Open PHACTS Easy API Christine Chichester Swiss Institute

Open PHACTS Easy API Christine Chichester Swiss Institute of Bioinformatics Community Workshop, June 25, 2014

Approach for analysis Concepts Data Sources API Use Cases

Use Cases “Let me compare MW, log. P and PSA for known oxidoreductase inhibitors” “What is the interaction profile of known p 38 inhibitors? ” “Find me compounds that inhibit targets in NFk. B pathway assayed in only functional assays with a potency <1 μM”

API Use Case Approach for analysis Data Sources s Concepts

Concepts Chemical compounds Pathways Biological targets Diseases

Approach for analysis API s Use Case Concepts Data Sources

Data Sources Ch. EMBL Ch. EBI Drug. Bank Gene Ontology Uni. Prot Chem. Spider Ch. EMBL Target Class ENZYME Concept. Wiki ne. Xt. Prot Dis. Ge. Net Wikipathways Clinical trials. org FDA adverse events

Approach for analysis es Use C as Concepts Data Sources API

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-4 c 10 a 810 -7 dfd 6 eb 05168 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: C 1=CC=C 2 C=CC=CC 2=C 1 In. Ch. I: In. Ch. I=1 S/C 10 H 8/c 1 -2 -6 -10 -8 -4 -3 -7 -9(10)5 -1/h 1 -8 H

"_about": "http: //www. conceptwiki. org/concept/60915889 -bbea-4 c 10 -a 810 -7 dfd 6 eb 05168”

"_about": "http: //rdf. chemspider. com/906" Entry with either Chemspider or Concept. Wiki URL (or others) into other API calls

API Results: Example with Compound APIs

Compound APIs: Results by Dataset “in. Dataset” Chembl Drug. Bank 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