Data Integration in a Big Data Context: An Open PHACTS Case Study

Data Integration in a Big Data ContextOpen PHACTS Case StudyAlasdair J G [email protected]@gray_alasdair

2

Big Data

@gray_alasdair Big Data Integration

Volume Velocity

Variety Veracity

http

://i.k

inja

-img.

com

/gaw

ker-m

edia

/imag

e/up

load

/lvzm

0afp

8kik

5dct

xiya

.jpg

Open PHACTS Use Case

“Let me compare MW, logP and PSA for launched inhibitors of human & mouse oxidoreductases”

Chemical Properties (Chemspider) Launched drugs (Drugbank) Human => Mouse (Homologene) Protein Families (Enzyme) Bioactivty Data (ChEMBL) … other info (Uniprot/Entrez etc.)

“Let me compare MW, logP and PSA for launched inhibitors of human & mouse oxidoreductases”

@gray_alasdair Big Data Integration 3

4

Open PHACTS Mission: Integrate Multiple Research Biomedical Data Resources

Into A Single Open & FreeAccess Point


5

LiteraturePubChem

GenbankPatents Databases

Downloads

Data Integration Data Analysis Firewalled Databases

Repeat @ each companyx

A single, shared solution.

Funded under• IMI: 2011-14• ENSO: 2014-16

Pre-competitive Data


6

http://dx.doi.org/10.1016/j.websem.2014.03.003

• Cloud-Based “Production” Level System.

• Secure & Private

• Guided By Business Questions

• Uses Semantic Web Technology

• Provides REST-ful API

http://dx.doi.org/10.1016/j.drudis.2013.05.008

Discovery Platform


7

Scientific Results

http://ceur-ws.org/Vol-1114/Demo_Dunlop.pdf

http://dx.doi.org/10.1016/j.drudis.2014.11.006 http://dx.doi.org/10.1002/minf.v31.8

http://dx.doi.org/10.1371/journal.pone.0115460


OPS Discovery Platform


Drug Discovery Platform

Apps

Domain API

Interactive responses

Production qualityintegration platform

MethodCalls

Standard Web Technologies

9

App Ecosystem

@gray_alasdair

An “App Store”?

Explorer Explorer2 ChemBioNavigator Target Dossier Pharmatrek Helium

MOE Collector Cytophacts Utopia Garfield SciBite

KNIME Mol. Data Sheets PipelinePilot scinav.it Taverna

Big Data Integration https://www.openphacts.org/2/sci/apps.html

Big Data Integration 10http://chembionavigator.com

ChemBioNavigator

@gray_alasdair

Big Data Integration 11@gray_alasdair

Big Data Integration 12@gray_alasdair

13

API Hits


Jan 2013

Feb 2013

Mar 2013

Apr 2013

May 2013

June 2013

July 2013

Aug 2013

Sept 2

013

Oct 2013

Nov 2013

Dec 2013

Jan 2014

Feb 2014

Mar 2014

Apr 2014

May 2014

June 2014

July 2014

Aug 2014

Sept 2

014

Oct 2014

Nov 2014

Dec 2014

Jan 2015

Feb 2015

Mar 2015

Apr 2015

May 2015

June 2015

0

10000000

20000000

30000000

40000000

50000000

60000000

Month

No

of H

its

Public launchof 1.2 API

1.3 API 1.4 API 1.5 API

14

OPS Discovery Platform

RDFNanopub

Db

VoID

Data Cache (Virtuoso Triple Store)

Semantic Workflow Engine

Linked Data API (RDF/XML, TTL, JSON)DomainSpecificServices

Identity Resolution

Service

Chemistry RegistrationNormalisation & Q/C

IdentifierManagement

Service

Indexing

Cor

e Pl

atfo

rm

P12374EC2.43.4

CS4532

“Adenosine receptor 2a”

RDF

VoID

Db

RDFNanopub

Db

VoID

RDF

Db

VoID

RDFNanopub

VoID

Public Content Commercial

Public Ontologies

User Annotations

Apps


15

Open PHACTS Data


John Wilbanks consulted for us

A framework built around STANDARD well-understood Creative Commons licences – and how they interoperate

Deal with the problems by:

Interoperable licences

Appropriate terms

Declare expectations to users and

data publishers

One size won‘t fit all requirements

Data Licensing (Or Lack Of!)

17

API: Complex Interactions


Disease

Tissue

Target

Compound

Pathway

18

STANDARD_TYPE UNIT_COUNT---------------- -------AC50 7 Activity 421 EC50 39 IC50 46 ID50 42 Ki 23 Log IC50 4 Log Ki 7 Potency 11 log IC50 0

STANDARD_TYPE STANDARD_UNITS COUNT(*)------------------ ------------------ --------IC50 nM 829448 IC50 ug.mL-1 41000 IC50 38521 IC50 ug/ml 2038 IC50 ug ml-1 509 IC50 mg kg-1 295 IC50 molar ratio 178 IC50 ug 117 IC50 % 113 IC50 uM well-1 52

~ 100 units>5000 types

Implemented using the Quantities, Units, Dimension, TypesOntology (http://www.qudt.org/)

Quantitative Data Challenges


19

Quality Assurance


Big Data Integration 20

P12047X31045 P12047

GB:29384RS_2353

Identity Mapping

@gray_alasdair

Andy Law's Third Law“The number of unique identifiers assigned to an individual is never less than the number of Institutions involved in the study”http://bioinformatics.roslin.ac.uk/lawslaws/

Gleevec®: Imatinib Mesylate


DrugbankChemSpider PubChem

Imatinib

MesylateImatinib MesylateYLMAHDNUQAMNNX-UHFFFAOYSA-N

Gleevec®: Imatinib Mesylate


DrugbankChemSpider PubChem

Imatinib

MesylateImatinib MesylateYLMAHDNUQAMNNX-UHFFFAOYSA-N

Are these records the same?It depends upon your task!


skos:exactMatch(InChI)

Strict Relaxed

Analysing Browsing

Structure Lens

@gray_alasdair

I need to perform an analysis, give me details of the active compound in

Gleevec.


skos:closeMatch(Drug Name)

skos:closeMatch(Drug Name)

skos:exactMatch(InChI)

Strict Relaxed

Analysing Browsing

Name Lens

@gray_alasdair

Which targets are known to interact with Gleevec?


Data Provenance

@gray_alasdair


Data Provenance

@gray_alasdair

29

dev.openphacts.org


31

Open PHACTS Approach1. Know your audience

Web developers2. Understand your use cases

Prioritised business questions3. Identify access pathways

Identify dataIdentify connectionsImplement API


32

QuestionsAlasdair J G [email protected]@gray_alasdair

Open [email protected]@open_phacts
