MiniProject:Testing and tracing in viral epidemics

Miniproject:

Testing and tracing in viral epidemics

Owner:

Vanisha Arora

Collaborators:

Om Prakash

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:

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

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

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

4. 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.

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.

**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