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MiniProject:Testing and tracing in viral epidemics

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vanishaarora881 edited this page Aug 10, 2020 · 39 revisions

Miniproject:

Testing and tracing in viral epidemics

Owner:

Vanisha Arora

Summary:

The project aims to extract the information about various "Tests" to diagnose the viral infections during the epidemic and also to encircle the ways to prevent its further spread. "Contact tracing" is the process of identification of persons who may have come into contact with an infected person ("contacts") and subsequent collection of further information about these contacts
The goals of contact tracing are:

  1. Interrupting ongoing transmission and reduce the spread of an infection

  2. Alerting contacts to the possibility of infection and offer preventive services or prophylactic care

  3. To offer diagnosis, counseling and treatment to already infected individuals

  4. If the infection is treatable, helping prevent reinfection of the originally infected patient

  5. To learn about the epidemiology of a disease in a particular population

  6. Interrupting ongoing transmission and reduce the spread of an infection.

Objective:

This miniproject is based on extracting information about testing and tracing done in the viral epidemics.

Methodology:

🟨 Conduct binary classification on communal corpus "EpidemicnoCov50" and create a spreadsheet.

🟨 Creating dictionaries for the project using AMI . Searching for the test names for disease diagnosis in the scientific literature.

🟨 Dictionary:Testing and tracing Dictionary (https://github.com/petermr/openVirus/blob/master/dictionaries/test/testing4.xml )

🟨 Downloading a corpus of 950 articles using getpapers and using the ami section for the Sectioning of the papers.

How I created my dictionary:

  • Create a text file (.txt) containing a list of Terms related to "Testing and contact tracing"(From wikipedia or through research papers.)
  • Meanwhile, create a directory by giving command in the command prompt as : mkdir mydictionaries This is the ouput directory where you are going to get the dictionary.
  • Open the command prompt and give the command as: amidict -v --dictionary testing_and_tracing --directory mydictionaries --input test_trace.txt create --informat list --outformats xml,html
  • The input file in the syntax is the file which was downloaded in Step 1.
  • After giving the command in Step 4, it took a while to create the dictionary.
  • Open the folder 'mydictionaries' in the system, the dictionary is created as both xml and html file.

Committing the corpus :

Tried committing through: ✔️ Github desktop

If you are using Github desktop to commit:Following steps are followed:

  • Installed Github desktop from : https://desktop.github.com
  • Cloned the repository openVirus into my system using Gitbash commandline : git clone https://github.com/petermr/openVirus.git
  • Open the folder where you want to upload your CProject.
  • Paste your project to the folder in openVirus repository(our remote repository) where you want to commit the files.
  • Open the Github desktop.
  • Go to 'File', then 'Add Local Repository'.
  • Now, choose the openVirus repository from your system.
  • Add a commit message and go to 'Commit to master'.
  • After committing, go to 'Push to origin'.
  • After completion of pushing the repository, your uploaded files can be viewed on the Github repository.

Issues faced:

  • Existence of the lock file in the repository, which has to be deleted to proceed. ✔️ Suggestion is to delete the file if any before starting to commit to avoid the wastage of time.
  • Connectivity issue : A good internet connection is required.

⚠️ PMR committed a corpus of 500 for me.

Used Git pull command in git bash to download the corpus for running ami section and ami search. git pull path.git

This command showed error in my windows . So, i used command prompt for cloning the repository.

PMR SUGGESTION: To Start working on corpus 100 to make things easy and avoid the time wastage.

Softwares used:

  1. AMI for creating dictionary and sectioning the corpus.

  2. KNIME for data extraction and Binary classification.

  3. KNIME, R for analysis.

Not started 🟫 :

Usage of knime and R

Started 🟨 :

Ami section for sectioning of corpus and Ami search for searching the tests in the corpus.

BLOCKED 🟥 :

  1. Ami search , The Testing and tracing being very rarely mentioned in the papers, so it is not searching the tests, hence, not getting the data tables. But trying the same in the corpus and searching for funders or countries is giving the results.

Tried ami search on the corpus of 100 and 150 as well but data tables still empty.

**PMR: I agree. This is a hard search. I think we need to collect terms iteratively from Wikipedia, from papers and gradually build a multi-term query. Use Wikipedia's "Contact tracing" as a good source of words and phrases.

FINISHED 🟩 :

  1. Binary classification for EpidemicnoCov50

  2. Creating a Corpus of 950 papers

  3. Dictionary for the Miniproject : https://github.com/petermr/openVirus/blob/master/dictionaries/test/testing4.xml

  4. AMI sectioning.

  5. Corpus commit by PMR

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