dwb2023/gtopdb-target-family-interaction-detail

Dataset Card for dwb2023/family-target-interaction-ligand-gtopdb

Dataset Details

Dataset Description

Dataset created using the IUPHAR database from the Guide to Pharmacology website

Dataset Sources

• Repository: https://www.guidetopharmacology.org/DATA/public_iuphardb_v2024.2.zip
• Paper: https://academic.oup.com/nar/article/52/D1/D1438/7332061?login=false

Dataset Creation

Source Data

Query used to create the dataset:

 SELECT f.family_id,
    f.type AS family_type,
    f.name AS family_name,
    o.object_id AS target_id,
    o.name AS target_name,
    l.ligand_id,
    l.name AS ligand_name,
    l.type AS ligand_type,
    i.interaction_id,
    i.type AS interaction_type,
    i.action AS interaction_action,
    l.approved AS ligand_approved,
    l.approved_source AS ligand_approval_source,
    l.pubchem_sid AS ligand_pubchem_sid,
    i.primary_target AS interaction_primary_target,
    i.affinity_median AS interaction_affinity_median,
    i.affinity_units AS interaction_affinity_units,
    r.reference_id,
    r.type AS reference_type,
    r.title AS reference_title,
    r.article_title AS reference_article_title,
    r.pubmed_id AS reference_pubmed_id,
    r.doi AS reference_doi,
    r.pmc_id AS reference_pmc_id
   FROM object o
     JOIN receptor2family rf ON o.object_id = rf.object_id
     JOIN family f ON rf.family_id = f.family_id
     JOIN interaction i ON o.object_id = i.object_id
     JOIN ligand l ON i.ligand_id = l.ligand_id
     LEFT JOIN interaction_affinity_refs ia ON i.interaction_id = ia.interaction_id
     LEFT JOIN reference r ON ia.reference_id = r.reference_id
  ORDER BY f.type, f.name, o.name, l.name;

Citation

BibTeX:

@article{10.1093/nar/gkad944,
    author = {Harding, Simon D and Armstrong, Jane F and Faccenda, Elena and Southan, Christopher and Alexander, Stephen P H and Davenport, Anthony P and Spedding, Michael and Davies, Jamie A},
    title = "{The IUPHAR/BPS Guide to PHARMACOLOGY in 2024}",
    journal = {Nucleic Acids Research},
    volume = {52},
    number = {D1},
    pages = {D1438-D1449},
    year = {2023},
    month = {10},
    abstract = "{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. Here, we report recent developments to the resource and describe expansion in content over the six database releases made during the last two years. The database update section of this paper focuses on two areas relating to important global health challenges. The first, SARS-CoV-2 COVID-19, remains a major concern and we describe our efforts to expand the database to include a new family of coronavirus proteins. The second area is antimicrobial resistance, for which we have extended our coverage of antibacterials in partnership with AntibioticDB, a collaboration that has continued through support from GARDP. We discuss other areas of curation and also focus on our external links to resources such as PubChem that bring important synergies to the resources.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkad944},
    url = {https://doi.org/10.1093/nar/gkad944},
    eprint = {https://academic.oup.com/nar/article-pdf/52/D1/D1438/55039511/gkad944.pdf},
}

Glossary

Here's a glossary for the dataset dwb2023/family_target_ligand_gtopdb based on the dataset description and the SQL query provided:

Glossary

• family_id: Unique identifier for a family in the IUPHAR database. A family groups related pharmacological targets based on their function or structure.

• family_type: The classification type of the family. This could refer to the specific category or class the family belongs to within the broader pharmacological context.

• family_name: The name of the family, which provides a descriptive label for the group of related targets.

• target_id: Unique identifier for a target in the IUPHAR database. A target is a biological entity, such as a receptor or enzyme, that a ligand interacts with.

• target_name: The name of the target, describing the specific protein or molecule that a ligand can bind to or influence.

• interaction_id: A unique identifier for an interaction in the IUPHAR database. An interaction refers to the relationship between a ligand and a target, where the ligand binds to or affects the target in some way.

• interaction_type: The type of interaction occurring between the ligand and the target. This might describe whether the interaction is inhibitory, stimulatory, or another type of effect that the ligand has on the target.

• interaction_action: The specific action that the ligand exerts on the target, such as activation, inhibition, modulation, or binding.

• ligand_id: Unique identifier for a ligand in the IUPHAR database. A ligand is a substance (such as a drug, hormone, or neurotransmitter) that forms a complex with a biomolecule to serve a biological purpose.

• ligand_name: The name of the ligand, describing the specific molecule that interacts with the target.

• ligand_type: The classification type of the ligand, which describes the nature of the ligand (e.g., small molecule, peptide, antibody, etc.).

• ligand_approved: A boolean indicator (True/False) that specifies whether the ligand has been approved by regulatory authorities for therapeutic use.

• ligand_approval_source: The source or agency that approved the ligand for therapeutic use, such as the FDA (Food and Drug Administration) or EMA (European Medicines Agency).

• ligand_pubchem_sid: The Substance ID (SID) in the PubChem database, which provides a unique identifier for substances recorded in PubChem. It links to detailed chemical and biological information about the ligand.

• interaction_primary_target: A boolean indicator (True/False) that specifies whether the target is the primary target for the ligand in the context of the recorded interaction. The primary target is usually the main biological entity that the ligand is designed to influence.

• interaction_affinity_median: The median value of the affinity data for the interaction, usually expressed as a numerical value that indicates how strongly the ligand binds to the target. Affinity is often measured in terms of concentration, such as in nanomolar (nM) units.

• interaction_affinity_units: The units in which the affinity of the ligand for the target is measured, such as nanomolar (nM), micromolar (μM), or other relevant concentration units.

• reference_id: A unique identifier for the reference or source of information about the interaction or ligand in the IUPHAR database.

• reference_type: The type or category of the reference, which could indicate whether it's a journal article, book, database entry, or another form of scientific literature.

• reference_title: The full title of the reference, which provides a brief description of the content of the source.

• reference_article_title: The title of the specific article within a larger publication, if applicable. This may be the same as the reference_title for journal articles.

• reference_pubmed_id: The unique identifier assigned to the reference in PubMed, a free full-text archive of biomedical and life sciences journal literature. This allows for easy lookup of the reference in the PubMed database.

• reference_doi: The Digital Object Identifier (DOI) for the reference, which is a persistent and unique identifier for the document that allows for reliable linking to its online location.

• reference_pmc_id: The unique identifier for the reference in PubMed Central (PMC), which is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM).