Project

Advanced Programming 2021/2022

Specification

The project consists in a three .py files, each one containing a different part:

1. part_1.py consists in a program able to:

   • Read the files;
   • Provide a registry of analytical operations that can be performed on the dataset and the link to the classes created in the part_2.py;
   • Links to part_3.py.

2. part_2.py consists in a program containing the classes and their associated methods for:

   • Recording the numerical metadata consisting of the number of rows and columns of each of the two files composing the data collection;
   • Recording the general semantics of the dataset, i.e. the labels of the columns of each of the two files composing the data collection;
   • Recording the number of different genes detected in literature. The list should be sorted in ascending order;
   • Given a gene symbol, provide the list of sentences that are an evidence in literature about the relation of this gene with COVID-19;
   • Recording the number of different disease detected in literature. The list should be sorted in ascending order;
   • Given a disease ID, provide the list of sentences that are an evidence in literature about the relation of this disease with COVID-19;
   • Recording the 10-top most frequent distinct association between genes and diseases;
   • Given a gene symbol, provide the list of diseases such a gene is associated with;
   • Given a disease name, provide the list of genes such a disease is associated with.

3. part_3.py consists in a program which implements the Web-based user interface (UI).

CRC Cards

We have provided a folder with CRC cards explaining each class built in part_2.py, each CRC card has been created with Visual Paradigm.

UML diagrams

We have provided a folder with an UML diagram explaining the connections between the classes built in part_2.py:

• DiagramProject.jpg is an image representing the UML diagram created with Visual Paradigm.
• UMLproject_final.vpp is the equivalent of DiagramProject.jpg but in format .vpp.

Templates

It is a folder with several templates used in order to implement the file part_3.py to create an HTML web page.

Data

The three parts will analyze the DisGeNET COVID-19 data collection. The .tsv files can be downloaded clicking onto the following links:

• disease_evidences.tsv
• gene_evidences.tsv

Libraries

Several libraries have been used:

import pandas as pd
from flask import Flask, render_template, request

In order to run the program, make sure to have them installed. If not, we have provided some tutorials to do so:

• Installing Flask;
• Installing pandas.

HTML page

Once running the part_3.py, the homepage will be available at the following link.

Authors

Corona Gaia, Storari Samuele, Verdesca Laura Claudia.