miniproject: viral epidemics and zoonoses

Which Viral Zoonoses lead to Viral Epidemic?

Owner

SANA SAIFI

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 based on various parameters- related to viral epidemic or not, funders named or not, country mentioned or not and so on.

◾ Re-run the query to get a corpus of 950 articles on the same.

◾ Create a dictionary on zoonotic diseases, specifically related to the Mini Project.

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

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

Software Used:

• nodejs nvm for installing get papers

• getpapers for retrieving 950 articles from EuPMC

• AMI for sectioning and searching.

• SPARQL and amidict

  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.

SEARCHING

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.

◾ amidict will be used for creating dictionaries.

◾ R for data analysis / KNIME

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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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