Biological database ICA

This is a biological database coursework for MSc Bioinformatics that searches the ENSEMBL, UNIPROT, GO, and STRING database. 10 gene identifier IDs are used to search through the databases and result tables of each search are loaded into the mysql database.

10 gene identifier IDs:
"ENSMUSG00000036061", "ENSMUSG00000000555", "ENSMUSG00000023055", "ENSMUSG00000075394",
"ENSMUSG00000001655", "ENSMUSG00000022485", "ENSMUSG00000001657", "ENSMUSG00000001661",
"ENSMUSG00000076010", "ENSMUSG00000023048"

Database searched:

1. ENSEMBL (http://www.ensembl.org)
2. UNIPROT (https://www.uniprot.org)
3. GO (https://geneontology.org)
4. STRING (https://string-db.org)

Steps

1. Database access

The search results from each database are organised into individual table and saved in the search_results folder. Depending on the database type, the databases are accessed using REST API (returns JSON) or directly using Biomart (returns pandas dataframe).

2. Loading into mysql server

The tables saved in the search_results folder are loaded into the mysql server by creating the gene_search_db database. When loading each results table, the ENSEMBL_id is set as the primary keys so ensure the relational design of the database so that different tables can be easily accessed with SQL query.

3. SQL query of gene_search_db

The final table that includes results from each database are queried using SQL queries and laoded into an integrated table integrated_table.csv