miniproject: viral epidemics and disease

What diseases co-occur with viral epidemics?

owner:

Priya

collaborators:

Dheeraj kumar

miniproject summary

proposed activities

• Use the communal corpus epidemic50noCov consisting of 50 articles.
• Scrutinizing the 50 articles to know the true positives and false positives, that is, whether the articles are about viral epidemic or not.
• Using ami search to find whether the articles mentioned any comorbidity in a viral epidemic or not.
• Sectioning the articles using ami:section to extract the relevant information on comorbidity. Annotating with dictionaries to create ami DataTables.
• Refining and rerunning the query to get a corpus of 950 articles.
• Using relevant ML technique for the classification of data whether the articles are based on viral epidemic and the diseases/disorders that co-occur.

outcomes

• A spreadsheet as well as a graph will be developed based on the comorbidity during a viral epidemic and their count.
• Development of the ML model for data classification on accuracy.

corpora

• Initially the communal corpus epidemic50noCov will be used.
• Later a corpus of 950 articles will be created.

dictionaries

• Disease (https://github.com/petermr/openVirus/wiki/Dictionary:-Diseases)

software

• getpapers to create the corpus of 950 articles from EuPMC.
• AMI for creating and using dictionaries, sectioning.
• SPARQL for creating dictionaries.
• KNIME for workflow and analytics.
• keras for binary classification.

constraints

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Initial Summary

(by collaborator Dheeraj)

The aim of the mini-project

What is our aim first of all, that if we recognize diseases, then we will be able to give medicines for it. In this mini project, we will be able to find diseases with the help of disease dictionary in times of "viral epidemic" by using ContentMine software ( getpapers and ami)

Resources

Dictionary

• The names of all diseases are updated in the dictionary of diseases which are helpful in searching particular diseases' words in the articles, just like the dictionary contains a store of words.
• It's source is ICD-10(by WHO) and Wikidata and it was created using ami.

Corpus 950

• This is a group of articles which is based on viral epidemics and diseases. These articles contain information regarding diseases which are to be simplified.
• This is a group of 950 articles that have been downloaded from EuPMC via getpapers.

Eupmc

This is a Pub Med Central website with a lot of scientific research knowledge articles. We are analyzing some of these articles for our mini-project, which are downloaded using getpapers.

Tools

getpapers

• It is a ContentMine software capable of downloading large number of articles from Eupmc.
• See https://github.com/petermr/openVirus/wiki/getpapers for using.

ami

• It is also a ContentMine software. It is used in creating a dictionary. It is useful for searching particular diseases' words that are updated in dictionary, sectioning downloaded articles and gathering information from them.
• Like in this, we have created a dictionary of disease.

Work done

• I have read about getpapers and EuPMC and also I have read about advanced search in EuPMC and Reading its articles too.
• I am reading wikidata and learning how to update the dictionary.

My goal

• As we said that if diseases are known, then we can give medicines accordingly. Therefore, our main goal will be to find out the names of diseases that co-occur during viral epidemics.
• In this mini-project my main goal is that updating dictionary with ICD-10 using Wikidata.

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Progress done

1. The 50 articles in communal corpus epidemic50noCov were binary classified as true and false positives manually and a spreadsheet was developed.
2. ami search was used in the corpus of 50 articles and the html DataTables on disease dictionary were created.
3. The corpus was sectioned using ami section as per the reference from https://github.com/petermr/openVirus/wiki/ami:section.
4. getpapers was used to create a corpus of 950 articles regarding human viral epidemics(expect COVID-19) by the syntax getpapers -q "viral epidemics AND human NOT COVID NOT corona virus NOT SARS-Cov-2" -o mpc -f mpc/log.txt -k 950 -x -p. JATS - 950 files, a log text document, XML -949 files & PDF -903 files were created.
5. ami search was used successfully in the 950 article corpus, which was segmented into 4 folders each containing 200-250 articles.
6. The 950 article corpus was sectioned successfully using ami section.
7. The 950 article corpus was uploaded in GitHub (Thanks to Ambreen).
8. Another disease dictionary was created with synonyms.

Things need to be done

(in the 950 article corpus)

1. To binary classify true and false positives manually (progressing).
2. To use KNIME software for binary classification.
3. To test the data classification on accuracy.

Blocking

1. Learning KNIME and Keras to use in binary classification.

Update

Uploading corpus to GitHub

(Reference from Ambreen's update )

1. Download VS code and clone the openVirus repository into your system.
2. Open the openVirus folder in VS code (don't close it).
3. Now open your openVirus folder in your directory and make your changes in it.
4. Reopen the VS code that was minimized. Now commit the changes by selecting the commit symbol. It might take time with respect to your size of uploading files.
5. After adding the remote repository, push the changes to GitHub. See this video for other clarification.

NOTE : If already had cloned the repository, first pull the repo and then push the changes.