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2015-05-19 Open PHACTS Drug Discovery Workflow Workshop - The API
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Open PHACTS API : Workflow Workshop Christine Chichester Swiss Institute of Bioinformatics May 19-20, 2015 1
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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
Concepts
Data Sources
Use Cases
API Approach for
analysis
“Give me all oxidoreductase inhibitors ac4ve <100nM in human and mouse”
Use Cases
Concepts D
ata Sources
Use
Cas
es
API
Approach for analysis
Concepts
Chemical compounds Biological targets
Pathways Diseases
Tissues
Con
cept
s
Data Sources
Use Cases
API
Approach for analysis
ChEMBL
DrugBank Gene
Ontology
Wikipathways
UniProt
ChemSpider
ChEMBL Target Class
ConceptWiki
ChEBI
DisGeNet
neXtProt
Data Sources
ENZYME
FDA adverse events
Concepts
Dat
a So
urce
s
Use C
ases API
Approach for analysis
Registering for API keys
API Overview
Entry Points: URLs
API Results
Getting Started with Compounds
Going Further
Open PHACTS API Basics
Get my API keys! https://dev.openphacts.org/
API Overview: Documentation https://dev.openphacts.org/docs/1.5
Response template legend for API calls results
API calls: Concept types
Many filtering options per call
Specific calls exposing filtering parameters
API Entry Points: URLs https://dev.openphacts.org/docs/1.5
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
Calls for: finding an initial 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
"_about": "http://www.conceptwiki.org/concept/60915889-bbea-4c10-a810-7dfd6eb05168”
"_about": "http://ops.rsc.org/OPS1356847"
API Results: Example with Compound APIs
Compound APIs: Results by Dataset “inDataset”
Chembl
ConceptWiki
OCRS
Compound Pharmacology API: Retrieve a target URL
Target URL
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
