Open PHACTS API Walkthrough

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A simple guide to the Open PHACTS Discovery Platform api (http://dev.openphacts.org) for accessing integrated drug discovery information

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  • Just a note, when using the documentation page watch out for spaces in your queries.
  • Just stick it in a browser 
  • _about is a central concept
  • Two important ones compount info and compound pharma paginated
  • https://beta.openphacts.org/compound?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5+&app_id=0e939a76&app_key=1004d9ef5f4ee1ab0bbfc02b623cb955
  • The Response is organized by data source with different properties selected from those different data sources
  • The Response is organized by data source with different properties selected from those different data sources
  • A lot of filtering options (point out that only bullets are required)https://beta.openphacts.org/compound/pharmacology/pages?uri=http%3A%2F%2Frdf.chemspider.com%2F187440&app_id=0e939a76&app_key=1004d9ef5f4ee1ab0bbfc02b623cb955&_pageSize=10
  • Pagination
  • Results
  • Pagination
  • Pagination
  • https://beta.openphacts.org/target?uri=http%3A%2F%2Fdata.kasabi.com%2Fdataset%2Fchembl-rdf%2Fchemblid%2FCHEMBL4226&app_id=0e939a76&app_key=1004d9ef5f4ee1ab0bbfc02b623cb955
  • https://beta.openphacts.org/target?uri=http%3A%2F%2Fdata.kasabi.com%2Fdataset%2Fchembl-rdf%2Fchemblid%2FCHEMBL4226&app_id=0e939a76&app_key=1004d9ef5f4ee1ab0bbfc02b623cb955
  • Open PHACTS API Walkthrough

    1. 1. Discovery Platform API Walkthrough Paul Groth @pgroth http://www.few.vu.nl/~pgroth/
    2. 2. Public Drug Discovery Data: Pharma are accessing, processing, storing & re-processing Literature PubChem Genbank Patents Databases Downloads Data Integration Data Analysis Firewalled Databases www.openphacts.org The Challenge
    3. 3. http://openphacts.org pmu@openphacts.org @Open_PHACTS
    4. 4. The Open PHACTS community ecosystem
    5. 5. Source Initial Records Chembl 1,149,792 ~1,091,462 cmpds ~8845 targets DrugBank 19,628 ~14,000 drugs ~5000 targets UniProt 536,789 ENZYME 6,187 ChEBI 35,584 GO/GOA 38,137 ChemSpider/ACD 1,194,437 ConceptWiki 2,828,966 Data Growing…..
    6. 6. Access to a wide range of interconnected data – easily jump between pharmacology, chemistry, disease, pathways and other databases without having to perform complex mapping operations Query by data type, not by data source (“Protein Information” not “Uniprot Information) API queries that seamlessly connect data (for instance the Pharmacology query draws data from Chembl, ChemSpider, ConceptWiki and Drugbank) Strong chemistry representation – all chemicals reprocessed via Open PHACTS chemical registry to ensure consistency across databases Built using open community standards, not an ad-hoc solution. Developed in conjuction with 8 major pharma (so your app will speak their language!) Simple, flexible data-joining (join compound data ignoring salt forms, join protein data ignoring species) Provenance everywhere – every single data point tagged with source, version, author, etc Nanopublication-enabled. Access to a rich dataset of established and emerging biomedical “assertions” Professionally Hosted (Continually Monitored) Developer-friendly JSON/XML methods. Consistent API for multiple services Seamless data upgrades. We manage updates so you don’t have to Community-curation tools to enhance and correct content Access to a rich application network (many different App builders) Toolkits to support many different languages, workflow engines and user applications Private and secure, suitable for confidential analyses Active & still growing through a unique public-private partnership Benefits
    7. 7. A Simple Restful API Registering The Hello World of Drug Discovery Apps Entry Points Compounds Targets Putting it together Going Further
    8. 8. Simple http calls for everything (you can put it in a browser) A RESTful API
    9. 9. Supports multiple formats Both params and content negotiation
    10. 10. DEVELOPER & APP KEYS
    11. 11. Hello World! Compound – Target App Sorafenib SMILIES: CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl
    12. 12. ENTRY POINTS
    13. 13. Where do I start? The API is URL centric - http://rdf.chemspider.com/187440 - http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a- 4ed1d7bdf9d5
    14. 14. Where do I start? The API is URL centric - http://rdf.chemspider.com/187440 - http://www.conceptwiki.org/concept/38932552-111f-4a4e- a46a-4ed1d7bdf9d5 Why? - Ensures precise identification - Allows for dereferencablity - Note: supports many URLs from different domains But what if I don’t have URL?
    15. 15. Entry Point APIs
    16. 16. Entry Point APIs Sorafenib
    17. 17. Entry Point APIs https://beta.openphacts.org/search/freetext?app_id=0e939a76& app_key=1004d9ef5f4ee1ab0bbfc02b623cb955&q=sorafenib&_ format=json
    18. 18. Entry Point APIs
    19. 19. "_about": "http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5", Entry Point APIs
    20. 20. CNC(=O)c1cc(ccn1)Oc2ccc(cc2 )NC(=O)Nc3ccc(c(c3)C(F)(F)F)C l Entry Point APIs
    21. 21. Entry Point APIs "_about": "http://rdf.chemspider.com/187440"
    22. 22. COMPOUND APIS
    23. 23. Compound APIs
    24. 24. Compound APIs: Compound Information We can use either: http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5 http://rdf.chemspider.com/187440
    25. 25. Compound APIs Chembl Chemspider
    26. 26. Compound APIs Drugbank provenance - inDataset property
    27. 27. Compound APIs Compound Pharmacology Paginated
    28. 28. Compound APIs Compound Pharmacology Paginated
    29. 29. Compound APIs Compound Pharmacology Paginated "items": [ { "_about": "http://data.kasabi.com/dataset/chembl-rdf/activity/a1650069", "pmid": "15711537", "forMolecule": {…}, "onAssay": { … "target": { "_about": "http://data.kasabi.com/dataset/chembl-rdf/chemblid/CHEMBL4226", "title": "Dual specificity protein kinase CLK3", "organism": "Homo sapiens" }, … }, … ]
    30. 30. Compound APIs Compound Pharmacology Paginated
    31. 31. TARGET APIS
    32. 32. Target APIs
    33. 33. Target APIs Target Information http://data.kasabi.com/dataset/chembl- rdf/chemblid/CHEMBL4226
    34. 34. Target APIs Target Information
    35. 35. PUTTING IT TOGETHER
    36. 36. Compound -> Target in 3 URLs 1. Keyword to a compound URL https://beta.openphacts.org/search/freetext?app_id=0e939a76&app_key=1004d9ef5f4ee1ab0bbfc0 2b623cb955&_format=json&q=sorafenib 1. Pharmacology for a compound https://beta.openphacts.org/compound/pharmacology/pages?uri=http%3A%2F%2Fwww.concept wiki.org%2Fconcept%2F38932552-111f-4a4e-a46a- 4ed1d7bdf9d5&app_id=0e939a76&app_key=1004d9ef5f4ee1ab0bbfc02b623cb955&_format=json &_pageSize=10 1. More information about a target https://beta.openphacts.org/target?uri=http%3A%2F%2Fdata.kasabi.com%2Fdataset%2Fchembl - rdf%2Fchemblid%2FCHEMBL4226&app_id=0e939a76&app_key=1004d9ef5f4ee1ab0bbfc02b623 cb955&_format=json
    37. 37. Sorafenib ` SMILIES: CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl Hello World! Compound – Target App Dual specificity protein kinase CLK3, sequence":"MPVLSARRRELADHAGSGRRSGPSPTARSGPHLSALRAQPARAAHLSGRGTYVRRDTAGGGPGQARPLGPPGTSLL GRGARRSGEGWCPGAFESGARAARPPSRVEPRLATAASREGAGLPRAEVAAGSGRGARSGEWGLAAAGAWETMHHCKRYRSP EPDPYLSYRWKRRRSYSREHEGRLRYPSRREPPPRRSRSRSHDRLPYQRRYRERRDSDTYRCEERSPSFGEDYYGPSRSRHRR RSRERGPYRTRKHAHHCHKRRTRSCSSASSRSQQSSKRSSRSVEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHA RGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAY QLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQP CDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLE HVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHTSRNPSR"
    38. 38. GOING FURTHER
    39. 39. More APIs Classification APIs Filtering
    40. 40. Client Libraries Support for multiple languages Still in development but useful to get started with Easy to create libraries Ruby - https://github.com/openphacts/ops_gems Javascript - https://github.com/openphacts/ops.js Java - https://github.com/openphacts/JavaLDAClient
    41. 41. Workflows https://dev.openphacts.org/workflow
    42. 42. https://github.com/openphacts
    43. 43. Coming Soon: 1.3 release • Pathways • CHEMBL Update • New chemistry registration system • Scientific Lenses • More hierarchy/classification support • Bonus :-)
    44. 44. Conclusion http://dev.openphacts.org Create!

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