Outline Data Management Description Data Analyses Contributing to EpidemiumDB

EpidemiumDB - Creating the Landscape ofCancer Epidemiology and Big Data

Data Management and Standardization in a Large-ScaleCollaborative Project

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye,Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi,

Pierre Mary, on behalf of the Epidemium Project

April 7, 2016

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

About EpidemiumDB

I Born from necessityI Standardise data to facilitate

their integration andreutilization

I Share all data and resourcescollected within Epidemiumprojects

I A collaboration betweenBD4Cancer and Baseline open toall Epidemium Projects

I The BD4Cancer is in charge ofcoordinating the project anddeveloping the database

I Baseline team is creating aninterface for data collection

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Data Management

Description

Data Analyses

Contributing to EpidemiumDB

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Creating the Landscape of Cancer Big Data andEpidemiology

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Data Management Issues in Large-Scale CollaborativeProjects - Example 1

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Data Management Issues in Large-Scale CollaborativeProjects - Example 2

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Sharing collected datasets (1)

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Sharing collected datasets (2)

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Why EpidemiumDB ?

I Share all data and resources collected within Epidemiumprojects

I Create a global and interactive map of all resources (results,datasets, studies, clinical trials, anti-cancer drugs, drugsdatabases, publications,..) available for cancer epidemiologyand Big Data

I Standardise data to facilitate their integration and reutilization

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Why EpidemiumDB ?

I Share all data and resources collected within Epidemiumprojects

I Create a global and interactive map of all resources (results,datasets, studies, clinical trials, anti-cancer drugs, drugsdatabases, publications,..) available for cancer epidemiologyand Big Data

I Standardise data to facilitate their integration and reutilization

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Why EpidemiumDB ?

I Share all data and resources collected within Epidemiumprojects

I Create a global and interactive map of all resources (results,datasets, studies, clinical trials, anti-cancer drugs, drugsdatabases, publications,..) available for cancer epidemiologyand Big Data

I Standardise data to facilitate their integration and reutilization

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Annotation and Metadata are important to report

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

EpidemiumDB content

I All cancer types, their classifications and codification (ICD-10,ICD-O-3, SNOMED, MeSH, externat links to OMIM,MedlinePlus,..)

I Anti-cancer drugs, their known or predicted (withinBD4Cancer) SEs, ADRs

I gene-cancer associations

I All known risk factors for cancers

I Cancer epidemiological data (provided by Epidemium orcollected within Baseline)

I Publications, reports, news about Big Data in oncology,

I Twitter data on cancer pharmacology

I ...

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

EpidemiumDB content

I All cancer types, their classifications and codification (ICD-10,ICD-O-3, SNOMED, MeSH, externat links to OMIM,MedlinePlus,..)

I Anti-cancer drugs, their known or predicted (withinBD4Cancer) SEs, ADRs

I gene-cancer associations

I All known risk factors for cancers

I Cancer epidemiological data (provided by Epidemium orcollected within Baseline)

I Publications, reports, news about Big Data in oncology,

I Twitter data on cancer pharmacology

I ...

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

EpidemiumDB content

I All cancer types, their classifications and codification (ICD-10,ICD-O-3, SNOMED, MeSH, externat links to OMIM,MedlinePlus,..)

I Anti-cancer drugs, their known or predicted (withinBD4Cancer) SEs, ADRs

I gene-cancer associations

I All known risk factors for cancers

I Cancer epidemiological data (provided by Epidemium orcollected within Baseline)

I Publications, reports, news about Big Data in oncology,

I Twitter data on cancer pharmacology

I ...

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

EpidemiumDB content

I All cancer types, their classifications and codification (ICD-10,ICD-O-3, SNOMED, MeSH, externat links to OMIM,MedlinePlus,..)

I Anti-cancer drugs, their known or predicted (withinBD4Cancer) SEs, ADRs

I gene-cancer associations

I All known risk factors for cancers

I Cancer epidemiological data (provided by Epidemium orcollected within Baseline)

I Publications, reports, news about Big Data in oncology,

I Twitter data on cancer pharmacology

I ...

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

EpidemiumDB content

I All cancer types, their classifications and codification (ICD-10,ICD-O-3, SNOMED, MeSH, externat links to OMIM,MedlinePlus,..)

I Anti-cancer drugs, their known or predicted (withinBD4Cancer) SEs, ADRs

I gene-cancer associations

I All known risk factors for cancers

I Cancer epidemiological data (provided by Epidemium orcollected within Baseline)

I Publications, reports, news about Big Data in oncology,

I Twitter data on cancer pharmacology

I ...

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

EpidemiumDB content

I All cancer types, their classifications and codification (ICD-10,ICD-O-3, SNOMED, MeSH, externat links to OMIM,MedlinePlus,..)

I Anti-cancer drugs, their known or predicted (withinBD4Cancer) SEs, ADRs

I gene-cancer associations

I All known risk factors for cancers

I Cancer epidemiological data (provided by Epidemium orcollected within Baseline)

I Publications, reports, news about Big Data in oncology,

I Twitter data on cancer pharmacology

I ...

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

EpidemiumDB content

I All cancer types, their classifications and codification (ICD-10,ICD-O-3, SNOMED, MeSH, externat links to OMIM,MedlinePlus,..)

I Anti-cancer drugs, their known or predicted (withinBD4Cancer) SEs, ADRs

I gene-cancer associations

I All known risk factors for cancers

I Cancer epidemiological data (provided by Epidemium orcollected within Baseline)

I Publications, reports, news about Big Data in oncology,

I Twitter data on cancer pharmacology

I ...

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

EpidemiumDB content

I All cancer types, their classifications and codification (ICD-10,ICD-O-3, SNOMED, MeSH, externat links to OMIM,MedlinePlus,..)

I Anti-cancer drugs, their known or predicted (withinBD4Cancer) SEs, ADRs

I gene-cancer associations

I All known risk factors for cancers

I Cancer epidemiological data (provided by Epidemium orcollected within Baseline)

I Publications, reports, news about Big Data in oncology,

I Twitter data on cancer pharmacology

I ...

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Data modeling - an ongoing process

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

EpidemiumDB/R Interface

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Sending us your requirements

I Prepare the database to receive the output of your projects(request specfic tables,..)

I Use standaridized data

I Approve and comment data modeling shared with Epidemiummembers

I Share your datasets

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Sending us your requirements

I Prepare the database to receive the output of your projects(request specfic tables,..)

I Use standaridized data

I Approve and comment data modeling shared with Epidemiummembers

I Share your datasets

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Sending us your requirements

I Prepare the database to receive the output of your projects(request specfic tables,..)

I Use standaridized data

I Approve and comment data modeling shared with Epidemiummembers

I Share your datasets

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Sending us your requirements

I Prepare the database to receive the output of your projects(request specfic tables,..)

I Use standaridized data

I Approve and comment data modeling shared with Epidemiummembers

I Share your datasets

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Contributing to EpidemiumDB

I The EpidemiumDB Wiki Pagehttp://wiki.epidemium.cc/wiki/EpidemiumDB. Thispage is used to discuss the design of the database

I EpidemiumDB Github repositoryhttps://github.com/Epidemium/EpidemiumDB

I To submit data to Baseline:http://baseline.epidemium.cc

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Contributing to EpidemiumDB

I The EpidemiumDB Wiki Pagehttp://wiki.epidemium.cc/wiki/EpidemiumDB. Thispage is used to discuss the design of the database

I EpidemiumDB Github repositoryhttps://github.com/Epidemium/EpidemiumDB

I To submit data to Baseline:http://baseline.epidemium.cc

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data

Outline Data Management Description Data Analyses Contributing to EpidemiumDB

Contributing to EpidemiumDB

I The EpidemiumDB Wiki Pagehttp://wiki.epidemium.cc/wiki/EpidemiumDB. Thispage is used to discuss the design of the database

I EpidemiumDB Github repositoryhttps://github.com/Epidemium/EpidemiumDB

I To submit data to Baseline:http://baseline.epidemium.cc

Seraya Maouche, Edouard Debonneuil, Olivier de Fresnoye, Augustin Terlinden, Peter-Mikhael Richard, Mehdi Benchoufi, Pierre Mary, on behalf of the Epidemium Project

EpidemiumDB - Creating the Landscape of Cancer Epidemiology and Big Data