open phacts api walkthrough

Discovery PlatformAPI WalkthroughPaul Groth

@pgroth

http://www.few.vu.nl/~pgroth/

Public Drug Discovery Data:Pharma are accessing, processing, storing & re-processing

LiteraturePubChem

GenbankPatents

DatabasesDownloads

Data Integration Data AnalysisFirewalled Databases

www.openphacts.org

The Challenge

http://openphacts.orgpmu@openphacts.org

@Open_PHACTS

The Open PHACTS community ecosystem

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…..

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

A Simple Restful API

Registering

The Hello World of Drug Discovery Apps

Entry Points

Compounds

Targets

Putting it together

Going Further

Simple http calls for everything (you can put it in a browser)

A RESTful API

Supports multiple formats

Both params and content negotiation

DEVELOPER & APP KEYS

Hello World!

Compound – Target App

Sorafenib

SMILIES:CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl

ENTRY POINTS

Where do I start?

The API is URL centric- http://rdf.chemspider.com/187440- http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-

4ed1d7bdf9d5

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?

Entry Point APIs

Entry Point APIs

Sorafenib

Entry Point APIs

https://beta.openphacts.org/search/freetext?app_id=0e939a76&app_key=1004d9ef5f4ee1ab0bbfc02b623cb955&q=sorafenib&_format=json

Entry Point APIs

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

Entry Point APIs

CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl

Entry Point APIs

Entry Point APIs

"_about": "http://rdf.chemspider.com/187440"

COMPOUND APIS

Compound APIs

Compound APIs:Compound Information

We can use either:http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5http://rdf.chemspider.com/187440

Compound APIs

Chembl

Chemspider

Compound APIs

Drugbank provenance - inDataset property

Compound APIsCompound Pharmacology Paginated

Compound APIsCompound Pharmacology Paginated

Compound APIsCompound 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" }, … },…]

Compound APIsCompound Pharmacology Paginated

TARGET APIS

Target APIs

Target APIsTarget Information

http://data.kasabi.com/dataset/chembl-rdf/chemblid/CHEMBL4226

Target APIsTarget Information

PUTTING IT TOGETHER

Compound -> Target in 3 URLs

1. Keyword to a compound URL

https://beta.openphacts.org/search/freetext?app_id=0e939a76&app_key=1004d9ef5f4ee1ab0bbfc02b623cb955&_format=json&q=sorafenib

2. Pharmacology for a compound

https://beta.openphacts.org/compound/pharmacology/pages?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5&app_id=0e939a76&app_key=1004d9ef5f4ee1ab0bbfc02b623cb955&_format=json&_pageSize=10

3. 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=1004d9ef5f4ee1ab0bbfc02b623cb955&_format=json

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":"MPVLSARRRELADHAGSGRRSGPSPTARSGPHLSALRAQPARAAHLSGRGTYVRRDTAGGGPGQARPLGPPGTSLLGRGARRSGEGWCPGAFESGARAARPPSRVEPRLATAASREGAGLPRAEVAAGSGRGARSGEWGLAAAGAWETMHHCKRYRSPEPDPYLSYRWKRRRSYSREHEGRLRYPSRREPPPRRSRSRSHDRLPYQRRYRERRDSDTYRCEERSPSFGEDYYGPSRSRHRRRSRERGPYRTRKHAHHCHKRRTRSCSSASSRSQQSSKRSSRSVEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVADFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLE

HVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHTSRNPSR"

GOING FURTHER

More APIs

Classification APIs

Filtering

Client Libraries

Support for multiple languagesStill in development but useful to get started withEasy to create libraries

Ruby- https://github.com/openphacts/ops_gems

Javascript- https://github.com/openphacts/ops.js

Java- https://github.com/openphacts/JavaLDAClient

Workflowshttps://dev.openphacts.org/workflow

https://github.com/openphacts

Coming Soon: 1.3 release

• Pathways• CHEMBL Update• New chemistry registration system• Scientific Lenses• More hierarchy/classification support• Bonus :-)

Conclusion

http://dev.openphacts.orgCreate!