Open PHACTS Easy API
Christine Chichester
Swiss Institute of Bioinformatics
Community Workshop, June 25, 2014
Approach for
analysis
“Let me compare
MW, logP and PSA
for known
oxidoreductase
inhibitors”
“What is the
interaction profile of
known p38 inhibitors?”
“Find me compounds
that inhibit targets in
NFkB pathway assayed
in only functional assays
with a potency <1 μM”
Approach for
analysis
Chemical compounds
Pathways
Biological targets
Diseases
Approach for
analysis
ChEMBL
ChEBI
DrugBank
neXtProt
Gene
Ontology
UniProt
ChemSpider
ChEMBL
Target Class
ENZYME
ConceptWiki
Clinical
trials.org
DisGeNet
FDA adverse
events
Wikipathways
Approach for
analysis
Open PHACTS API Basics
Registering for API keys
API Overview
Entry Points: URLs
API Results
Getting Started with Compounds
Going Further
Get my API keys!
https://dev.openphacts.org/admin
API Overview: Documentation
https://dev.openphacts.org/docs/1.3
The Linked Data API – Simple Rest-ful API
Advantages of the linked data approach while providing a more
familiar API
Lowers the barrier to data access
Based on community standards
REST
JSON, XML, TSV
Not just data access, but complex queries allowing filtering,
pagination, export, etc.
Response template legend for API calls results
1.3 API calls: Concept types
Multiple result formats
Many filtering options per call
Calls that provide filtering parameters
API Entry Points: URLs
https://dev.openphacts.org/docs/1.3
What’s needed to get started?
The API is URL centric
- http://rdf.chemspider.com/906
- http://www.conceptwiki.org/concept/60915889-bbea-4c10a810-7dfd6eb05168
Why?
- Ensures precise identification of the concept
- Allows for dereferencablity
- supports many URLs from different domains
Next: Getting a URL
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://rdf.chemspider.com/906"
Entry with either Chemspider or ConceptWiki URL (or others) into other API calls
API Results: Example with Compound APIs
Compound APIs: Results by Dataset
“inDataset”
Chembl
DrugBank
OPS: Open PHACTS
Chemical Registry
Compound Pharmacology API: Retrieve a target URL
Target URL
Target Information API: Using target URL from previous call
Target URL
Target Information API: results (continued)
Compound -> Target in 3 URLs
1. Free text to retrieve a compound URL
1. Pharmacology for the compound: results include a target URLs
1. More information about a target
Thank you