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

Open PHACTS Easy API

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Open PHACTS Easy API. Christine Chichester Swiss Institute of Bioinformatics. Community Workshop , June 25, 2014. Concepts. Data Sources. Approach for analysis. Use Cases. API. “Let me compare MW, logP and PSA for known oxidoreductase inhibitors”. - PowerPoint PPT Presentation

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Page 1: Open  PHACTS  Easy API

Open PHACTS Easy API

Community Workshop, June 25, 2014

Christine ChichesterSwiss Institute of Bioinformatics

Page 2: Open  PHACTS  Easy API

Concepts

Data Sources

Use Cases

AP

I Approach for analysis

Page 3: Open  PHACTS  Easy API

“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

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ConceptsD

ata Sources

Use

Cas

es

API

Approach for analysis

Page 5: Open  PHACTS  Easy API

Concepts

Chemical compoundsBiological targets

Pathways Diseases

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Con

c ept

s

Data Sources

Use Cases

AP

IApproach for analysis

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ChEMBL

DrugBankGene

Ontology

Wikipathways

UniProt

ChemSpider

ChEMBLTarget Class

ConceptWiki

ChEBI

DisGeNet

neXtProt

Data Sources

ENZYME

FDA adverseevents

Clinical trials.org

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Concepts

Dat

a S

ourc

es

Use C

asesAPI

Approach for analysis

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Registering for API keys

API Overview

Entry Points: URLs

API Results

Getting Started with Compounds

Going Further

Open PHACTS API Basics

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Get my API keys!https://dev.openphacts.org/admin

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API Overview: Documentationhttps://dev.openphacts.org/docs/1.3

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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.

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Response template legend for API calls results

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1.3 API calls: Concept types

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Multiple result formats

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Many filtering options per call

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Calls that provide filtering parameters

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API Entry Points: URLs https://dev.openphacts.org/docs/1.3

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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

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Finding an initial URL

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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

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"_about": "http://www.conceptwiki.org/concept/60915889-bbea-4c10-a810-7dfd6eb05168”

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

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

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API Results: Example with Compound APIs

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Compound APIs: Results by Dataset

Chembl

DrugBank

OPS: Open PHACTSChemical Registry

“inDataset”

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Compound Pharmacology API: Retrieve a target URL

Target URL

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Target Information API: Using target URL from previous callTarget URL

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Target Information API: results (continued)

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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

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Thank you