NeuroTransDB

Highly Curated and Structured Transcriptomic Meta-Data for Neurodegenerative Diseases

More details about the database content can be found here:

Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius and Philipp Senger (2015):
NeuroTransDB: Highly Curated and Structured Transcriptomic Meta-data for Neurodegenerative Diseases . DATABASE (submitted)

Please cite NeuroTransDB if the data is used.

NeuroTransDB SQLDump

Below are the SQLDump files, along with the table names:

• integrated_view_human: human_AD1.sql
• integrated_view_mouse: mouse_AD1.sql
• integrated_view_rat: rat_AD1.sql

NeuroTransDB as Excel

Here are the tables for Human, Mouse and Rat as Excel/CSV files:

• integrated_view_human: human_AD1.csv
• integrated_view_mouse: mouse_AD1.csv
• integrated_view_rat: rat_AD1.csv

NeuroTransDB Normalized Human Data

Below is the SQLDump file and Excel sheet data for Human Normalized meta-data for AD1 studies:

• NeuroTransDB Human normalized SQL Dump
• NeuroTransDB Human normalized Excel file

Additional Information

Meta-Data Curation Guidelines With Illustrations

To download the guidelines for meta-data curation, please click here. This file contains information for each curated field and how the curation was carried out.

List of Experiments Retrieved From Public Repositories for Alzheimer’s Disease:

To download the list of experiments, that were retrieved using automated method (please refer to Data Retrieval Section in the publication), which were further prioritized and curated, click here.

Priority 1 Experiment IDs:

To download a list of Priority 1 experiment IDs for which NeuroTransDB provides manually curated meta-data information, please click here to download.

MySQL Installation and Data Upload

Please refer to the below link to install MySQL

http://dev.mysql.com/doc/refman/5.6/en/installing.html

MySQLDump Usage:

Below, we describe simple steps for loading the provided SQLDumps into your installed MySQL. 

Step 1: Start mysql  with a username (e.g. myname) and password (if given)

mysql -u myname  -p

For more details please see: https://dev.mysql.com/doc/refman/5.0/en/connecting-disconnecting.html 

Step 2: Create a new empty database of your choice (e.g. test), and then exit MYSQL

CREATE DATABASE test;
exit;

Step 3: Import the given SQLDump table into this created database

mysql -u myname -p test <human_AD1.sql

Please refer to the below link on how to use MySQL database:

https://dev.mysql.com/doc/refman/5.0/en/tutorial.html