Matt Mulvahill
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/multiMiR |
| git_branch: RELEASE_3_14 |
| git_last_commit: 56f3190 |
| git_last_commit_date: 2021-10-26 12:38:12 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:58 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the multiMiR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/multiMiR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1246/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| multiMiR 1.16.0 (landing page) Matt Mulvahill
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: multiMiR |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiMiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings multiMiR_1.16.0.tar.gz |
| StartedAt: 2022-04-12 23:27:53 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 23:31:12 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 198.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: multiMiR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiMiR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings multiMiR_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/multiMiR.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'multiMiR/DESCRIPTION' ... OK * this is package 'multiMiR' version '1.16.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'multiMiR' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... Running 'testthat.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK
multiMiR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/multiMiR_1.16.0.tar.gz && rm -rf multiMiR.buildbin-libdir && mkdir multiMiR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multiMiR.buildbin-libdir multiMiR_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL multiMiR_1.16.0.zip && rm multiMiR_1.16.0.tar.gz multiMiR_1.16.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 51439 100 51439 0 0 324k 0 --:--:-- --:--:-- --:--:-- 324k
install for i386
* installing *source* package 'multiMiR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'multiMiR'
finding HTML links ... done
add.multimir.links html
all_tables html
as.mmquery html
as_mmsql_components html
build_mmsql html
default_cutoff html
deprecate_arg html
extract_mmquery html
get.multimir.cutoffs html
get_multimir html
list_multimir html
mmquery_bioc-class html
multiMiR html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/multiMiR.buildbin-libdir/00LOCK-multiMiR/00new/multiMiR/help/multimir.html
multimir.summary html
multimir_dbInfo html
multimir_switchDBVersion html
null_to_df html
pad html
parens_quote html
parens_wrap html
parse_orgs html
parse_response html
query_multimir html
quote_wrap html
remove_empty_strings html
remove_table html
search_multimir html
split_by html
sql_org html
sql_validated html
submit_request html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'multiMiR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'multiMiR' as multiMiR_1.16.0.zip
* DONE (multiMiR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'multiMiR' successfully unpacked and MD5 sums checked
|
multiMiR.Rcheck/tests_i386/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(multiMiR)
Welcome to multiMiR.
multiMiR database URL has been set to the
default value: http://multimir.org/
Database Version: 2.3.0 Updated: 2020-04-15
>
> test_check("multiMiR")
--
-- Table structure for table `mirna`
--
DROP TABLE IF EXISTS `mirna`;
CREATE TABLE `mirna` (
mature_mirna_uid INTEGER UNSIGNED AUTO_INCREMENT, -- mature miRNA unique ID
org VARCHAR(4) NOT NULL, -- organism abbreviation
mature_mirna_acc VARCHAR(20) default NULL, -- mature miRNA accession
mature_mirna_id VARCHAR(20) default NULL, -- mature miRNA ID/name
PRIMARY KEY (mature_mirna_uid),
KEY org (org),
KEY mature_mirna_acc (mature_mirna_acc),
KEY mature_mirna_id (mature_mirna_id)
);
--
-- Table structure for table `target`
--
DROP TABLE IF EXISTS `target`;
CREATE TABLE `target` (
target_uid INTEGER UNSIGNED AUTO_INCREMENT, -- target gene unique ID
org VARCHAR(4) NOT NULL, -- organism abbreviation
target_symbol VARCHAR(80) default NULL, -- target gene symbol
target_entrez VARCHAR(10) default NULL, -- target gene Entrez gene ID
target_ensembl VARCHAR(20) default NULL, -- target gene Ensembl gene ID
PRIMARY KEY (target_uid),
KEY org (org),
KEY target_symbol (target_symbol),
KEY target_entrez (target_entrez),
KEY target_ensembl (target_ensembl)
);
--
-- Table structure for table `mirecords`
--
DROP TABLE IF EXISTS `mirecords`;
CREATE TABLE `mirecords` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
target_site_number INT(10) default NULL, -- target site number
target_site_position INT(10) default NULL, -- target site position
experiment VARCHAR(160) default NULL, -- supporting experiment
support_type VARCHAR(40) default NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `mirtarbase`
--
DROP TABLE IF EXISTS `mirtarbase`;
CREATE TABLE `mirtarbase` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
experiment VARCHAR(160) NOT NULL, -- supporting experiment
support_type VARCHAR(40) NOT NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `tarbase`
--
DROP TABLE IF EXISTS `tarbase`;
CREATE TABLE `tarbase` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
experiment VARCHAR(160) NOT NULL, -- supporting experiment
support_type VARCHAR(40) NOT NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `miranda`
--
DROP TABLE IF EXISTS `miranda`;
CREATE TABLE `miranda` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
conservation REAL NOT NULL, -- conservation score
mirsvr_score REAL NOT NULL, -- mirSVR downregulation score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY conservation (conservation),
KEY mirsvr_score (mirsvr_score)
);
--
-- Table structure for table `targetscan`
--
DROP TABLE IF EXISTS `targetscan`;
CREATE TABLE `targetscan` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
site_type INTEGER UNSIGNED NOT NULL, -- site type (see http://www.targetscan.org/faqs.html)
context_plus_score REAL NOT NULL, -- context+ score
conserved_site ENUM('N','Y'), -- whether the target site is conserved
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY context_plus_score (context_plus_score),
KEY conserved_site (conserved_site)
);
--
-- Table structure for table `diana_microt`
--
DROP TABLE IF EXISTS `diana_microt`;
CREATE TABLE `diana_microt` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
miTG_score REAL NOT NULL, -- miRNA target gene score
UTR3_hit INTEGER UNSIGNED NOT NULL, -- number of 3'-UTR binding sites
CDS_hit INTEGER UNSIGNED NOT NULL, -- number of CDS binding sites
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY miTG_score (miTG_score)
);
--
-- Table structure for table `elmmo`
--
DROP TABLE IF EXISTS `elmmo`;
CREATE TABLE `elmmo` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
p REAL NOT NULL, -- "the posterior probability that the site is under evolutionnary selective pressure"
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY p (p)
);
--
-- Table structure for table `pita`
--
DROP TABLE IF EXISTS `pita`;
CREATE TABLE `pita` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
ddG REAL NOT NULL, -- ddG = dGduplex (microRNA-target hybridization energy) - dGopen (energy required to make the target site accessible)
conservation REAL NOT NULL, -- site conservation (range 0~1)
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY ddG (ddG),
KEY conservation (conservation)
);
--
-- Table structure for table `microcosm`
--
DROP TABLE IF EXISTS `microcosm`;
CREATE TABLE `microcosm` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- miRanda score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `pictar`
--
DROP TABLE IF EXISTS `pictar`;
CREATE TABLE `pictar` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `mirdb`
--
DROP TABLE IF EXISTS `mirdb`;
CREATE TABLE `mirdb` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `mir2disease`
--
DROP TABLE IF EXISTS `mir2disease`;
CREATE TABLE `mir2disease` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
disease VARCHAR(100) NOT NULL, -- disease
mirna_regulation VARCHAR(20) NOT NULL, -- how miRNA is regulated in the disease (up-regulated, down-regulated or normal)
experiment VARCHAR(40) NOT NULL, -- supporting experiment
year INTEGER UNSIGNED NOT NULL, -- year of the paper
title TEXT NOT NULL, -- title of the paper
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY disease (disease)
);
--
-- Table structure for table `pharmaco_mir`
--
DROP TABLE IF EXISTS `pharmaco_mir`;
CREATE TABLE `pharmaco_mir` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
drug VARCHAR(40) NOT NULL, -- disease
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY drug (drug)
);
--
-- Table structure for table `phenomir`
--
DROP TABLE IF EXISTS `phenomir`;
CREATE TABLE `phenomir` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
pre_mirna_acc VARCHAR(20) default NULL, -- precursor miRNA accession
pre_mirna_id VARCHAR(20) default NULL, -- precursor miRNA ID
disease VARCHAR(60) NOT NULL, -- disease
disease_class VARCHAR(20) NOT NULL, -- disease class
mirna_expression VARCHAR(30) NOT NULL, -- how miRNA is expressed in the disease
study VARCHAR(40) NOT NULL, -- type of study (in cells, patients, etc)
experiment VARCHAR(40) NOT NULL, -- supporting experiment
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY disease (disease),
KEY disease_class (disease_class)
);
--
-- Table structure for table `metadata`
--
DROP TABLE IF EXISTS `metadata`;
CREATE TABLE metadata (
name VARCHAR(80) PRIMARY KEY,
value VARCHAR(255)
);
--
-- Table structure for table `map_metadata`
--
DROP TABLE IF EXISTS `map_metadata`;
CREATE TABLE map_metadata (
map_name VARCHAR(80) PRIMARY KEY,
source_name VARCHAR(80) NOT NULL,
source_version VARCHAR(20),
source_date VARCHAR(20),
source_url VARCHAR(255) NOT NULL
);
--
-- Table structure for table `map_counts`
--
DROP TABLE IF EXISTS `map_counts`;
CREATE TABLE map_counts (
map_name VARCHAR(80) PRIMARY KEY,
human_count INTEGER UNSIGNED NOT NULL,
mouse_count INTEGER UNSIGNED NOT NULL,
total_count INTEGER UNSIGNED NOT NULL
);
--
-- Table structure for table `mirna`
--
DROP TABLE IF EXISTS `mirna`;
CREATE TABLE `mirna` (
mature_mirna_uid INTEGER UNSIGNED AUTO_INCREMENT, -- mature miRNA unique ID
org VARCHAR(4) NOT NULL, -- organism abbreviation
mature_mirna_acc VARCHAR(20) default NULL, -- mature miRNA accession
mature_mirna_id VARCHAR(20) default NULL, -- mature miRNA ID/name
PRIMARY KEY (mature_mirna_uid),
KEY org (org),
KEY mature_mirna_acc (mature_mirna_acc),
KEY mature_mirna_id (mature_mirna_id)
);
--
-- Table structure for table `target`
--
DROP TABLE IF EXISTS `target`;
CREATE TABLE `target` (
target_uid INTEGER UNSIGNED AUTO_INCREMENT, -- target gene unique ID
org VARCHAR(4) NOT NULL, -- organism abbreviation
target_symbol VARCHAR(80) default NULL, -- target gene symbol
target_entrez VARCHAR(10) default NULL, -- target gene Entrez gene ID
target_ensembl VARCHAR(20) default NULL, -- target gene Ensembl gene ID
PRIMARY KEY (target_uid),
KEY org (org),
KEY target_symbol (target_symbol),
KEY target_entrez (target_entrez),
KEY target_ensembl (target_ensembl)
);
--
-- Table structure for table `mirecords`
--
DROP TABLE IF EXISTS `mirecords`;
CREATE TABLE `mirecords` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
target_site_number INT(10) default NULL, -- target site number
target_site_position INT(10) default NULL, -- target site position
experiment VARCHAR(160) default NULL, -- supporting experiment
support_type VARCHAR(40) default NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `mirtarbase`
--
DROP TABLE IF EXISTS `mirtarbase`;
CREATE TABLE `mirtarbase` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
experiment VARCHAR(160) NOT NULL, -- supporting experiment
support_type VARCHAR(40) NOT NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `tarbase`
--
DROP TABLE IF EXISTS `tarbase`;
CREATE TABLE `tarbase` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
experiment VARCHAR(160) NOT NULL, -- supporting experiment
support_type VARCHAR(40) NOT NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `miranda`
--
DROP TABLE IF EXISTS `miranda`;
CREATE TABLE `miranda` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
conservation REAL NOT NULL, -- conservation score
mirsvr_score REAL NOT NULL, -- mirSVR downregulation score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY conservation (conservation),
KEY mirsvr_score (mirsvr_score)
);
--
-- Table structure for table `targetscan`
--
DROP TABLE IF EXISTS `targetscan`;
CREATE TABLE `targetscan` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
site_type INTEGER UNSIGNED NOT NULL, -- site type (see http://www.targetscan.org/faqs.html)
context_plus_score REAL NOT NULL, -- context+ score
conserved_site ENUM('N','Y'), -- whether the target site is conserved
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY context_plus_score (context_plus_score),
KEY conserved_site (conserved_site)
);
--
-- Table structure for table `diana_microt`
--
DROP TABLE IF EXISTS `diana_microt`;
CREATE TABLE `diana_microt` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
miTG_score REAL NOT NULL, -- miRNA target gene score
UTR3_hit INTEGER UNSIGNED NOT NULL, -- number of 3'-UTR binding sites
CDS_hit INTEGER UNSIGNED NOT NULL, -- number of CDS binding sites
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY miTG_score (miTG_score)
);
--
-- Table structure for table `elmmo`
--
DROP TABLE IF EXISTS `elmmo`;
CREATE TABLE `elmmo` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
p REAL NOT NULL, -- "the posterior probability that the site is under evolutionnary selective pressure"
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY p (p)
);
--
-- Table structure for table `pita`
--
DROP TABLE IF EXISTS `pita`;
CREATE TABLE `pita` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
ddG REAL NOT NULL, -- ddG = dGduplex (microRNA-target hybridization energy) - dGopen (energy required to make the target site accessible)
conservation REAL NOT NULL, -- site conservation (range 0~1)
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY ddG (ddG),
KEY conservation (conservation)
);
--
-- Table structure for table `microcosm`
--
DROP TABLE IF EXISTS `microcosm`;
CREATE TABLE `microcosm` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- miRanda score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `pictar`
--
DROP TABLE IF EXISTS `pictar`;
CREATE TABLE `pictar` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `mirdb`
--
DROP TABLE IF EXISTS `mirdb`;
CREATE TABLE `mirdb` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `mir2disease`
--
DROP TABLE IF EXISTS `mir2disease`;
CREATE TABLE `mir2disease` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
disease VARCHAR(100) NOT NULL, -- disease
mirna_regulation VARCHAR(20) NOT NULL, -- how miRNA is regulated in the disease (up-regulated, down-regulated or normal)
experiment VARCHAR(40) NOT NULL, -- supporting experiment
year INTEGER UNSIGNED NOT NULL, -- year of the paper
title TEXT NOT NULL, -- title of the paper
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY disease (disease)
);
--
-- Table structure for table `pharmaco_mir`
--
DROP TABLE IF EXISTS `pharmaco_mir`;
CREATE TABLE `pharmaco_mir` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
drug VARCHAR(40) NOT NULL, -- disease
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY drug (drug)
);
--
-- Table structure for table `phenomir`
--
DROP TABLE IF EXISTS `phenomir`;
CREATE TABLE `phenomir` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
pre_mirna_acc VARCHAR(20) default NULL, -- precursor miRNA accession
pre_mirna_id VARCHAR(20) default NULL, -- precursor miRNA ID
disease VARCHAR(60) NOT NULL, -- disease
disease_class VARCHAR(20) NOT NULL, -- disease class
mirna_expression VARCHAR(30) NOT NULL, -- how miRNA is expressed in the disease
study VARCHAR(40) NOT NULL, -- type of study (in cells, patients, etc)
experiment VARCHAR(40) NOT NULL, -- supporting experiment
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY disease (disease),
KEY disease_class (disease_class)
);
--
-- Table structure for table `metadata`
--
DROP TABLE IF EXISTS `metadata`;
CREATE TABLE metadata (
name VARCHAR(80) PRIMARY KEY,
value VARCHAR(255)
);
--
-- Table structure for table `map_metadata`
--
DROP TABLE IF EXISTS `map_metadata`;
CREATE TABLE map_metadata (
map_name VARCHAR(80) PRIMARY KEY,
source_name VARCHAR(80) NOT NULL,
source_version VARCHAR(20),
source_date VARCHAR(20),
source_url VARCHAR(255) NOT NULL
);
--
-- Table structure for table `map_counts`
--
DROP TABLE IF EXISTS `map_counts`;
CREATE TABLE map_counts (
map_name VARCHAR(80) PRIMARY KEY,
human_count INTEGER UNSIGNED NOT NULL,
mouse_count INTEGER UNSIGNED NOT NULL,
total_count INTEGER UNSIGNED NOT NULL
);
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ]
>
> proc.time()
user system elapsed
6.07 0.59 8.79
|
multiMiR.Rcheck/tests_x64/testthat.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(multiMiR)
Welcome to multiMiR.
multiMiR database URL has been set to the
default value: http://multimir.org/
Database Version: 2.3.0 Updated: 2020-04-15
>
> test_check("multiMiR")
--
-- Table structure for table `mirna`
--
DROP TABLE IF EXISTS `mirna`;
CREATE TABLE `mirna` (
mature_mirna_uid INTEGER UNSIGNED AUTO_INCREMENT, -- mature miRNA unique ID
org VARCHAR(4) NOT NULL, -- organism abbreviation
mature_mirna_acc VARCHAR(20) default NULL, -- mature miRNA accession
mature_mirna_id VARCHAR(20) default NULL, -- mature miRNA ID/name
PRIMARY KEY (mature_mirna_uid),
KEY org (org),
KEY mature_mirna_acc (mature_mirna_acc),
KEY mature_mirna_id (mature_mirna_id)
);
--
-- Table structure for table `target`
--
DROP TABLE IF EXISTS `target`;
CREATE TABLE `target` (
target_uid INTEGER UNSIGNED AUTO_INCREMENT, -- target gene unique ID
org VARCHAR(4) NOT NULL, -- organism abbreviation
target_symbol VARCHAR(80) default NULL, -- target gene symbol
target_entrez VARCHAR(10) default NULL, -- target gene Entrez gene ID
target_ensembl VARCHAR(20) default NULL, -- target gene Ensembl gene ID
PRIMARY KEY (target_uid),
KEY org (org),
KEY target_symbol (target_symbol),
KEY target_entrez (target_entrez),
KEY target_ensembl (target_ensembl)
);
--
-- Table structure for table `mirecords`
--
DROP TABLE IF EXISTS `mirecords`;
CREATE TABLE `mirecords` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
target_site_number INT(10) default NULL, -- target site number
target_site_position INT(10) default NULL, -- target site position
experiment VARCHAR(160) default NULL, -- supporting experiment
support_type VARCHAR(40) default NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `mirtarbase`
--
DROP TABLE IF EXISTS `mirtarbase`;
CREATE TABLE `mirtarbase` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
experiment VARCHAR(160) NOT NULL, -- supporting experiment
support_type VARCHAR(40) NOT NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `tarbase`
--
DROP TABLE IF EXISTS `tarbase`;
CREATE TABLE `tarbase` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
experiment VARCHAR(160) NOT NULL, -- supporting experiment
support_type VARCHAR(40) NOT NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `miranda`
--
DROP TABLE IF EXISTS `miranda`;
CREATE TABLE `miranda` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
conservation REAL NOT NULL, -- conservation score
mirsvr_score REAL NOT NULL, -- mirSVR downregulation score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY conservation (conservation),
KEY mirsvr_score (mirsvr_score)
);
--
-- Table structure for table `targetscan`
--
DROP TABLE IF EXISTS `targetscan`;
CREATE TABLE `targetscan` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
site_type INTEGER UNSIGNED NOT NULL, -- site type (see http://www.targetscan.org/faqs.html)
context_plus_score REAL NOT NULL, -- context+ score
conserved_site ENUM('N','Y'), -- whether the target site is conserved
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY context_plus_score (context_plus_score),
KEY conserved_site (conserved_site)
);
--
-- Table structure for table `diana_microt`
--
DROP TABLE IF EXISTS `diana_microt`;
CREATE TABLE `diana_microt` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
miTG_score REAL NOT NULL, -- miRNA target gene score
UTR3_hit INTEGER UNSIGNED NOT NULL, -- number of 3'-UTR binding sites
CDS_hit INTEGER UNSIGNED NOT NULL, -- number of CDS binding sites
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY miTG_score (miTG_score)
);
--
-- Table structure for table `elmmo`
--
DROP TABLE IF EXISTS `elmmo`;
CREATE TABLE `elmmo` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
p REAL NOT NULL, -- "the posterior probability that the site is under evolutionnary selective pressure"
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY p (p)
);
--
-- Table structure for table `pita`
--
DROP TABLE IF EXISTS `pita`;
CREATE TABLE `pita` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
ddG REAL NOT NULL, -- ddG = dGduplex (microRNA-target hybridization energy) - dGopen (energy required to make the target site accessible)
conservation REAL NOT NULL, -- site conservation (range 0~1)
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY ddG (ddG),
KEY conservation (conservation)
);
--
-- Table structure for table `microcosm`
--
DROP TABLE IF EXISTS `microcosm`;
CREATE TABLE `microcosm` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- miRanda score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `pictar`
--
DROP TABLE IF EXISTS `pictar`;
CREATE TABLE `pictar` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `mirdb`
--
DROP TABLE IF EXISTS `mirdb`;
CREATE TABLE `mirdb` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `mir2disease`
--
DROP TABLE IF EXISTS `mir2disease`;
CREATE TABLE `mir2disease` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
disease VARCHAR(100) NOT NULL, -- disease
mirna_regulation VARCHAR(20) NOT NULL, -- how miRNA is regulated in the disease (up-regulated, down-regulated or normal)
experiment VARCHAR(40) NOT NULL, -- supporting experiment
year INTEGER UNSIGNED NOT NULL, -- year of the paper
title TEXT NOT NULL, -- title of the paper
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY disease (disease)
);
--
-- Table structure for table `pharmaco_mir`
--
DROP TABLE IF EXISTS `pharmaco_mir`;
CREATE TABLE `pharmaco_mir` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
drug VARCHAR(40) NOT NULL, -- disease
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY drug (drug)
);
--
-- Table structure for table `phenomir`
--
DROP TABLE IF EXISTS `phenomir`;
CREATE TABLE `phenomir` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
pre_mirna_acc VARCHAR(20) default NULL, -- precursor miRNA accession
pre_mirna_id VARCHAR(20) default NULL, -- precursor miRNA ID
disease VARCHAR(60) NOT NULL, -- disease
disease_class VARCHAR(20) NOT NULL, -- disease class
mirna_expression VARCHAR(30) NOT NULL, -- how miRNA is expressed in the disease
study VARCHAR(40) NOT NULL, -- type of study (in cells, patients, etc)
experiment VARCHAR(40) NOT NULL, -- supporting experiment
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY disease (disease),
KEY disease_class (disease_class)
);
--
-- Table structure for table `metadata`
--
DROP TABLE IF EXISTS `metadata`;
CREATE TABLE metadata (
name VARCHAR(80) PRIMARY KEY,
value VARCHAR(255)
);
--
-- Table structure for table `map_metadata`
--
DROP TABLE IF EXISTS `map_metadata`;
CREATE TABLE map_metadata (
map_name VARCHAR(80) PRIMARY KEY,
source_name VARCHAR(80) NOT NULL,
source_version VARCHAR(20),
source_date VARCHAR(20),
source_url VARCHAR(255) NOT NULL
);
--
-- Table structure for table `map_counts`
--
DROP TABLE IF EXISTS `map_counts`;
CREATE TABLE map_counts (
map_name VARCHAR(80) PRIMARY KEY,
human_count INTEGER UNSIGNED NOT NULL,
mouse_count INTEGER UNSIGNED NOT NULL,
total_count INTEGER UNSIGNED NOT NULL
);
--
-- Table structure for table `mirna`
--
DROP TABLE IF EXISTS `mirna`;
CREATE TABLE `mirna` (
mature_mirna_uid INTEGER UNSIGNED AUTO_INCREMENT, -- mature miRNA unique ID
org VARCHAR(4) NOT NULL, -- organism abbreviation
mature_mirna_acc VARCHAR(20) default NULL, -- mature miRNA accession
mature_mirna_id VARCHAR(20) default NULL, -- mature miRNA ID/name
PRIMARY KEY (mature_mirna_uid),
KEY org (org),
KEY mature_mirna_acc (mature_mirna_acc),
KEY mature_mirna_id (mature_mirna_id)
);
--
-- Table structure for table `target`
--
DROP TABLE IF EXISTS `target`;
CREATE TABLE `target` (
target_uid INTEGER UNSIGNED AUTO_INCREMENT, -- target gene unique ID
org VARCHAR(4) NOT NULL, -- organism abbreviation
target_symbol VARCHAR(80) default NULL, -- target gene symbol
target_entrez VARCHAR(10) default NULL, -- target gene Entrez gene ID
target_ensembl VARCHAR(20) default NULL, -- target gene Ensembl gene ID
PRIMARY KEY (target_uid),
KEY org (org),
KEY target_symbol (target_symbol),
KEY target_entrez (target_entrez),
KEY target_ensembl (target_ensembl)
);
--
-- Table structure for table `mirecords`
--
DROP TABLE IF EXISTS `mirecords`;
CREATE TABLE `mirecords` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
target_site_number INT(10) default NULL, -- target site number
target_site_position INT(10) default NULL, -- target site position
experiment VARCHAR(160) default NULL, -- supporting experiment
support_type VARCHAR(40) default NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `mirtarbase`
--
DROP TABLE IF EXISTS `mirtarbase`;
CREATE TABLE `mirtarbase` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
experiment VARCHAR(160) NOT NULL, -- supporting experiment
support_type VARCHAR(40) NOT NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `tarbase`
--
DROP TABLE IF EXISTS `tarbase`;
CREATE TABLE `tarbase` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
experiment VARCHAR(160) NOT NULL, -- supporting experiment
support_type VARCHAR(40) NOT NULL, -- type of supporting experiment
pubmed_id VARCHAR(10) default NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT
);
--
-- Table structure for table `miranda`
--
DROP TABLE IF EXISTS `miranda`;
CREATE TABLE `miranda` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
conservation REAL NOT NULL, -- conservation score
mirsvr_score REAL NOT NULL, -- mirSVR downregulation score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY conservation (conservation),
KEY mirsvr_score (mirsvr_score)
);
--
-- Table structure for table `targetscan`
--
DROP TABLE IF EXISTS `targetscan`;
CREATE TABLE `targetscan` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
site_type INTEGER UNSIGNED NOT NULL, -- site type (see http://www.targetscan.org/faqs.html)
context_plus_score REAL NOT NULL, -- context+ score
conserved_site ENUM('N','Y'), -- whether the target site is conserved
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY context_plus_score (context_plus_score),
KEY conserved_site (conserved_site)
);
--
-- Table structure for table `diana_microt`
--
DROP TABLE IF EXISTS `diana_microt`;
CREATE TABLE `diana_microt` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
miTG_score REAL NOT NULL, -- miRNA target gene score
UTR3_hit INTEGER UNSIGNED NOT NULL, -- number of 3'-UTR binding sites
CDS_hit INTEGER UNSIGNED NOT NULL, -- number of CDS binding sites
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY miTG_score (miTG_score)
);
--
-- Table structure for table `elmmo`
--
DROP TABLE IF EXISTS `elmmo`;
CREATE TABLE `elmmo` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
p REAL NOT NULL, -- "the posterior probability that the site is under evolutionnary selective pressure"
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY p (p)
);
--
-- Table structure for table `pita`
--
DROP TABLE IF EXISTS `pita`;
CREATE TABLE `pita` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
ddG REAL NOT NULL, -- ddG = dGduplex (microRNA-target hybridization energy) - dGopen (energy required to make the target site accessible)
conservation REAL NOT NULL, -- site conservation (range 0~1)
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY ddG (ddG),
KEY conservation (conservation)
);
--
-- Table structure for table `microcosm`
--
DROP TABLE IF EXISTS `microcosm`;
CREATE TABLE `microcosm` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- miRanda score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `pictar`
--
DROP TABLE IF EXISTS `pictar`;
CREATE TABLE `pictar` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `mirdb`
--
DROP TABLE IF EXISTS `mirdb`;
CREATE TABLE `mirdb` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
score REAL NOT NULL, -- score
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY score (score)
);
--
-- Table structure for table `mir2disease`
--
DROP TABLE IF EXISTS `mir2disease`;
CREATE TABLE `mir2disease` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
disease VARCHAR(100) NOT NULL, -- disease
mirna_regulation VARCHAR(20) NOT NULL, -- how miRNA is regulated in the disease (up-regulated, down-regulated or normal)
experiment VARCHAR(40) NOT NULL, -- supporting experiment
year INTEGER UNSIGNED NOT NULL, -- year of the paper
title TEXT NOT NULL, -- title of the paper
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY disease (disease)
);
--
-- Table structure for table `pharmaco_mir`
--
DROP TABLE IF EXISTS `pharmaco_mir`;
CREATE TABLE `pharmaco_mir` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
target_uid INTEGER UNSIGNED NOT NULL, -- target gene unique ID
drug VARCHAR(40) NOT NULL, -- disease
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
FOREIGN KEY (target_uid)
REFERENCES target(target_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY drug (drug)
);
--
-- Table structure for table `phenomir`
--
DROP TABLE IF EXISTS `phenomir`;
CREATE TABLE `phenomir` (
mature_mirna_uid INTEGER UNSIGNED NOT NULL, -- mature miRNA unique ID
pre_mirna_acc VARCHAR(20) default NULL, -- precursor miRNA accession
pre_mirna_id VARCHAR(20) default NULL, -- precursor miRNA ID
disease VARCHAR(60) NOT NULL, -- disease
disease_class VARCHAR(20) NOT NULL, -- disease class
mirna_expression VARCHAR(30) NOT NULL, -- how miRNA is expressed in the disease
study VARCHAR(40) NOT NULL, -- type of study (in cells, patients, etc)
experiment VARCHAR(40) NOT NULL, -- supporting experiment
pubmed_id VARCHAR(10) NOT NULL, -- PubMed ID
FOREIGN KEY (mature_mirna_uid)
REFERENCES mirna(mature_mirna_uid)
ON UPDATE CASCADE ON DELETE RESTRICT,
KEY disease (disease),
KEY disease_class (disease_class)
);
--
-- Table structure for table `metadata`
--
DROP TABLE IF EXISTS `metadata`;
CREATE TABLE metadata (
name VARCHAR(80) PRIMARY KEY,
value VARCHAR(255)
);
--
-- Table structure for table `map_metadata`
--
DROP TABLE IF EXISTS `map_metadata`;
CREATE TABLE map_metadata (
map_name VARCHAR(80) PRIMARY KEY,
source_name VARCHAR(80) NOT NULL,
source_version VARCHAR(20),
source_date VARCHAR(20),
source_url VARCHAR(255) NOT NULL
);
--
-- Table structure for table `map_counts`
--
DROP TABLE IF EXISTS `map_counts`;
CREATE TABLE map_counts (
map_name VARCHAR(80) PRIMARY KEY,
human_count INTEGER UNSIGNED NOT NULL,
mouse_count INTEGER UNSIGNED NOT NULL,
total_count INTEGER UNSIGNED NOT NULL
);
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ]
>
> proc.time()
user system elapsed
6.32 0.29 8.76
|
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multiMiR.Rcheck/examples_i386/multiMiR-Ex.timings
|
multiMiR.Rcheck/examples_x64/multiMiR-Ex.timings
|