2015-05-19 Open PHACTS Drug Discovery Workflow Workshop - The API
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Transcript of 2015-05-19 Open PHACTS Drug Discovery Workflow Workshop - The API
Open PHACTS API : Workflow Workshop
Christine Chichester Swiss Institute of Bioinformatics
May 19-20, 2015 1
ChEMBL
DrugBank Gene
Ontology
Wikipathways
UniProt
ChemSpider
ChEMBL Target Class
ConceptWiki
ChEBI
DisGeNet
neXtProt
Data Sources
ENZYME
FDA adverse events
Registering for API keys
API Overview
Entry Points: URLs
API Results
Getting Started with Compounds
Going Further
Open PHACTS API Basics
What’s needed to get started?
The API is URL centric - http://rdf.chemspider.com/906 - http://www.conceptwiki.org/concept/60915889-bbea-4c10-
a810-7dfd6eb05168
Next: Getting a URL
Compound example: Naphthalene
Textual name: Naphthalene SMILES: C1=CC=C2C=CC=CC2=C1 InChI: InChI=1S/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H
Target Information API: Using target URL from previous call: http://rdf.ebi.ac.uk/resource/chembl/target/CHEMBL1293278
The target type, single_protein, can be used as filter parameter in pharmacology calls
GO classifications : http://purl.uniprot.org/go/0003714 Can be used in Target Class Members
Target Information API: results (continued)
InteractsWith: protein-protein interaction partners
Sequence
Molecular Weight
Textual name
Compound name-> Target: 3 URLs 1. Free text to retrieve a compound URL
2. Pharmacology for the compound: Results include the target URLs
3. More information about the target
API call Data Dataset Target Information
Amino acid sequence, number of residues, theoretical pI, mass, textual labels, functional annotation, interacting proteins, target components, cellular localization, GO terms, UniProt keywords, drugs specific for the target, links to other datasets: GO annotations, Protein Databank
SwissProt, Chembl, DrugBank
Compound Information
SMILES, InChI, InChIKey, molecular formula, textual labels, hydrogen bond donors/acceptors, molecular weight, rule of 5 violations, rotatable bonds, logP, polar surface area, melting point, metabolism, toxicity, protein binding, description, classification as per drug approval process, drug-drug interactions, adverse events
OPS Chemical Registry DrugBank
API call Data Dataset Target Pharmacology
Target, target textual name, compound, published activity type, published activity value, activity units, pChEMBL value, assay, assay comment, assay organism, DOI, target type
Chembl
Compound Pharmacology
Compound, target, Published activity type, published activity value, activity units, pChEMBL value, assay, assay description, assay comment, assay organism, DOI, drug type, drug generic name
Chembl, DrugBank
API call Data Dataset Tissue Information (tissue expression information)
Tissue description, Links to other datasets (cross-references): Foundational model of anatomy, Brenda tissue ontology, UBERON, Medical subject headings Filters for quality of evidence and level of expression
neXtProt
Disease Information
Textual label, disease class DisGeNet
Pathway Information
Textual label, pathway organism, pathway elements, pathway description, Pathway Ontology terms
WikiPathways