open phacts easy api
DESCRIPTION
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 PresentationTRANSCRIPT
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