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Open PHACTS Easy API

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”.

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Open PHACTS Easy API

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

  2. Concepts Data Sources Approach for analysis Use Cases API

  3. “Let me compare MW, logP and PSA for known oxidoreductase inhibitors” “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?” Use Cases

  4. Concepts Data Sources Approach for analysis Use Cases API

  5. Concepts Chemical compounds Biological targets Pathways Diseases

  6. Concepts Data Sources Approach for analysis Use Cases API

  7. Data Sources ChEMBL ChEBI neXtProt DrugBank Clinical trials.org Gene Ontology DisGeNet UniProt FDA adverse events ChEMBL Target Class Wikipathways ChemSpider ENZYME ConceptWiki

  8. Concepts Data Sources Approach for analysis Use Cases API

  9. Open PHACTS API Basics • Registering for API keys • API Overview • Entry Points: URLs • API Results • Getting Started with Compounds • Going Further

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

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

  12. 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.

  13. Response template legend for API calls results

  14. 1.3 API calls: Concept types

  15. Multiple result formats

  16. Many filtering options per call

  17. Calls that provide filtering parameters

  18. API Entry Points: URLshttps://dev.openphacts.org/docs/1.3

  19. 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

  20. Finding an initial URL

  21. 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

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

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

  24. API Results: Example with Compound APIs

  25. Compound APIs: Results by Dataset “inDataset” Chembl DrugBank OPS: Open PHACTS Chemical Registry

  26. Compound Pharmacology API: Retrieve a target URL Target URL

  27. Target Information API: Using target URL from previous call Target URL

  28. Target Information API: results (continued)

  29. Compound -> Target in 3 URLs • Free text to retrieve a compound URL • Pharmacology for the compound: results include a target URLs • More information about a target

  30. Thank you

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