Dataset Card for dwb2023/family_target_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 [optional]: 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.pubchem_sid
FROM
    public.object o
JOIN
    public.receptor2family rf ON o.object_id = rf.object_id
JOIN
    public.family f ON rf.family_id = f.family_id
JOIN
    public.interaction i ON o.object_id = i.object_id
JOIN
    public.ligand l ON i.ligand_id = l.ligand_id
ORDER BY f.type, f.name, o.name, l.name

Citation [optional]

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.

• 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.

• 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.