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

1. Discovery Platform
API Walkthrough
Paul Groth
@pgroth
http://www.few.vu.nl/~pgroth/

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. http://openphacts.org
pmu@openphacts.org
@Open_PHACTS

4. The Open PHACTS community ecosystem

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. 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. A Simple Restful API
Registering
The Hello World of Drug Discovery Apps
Entry Points
Compounds
Targets
Putting it together
Going Further

8. Simple http calls for
everything (you can put it in
a browser)
A RESTful API

9. Supports multiple formats
Both params and content negotiation

10. DEVELOPER & APP KEYS

14. Hello World!
Compound –
Target App
Sorafenib
SMILIES:
CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl

15. ENTRY POINTS

16. Where do I start?
The API is URL centric
- http://rdf.chemspider.com/187440
- http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-
4ed1d7bdf9d5

17. 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?

18. Entry Point APIs

19. Entry Point APIs
Sorafenib

20. Entry Point APIs
https://beta.openphacts.org/search/freetext?app_id=0e939a76&
app_key=1004d9ef5f4ee1ab0bbfc02b623cb955&q=sorafenib&_
format=json

21. Entry Point APIs

22. "_about": "http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5",
Entry Point APIs

23. CNC(=O)c1cc(ccn1)Oc2ccc(cc2
)NC(=O)Nc3ccc(c(c3)C(F)(F)F)C
l
Entry Point APIs

24. Entry Point APIs
"_about": "http://rdf.chemspider.com/187440"

25. COMPOUND APIS

26. Compound APIs

27. Compound APIs:
Compound Information
We can use either:
http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5
http://rdf.chemspider.com/187440

28. Compound APIs
Chembl
Chemspider

29. Compound APIs
Drugbank provenance - inDataset property

30. Compound APIs
Compound Pharmacology Paginated

31. Compound APIs
Compound Pharmacology Paginated

32. 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"
},
…
},
…
]

33. Compound APIs
Compound Pharmacology Paginated

34. TARGET APIS

35. Target APIs

36. Target APIs
Target Information
http://data.kasabi.com/dataset/chembl-
rdf/chemblid/CHEMBL4226

37. Target APIs
Target Information

38. PUTTING IT TOGETHER

39. 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

40. 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"

41. GOING FURTHER

42. More APIs
Classification APIs
Filtering

43. 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

44. Workflows
https://dev.openphacts.org/workflow

45. https://github.com/openphacts

46. Coming Soon: 1.3 release
• Pathways
• CHEMBL Update
• New chemistry registration system
• Scientific Lenses
• More hierarchy/classification support
• Bonus :-)

47. Conclusion
http://dev.openphacts.org
Create!