Open PHACTS Easy API

Open PHACTS Easy API

Community Workshop, June 25, 2014

Christine ChichesterSwiss Institute of Bioinformatics

Concepts

Data Sources

Use Cases

AP

I Approach for analysis

“Find me compounds that inhibit targets in NFkB pathway assayed in only functional assays with a potency <1 μM”

“What is the interaction profile of known p38 inhibitors?”

“Let me compare MW, logP and PSA for known oxidoreductase inhibitors”

Use Cases

ConceptsD

ata Sources

Use

Cas

es

API

Approach for analysis

Concepts

Chemical compoundsBiological targets

Pathways Diseases

Con

c ept

s

Data Sources

Use Cases

AP

IApproach for analysis

ChEMBL

DrugBankGene

Ontology

Wikipathways

UniProt

ChemSpider

ChEMBLTarget Class

ConceptWiki

ChEBI

DisGeNet

neXtProt

Data Sources

ENZYME

FDA adverseevents

Clinical trials.org

Concepts

Dat

a S

ourc

es

Use C

asesAPI

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/admin

API Overview: Documentationhttps://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-4c10-

a810-7dfd6eb05168

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”

Entry with either Chemspider or ConceptWiki URL (or others) into other API calls

"_about": "http://rdf.chemspider.com/906"

API Results: Example with Compound APIs

Compound APIs: Results by Dataset

Chembl

DrugBank

OPS: Open PHACTSChemical Registry

“inDataset”

Compound Pharmacology API: Retrieve a target URL

Target URL

Target Information API: Using target URL from previous callTarget URL

Target Information API: results (continued)

Compound -> Target in 3 URLs

1. Free text to retrieve a compound URL

2. Pharmacology for the compound: results include a target URLs

3. More information about a target

Thank you