EpidemiumDB SQLite

Sqlite version of EpidemiumDB (version 1.0)

SQLite version contains EpidemiumDB tables that are needed for analyses. The current version contains 7 tables from BD4Cancer and Baseline projects.

Latest update

The current version was generated on May, 9th, 2016

Download current version

• The current version of EpidemiumDB SQLite version is available at http://data.epidemium.cc/files/epidemiumDBSqlite/EpidemiumDB_v1.0.db
• R code to use EpidemiumDB in R has been provided here.

Using EpidemiumDB SQLite in R

To use EpidemiumDB (SQLite version) in R, the two packages RSQLite and DBI need to be installed.

• RSQLITE (CRAN) : https://cran.r-project.org/web/packages/RSQLite/index.html
• RSQLITE on Github : https://github.com/rstats-db/RSQLite
• DBI: https://cran.r-project.org/web/packages/DBI/index.html
• Documentation: https://cran.r-project.org/web/packages/RSQLite/RSQLite.pdf

#### Install DBI and RSQLite
install.packages("RSQLite")
install.packages("DBI")

# Load required libraries
library(DBI)
library(RSQLite)

# Connecting to EpidemiumDB_v1.0.db
setwd(path_to_EpidemiumDB_v1.0.db)
system("ls *.db", show=TRUE)

sqlite      <- dbDriver("SQLite")
EpidemiumDB <- dbConnect(sqlite,"EpidemiumDB_v1.0.db")

# List of tables
dbListTables(EpidemiumDB)
# [1] "baselineCondition" "cancerType"        "collectedData"    
# [4] "country"           "location"          "locationPartOf"   
# [7] "metadata"

# List of fields in CancerType Table
dbListFields(EpidemiumDB, "cancerType")
# [1] "cancerType_id"                   "cancerType_name"                
# [3] "cancerType_otherName"            "cancerType_frenchName"          
# [5] "cancerType_bodySystem"           "cancerType_ICD10"               
# [7] "cancerType_ICDO3"                "cancerType_SNOMED"              
# [9] "cancerType_MeSH"                 "cancerType_OMIM"                
# [11] "cancerType_medlinePlus"          "cancerType_WHOpage"             
# [13] "cancerType_createdBy"            "cancerType_creationDate"        
# [15] "cancerType_lastModifiedBy"       "cancerType_lastModificationDate"
# [17] "cancerType_validationStatus"  

# Examples of queries to use of EpidemiumDB RSQLite
# Table Country
dbGetQuery(EpidemiumDB, "select * from country where country_name = 'France'")

#country_id country_name country_iso2 country_iso3 country_numericCode
# 1          1       France           FR          FRA                 250
# country_WHOcancerCountryProfile
# 1 http://who.int/cancer/country-profiles/fra_en.pdf?ua=1
#              country_statsData
# 1 http://lesdonnees.e-cancer.fr

results <- dbGetQuery(EpidemiumDB, 
                      "select * from country where country_name = 'France'")

query4="select * from collectedData"
rs4=dbSendQuery(EpidemiumDB,query4)
res4=fetch(rs4,n=-1)
head(res4)

Using the SQLite Database Browser

SQLite Database Browser is multi-platforms open source software to use SQLite databases. This SQLite client can be used to explore EpidemiumDB. Instructions to install SQLite Database Browser are available at https://github.com/sqlitebrowser/sqlitebrowser

Using Epidemium CKAN-based Open Data platform using the API

EpidemiumDB provide a link to the CKAN-based Open Data Platform. The table datasets provide a description and links to cancer datasets availables at data.epidemium.cc We developed an R script that provide functionalities to query and search CKAN https://github.com/Epidemium/SQLite/blob/master/RSQLiteEpidemiumDB.R

Citing EpidemiumDB

Citing EpidemiumDB or code on this Github repository

Maouche S, Debonneuil E, de Fresnoye O, Richard PM, Terlinden A, Couderc C, Mary P, BD4Cancer, Baseline, Epidemium (2016), GitHub repository, https://github.com/Epidemium/SQLite

• A respective BibTeX entry

@misc{Maouche2016,
  author = {Maouche S, Debonneuil E, de Fresnoye O, Richard PM, Terlinden A, Couderc C, Mary P, BD4Cancer, Baseline, Epidemium},
  title = {EpidemiumDB},
  year = {2016},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/Epidemium/SQLite}},
  commit = {}
}

Releases

Version 1.0 released - 2016-05-09