miniproject: viral epidemics and zoonoses

Which Viral Zoonoses lead to Viral Epidemic?

Owner

SANA SAIFI

Collaborator

_ 

Background !

Zoonoses are diseases transmissible from animals, to Humans. Both new and old viral zoonoses are important in emerging and reemerging virus diseases leading to a epidemic. Scientists estimate that more than 6 out of every 10 known infectious diseases in people can be spread from animals , and 3 out of every 4 new or emerging infectious diseases in people come from animals.

Mini Project Summary

OBJECTIVE

This Mini Project is set to find, How and which zoonotic diseases lead to the Viral Epidemic.

METHODOLOGY

• Using the communal corpus Viral Epidemic 50 articles were downloaded using get papers.

• Binary Classification of the 50 articles into True Positives/ False Positivesi.e, the articles are based on Viral Epidemics or not.

• Using ami search to find whether the articles mentioned any comorbidity in a viral epidemic or not, annotating with dictionaries to create ami DataTables.

• Sectioning the articles using ami sectionto split a document in aCtreeinto sections. Based on tags from JATS, etc.

• Re-run the query to get a corpus of 950 articles on the _ Viral Epidemics and Zoonoses_.

• Scrutinizing the 950 articles for true positives and false positives and creating a spreadsheet.

• Using ami search to create DataTables and ami section for sectioning the 950 articles.

• Create a dictionary, specifically related to the Mini Project.

• Sectioning the papers on the basis of the diseases related to animals.

• Use relevant machine learning techniques for the classification of data based on whether the papers are related to viral epidemics and the which Viral Zoonotic Disease were reported.

PROGRESS

◾ Spreadsheet of 50 articles classified into the subcategories of viruses, funders, countries, year of publish, testing and tracing, and type of paper is done.

Corpora

◾ Initially the communal corpus of 50 articles on viral epidemics.

                getpapers -q viral epidemics -k 950 -o viral epidemics -x -p

◾ Next, a new corpus of 950 articles using the Dictionary Zoonoses.

◾ Downloaded the corpus of 950 articles using getpapers with the syntax:

                getpapers -q "Zoonoses in Viral epidemics" -k 950 -o viral epidemics -x -p

Dictionary

• How to create dictionary?

• Test Dictionary was created using amidict .

• Again dictionary was created using SPARQL Query Service from Wikidata.

Software Used:

• nodejs nvm for installing get papers
• getpapers for retrieving 950 articles from EuPMC
• AMI for sectioning and searching.
• SPARQL and amidict for creating dictionaries.
• KNIME for displaying results.

AMI SECTIONING :

Sectioning of the dataset is usually done for greater precision.

1. Downloaded the corpus of 950 papers using getpapers in XML, PDF and JSON file.

                    getpapers -q "Zoonoses in Viral epidemics" -k 950 -o viral epidemics -x -p
   

2. To easy the process, made 5 subfolders of 200 corpus.

3. To divide the content of papers into sections of front, body, back and float groups, again open the Command Prompt and give the syntax:

                         ami -p <name of directory> section
   

4. This will create a subfolder of sections in each folder of the scientific paper which is there in your directory.

AMI SEARCH

1. Downloaded the corpus of 950 papers using the above same syntax in XML, PDF and JSON file.

2. To search the dictionary of country drugs funders diseases, open the command prompt and give syntax:

                   ami -p <name of directory> search --dictionary country drugs funders diseases 
   

3. Open the directory and at the end of folder you will find various HTML Document.

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NOT STARTED: KNIME, Keras, R

STARTED : dictionary

BLOCKED : .

FINISHED : downloading and installing get papers, manual classification, list of zoonotic diseases, installing ami, getpapers, maven, jdk, sectioning of corpus950, ami search of corpus 950.

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