GtoPdb ELIXIR-All Hands 2018
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The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) is an open, expert-driven database that contains information on over 1,700 pharmacological targets and the substances that act on them. The database provides overviews and detailed information on targets that is manually curated from literature and reviewed by experts. It aims to cover human drug targets and potential future therapeutic targets. New features of the database include search tools to find targets and ligands, information on diseases associated with targets and ligands, organization of ligand families, and comparison of ligand activity across species. The database content is available to download in various formats and its interoperability has been increased through developing an RDF version and submitting data to other sources
![Contact
IUPHAR/BPS
Guide to PHARMACOLOGY
Title
Title
Simon D. Harding1
, Jane Armstrong1
, Elena Faccenda1
, Adam J. Pawson1
, Joanna L. Sharman1
,
Christopher Southan1
, Stephen P.H. Alexander2
, Anthony P. Davenport3
, Michael Spedding4
, Jamie A.
Davies1
and NC-IUPHAR*
1
Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK. 2
School of Life Sciences, University of Notngham Medical School, Notngham, UK. 3
Experimental Medicine and
Immunotherapeutcs, University of Cambridge, Cambridge. 4
Spedding Research Solutons SAS, Paris, France. * The Internatonal Union of Basic and Clinical Pharmacology Commitee on Receptor
Nomenclature and Drug Classifcaton.
1. Introducton
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) is an open, expert-driven
database of pharmacological targets and the substances that act on them [1]. It is a
joint initatve between the Britsh Pharmacological Society (BPS) and the Internatonal
Union of Basic and Clinical Pharmacology (IUPHAR), which aims to cover the human
targets of licensed drugs and other likely targets of future therapeutcs.
The informaton is presented at two levels:
1. Overviews of the key propertes, selectve ligands and further reading for a wide
range of human biological targets, which form the basis for the Concise Guide to
PHARMACOLOGY (CGTP) [2].
2. Detailed pharmacological, functonal and clinical informaton for a subset of
important targets.
All data are manually curated from the primary literature and reviewed by an
internatonal network of >500 experts in 96 subcommitees of the IUPHAR Commitee
on Receptor Nomenclature and Drug Classifcaton (NC-IUPHAR).
2. Current database content
~ 1,700 established or potental data-supported drug targets
~ 1,100 additonal related proteins
> 9,000 ligands, over 5,500 with quanttatve interacton data
> 1,300 approved drugs, >800 with quanttatve informaton
Title
3. New search tools
Various search tools are available to fnd targets and ligands by name, ID, reference,
chemical structure similarity, or BLAST sequence search. A new Pharmacology Search
Tool (Fig. 1) allows users to upload lists of protein IDs and fnd ligands that modulate
them, from both the GtoPdb and ChEMBL [3] databases.
Title
Title
4. Disease informaton
A list of diseases associated to targets and ligands in GtoPdb is now available.
(A) Disease list (B) A disease summary for ALL
A
B
(A) Pharmacology Search Tool with
searching restricted to 3 interactons per
target. (B) Results show actvity data
summarised from GtoPdb and ChEMBL
Results from searches can be
downloaded as a CSV fle
Tip
B
A
Title
5. Navigatng target and ligand families
Targets are organised by class, which can be browsed as a tree with families and
subfamilies (A). Ligands have recently been organised into related families and groups
(B). Each family/group page lists summary informaton for the ligands, with links to
more detailed pages (C).
B
A C
Title
6. Comparing ligand afnity across species
Ligand actvity graphs provide a quick way to visualise afntty at diferent targets and
across species. Box plots (A) summaries standardised actvity data from GtoPdb and
ChEMBL. Individual data points, assay details and references are provided in an
accompanying table (B).
B
A
Chart and table showing palosuran actvity at human and rat UT receptors
Title
7. Interoperability, RDF and data access
As part of our contnuing efort to increase interoperability of GtoPdb we have:
Created an RDF version of GtoPdb
Submited ligands to WikiPathways
Worked with Bioschemas to implement Schema.org mark-up
Set up a new subcommitee of Data Interoperability (Chaired by Dr. Alasdair Gray)
GtoPdb RDF provided in N3 format with metadata generate in accordance with W3C
HCLS Profle to ensure FAIR compliance. Development of SPARQL end-point is
planned.
Data access
GtoPdb data are available to download in various formats:
Lists of targets, ligands and interactons in CSV format
REST web services for computatonal access to data in JSON format
SQL database dump fles
Interacton data are now available in RDF format for semantc integraton
8. References
1. Harding SD, et al. (2018). Nucl. Acids Res. 46 (Issue D1): D1091-D1106.
2. Alexander SPH, et al. (2017). Br J Pharmacol. 174 (Suppl 1): S1-S446.
3. Bento AP, et al. (2014). Nucl. Acids Res. 42 (Database Issue): D1083-D1090.
In additon, for a “how-to” guide on using GtoPdb see: Sharman JL, et al. (2018) Accessing
Expert Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY.‐ Curr
Protoc Bioinformatcs. 61: 1.34.1-1.34.46.
www.guidetopharmacology.org enquiries@guidetopharmacology.org @GuidetoPHARM](https://image.slidesharecdn.com/elixirgtopdballhands2018-180601155955/85/GtoPdb-ELIXIR-All-Hands-2018-1-320.jpg)
GtoPdb ELIXIR-All Hands 2018
- 1. Contact IUPHAR/BPS Guide to PHARMACOLOGY Title Title Simon D. Harding1 , Jane Armstrong1 , Elena Faccenda1 , Adam J. Pawson1 , Joanna L. Sharman1 , Christopher Southan1 , Stephen P.H. Alexander2 , Anthony P. Davenport3 , Michael Spedding4 , Jamie A. Davies1 and NC-IUPHAR* 1 Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK. 2 School of Life Sciences, University of Notngham Medical School, Notngham, UK. 3 Experimental Medicine and Immunotherapeutcs, University of Cambridge, Cambridge. 4 Spedding Research Solutons SAS, Paris, France. * The Internatonal Union of Basic and Clinical Pharmacology Commitee on Receptor Nomenclature and Drug Classifcaton. 1. Introducton The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) is an open, expert-driven database of pharmacological targets and the substances that act on them [1]. It is a joint initatve between the Britsh Pharmacological Society (BPS) and the Internatonal Union of Basic and Clinical Pharmacology (IUPHAR), which aims to cover the human targets of licensed drugs and other likely targets of future therapeutcs. The informaton is presented at two levels: 1. Overviews of the key propertes, selectve ligands and further reading for a wide range of human biological targets, which form the basis for the Concise Guide to PHARMACOLOGY (CGTP) [2]. 2. Detailed pharmacological, functonal and clinical informaton for a subset of important targets. All data are manually curated from the primary literature and reviewed by an internatonal network of >500 experts in 96 subcommitees of the IUPHAR Commitee on Receptor Nomenclature and Drug Classifcaton (NC-IUPHAR). 2. Current database content ~ 1,700 established or potental data-supported drug targets ~ 1,100 additonal related proteins > 9,000 ligands, over 5,500 with quanttatve interacton data > 1,300 approved drugs, >800 with quanttatve informaton Title 3. New search tools Various search tools are available to fnd targets and ligands by name, ID, reference, chemical structure similarity, or BLAST sequence search. A new Pharmacology Search Tool (Fig. 1) allows users to upload lists of protein IDs and fnd ligands that modulate them, from both the GtoPdb and ChEMBL [3] databases. Title Title 4. Disease informaton A list of diseases associated to targets and ligands in GtoPdb is now available. (A) Disease list (B) A disease summary for ALL A B (A) Pharmacology Search Tool with searching restricted to 3 interactons per target. (B) Results show actvity data summarised from GtoPdb and ChEMBL Results from searches can be downloaded as a CSV fle Tip B A Title 5. Navigatng target and ligand families Targets are organised by class, which can be browsed as a tree with families and subfamilies (A). Ligands have recently been organised into related families and groups (B). Each family/group page lists summary informaton for the ligands, with links to more detailed pages (C). B A C Title 6. Comparing ligand afnity across species Ligand actvity graphs provide a quick way to visualise afntty at diferent targets and across species. Box plots (A) summaries standardised actvity data from GtoPdb and ChEMBL. Individual data points, assay details and references are provided in an accompanying table (B). B A Chart and table showing palosuran actvity at human and rat UT receptors Title 7. Interoperability, RDF and data access As part of our contnuing efort to increase interoperability of GtoPdb we have: Created an RDF version of GtoPdb Submited ligands to WikiPathways Worked with Bioschemas to implement Schema.org mark-up Set up a new subcommitee of Data Interoperability (Chaired by Dr. Alasdair Gray) GtoPdb RDF provided in N3 format with metadata generate in accordance with W3C HCLS Profle to ensure FAIR compliance. Development of SPARQL end-point is planned. Data access GtoPdb data are available to download in various formats: Lists of targets, ligands and interactons in CSV format REST web services for computatonal access to data in JSON format SQL database dump fles Interacton data are now available in RDF format for semantc integraton 8. References 1. Harding SD, et al. (2018). Nucl. Acids Res. 46 (Issue D1): D1091-D1106. 2. Alexander SPH, et al. (2017). Br J Pharmacol. 174 (Suppl 1): S1-S446. 3. Bento AP, et al. (2014). Nucl. Acids Res. 42 (Database Issue): D1083-D1090. In additon, for a “how-to” guide on using GtoPdb see: Sharman JL, et al. (2018) Accessing Expert Curated Pharmacological Data in the IUPHAR/BPS Guide to PHARMACOLOGY.‐ Curr Protoc Bioinformatcs. 61: 1.34.1-1.34.46. www.guidetopharmacology.org enquiries@guidetopharmacology.org @GuidetoPHARM