession (UniProtKB prefix), taken from the Target UniProt ID column of interactions.csv. |
Future Modeling Considerations¶
node_properties: Consider future new Biolink node types (e.g. stimulus and fusion protein) for more accurate mapping of GtoPdb target/ligand types into the Biolink Model.
spoq_pattern: Revisit the generic 'related_to' fallback edge (Type = 'None', Action = 'None') to decide whether these low-information edges should be retained, refined, or filtered.
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 - Data Examples: https://docs.google.com/spreadsheets/d/1c6M71yrPNGTvH-LeKR75nf5iFOfz0IOOJLpGMy62t4Y/edit?gid=377376877#gid=377376877 - Predicate/qualifier mapping: https://docs.google.com/spreadsheets/d/1DeAE04O1mz3R9s3dCZpG2hQp9hwif5WjdkUMsBci-u8/edit?gid=461277142#gid=461277142