jonherke-tg / covid19-1

COVID19

Modeling the Spread & Impact of COVID-19

_{This Database Initiative Community Chat → https://discord.gg/KBerGfE}

_{Largest COVID-19 Community Chat → https://discord.gg/Bphw4dF}

The threat of COVID-19 from spreading and affecting those around us, especially our loved ones that are over the age of 60+ with the exponential mortality rate of COVID 19 rising to 15% in those around the age of 80.

The biggest impact is not only the impact on the health around us, but the stability of the global economy itself.

Proposal: Build the world's richest inter-connected data set that allows the world's smartest researchers to build virus spread models, economic impact models, reporting dashboards, drug vaccine effectiveness models to supply-chain models.

Additional Information Presented by Professor Victor Lee Coronavirus-a-serious-need-for-analyzing-connections

Click Here to See Where You Can Help!

Spread Prediction:

Transportation Data

Viruses spread through means of transportation. The biggest transportation networks are airlines. If we pull the last year of all flight data from every plane to every airport the flew in and out of. Along with the path of virus spread we may begin to identify where the

This data can be extracted from OpenSky API.

Open Sky Documentation

https://opensky-network.org/apidoc/rest.html

The missing data from open sky is the ICAO which are International Airport Codes

https://docs.google.com/spreadsheets/d/1CGENTf6vbRkXeXhEuPRq6uIjpNRH_u-0ql5h90qzCoA/edit?usp=sharing

Sample Data - Pulled from Open Sky https://colab.research.google.com/drive/16NCKbgVTZIrBj-CasNI7ZycpBZdghJqp#scrollTo=b-flVhevP2IJ

    [{
    'icao24': 'e48bb0',
    'firstSeen': 1517227957,
    'estDepartureAirport': 'SBSP',
    'lastSeen': 1517229087,
    'estArrivalAirport': None,
    'callsign': 'ONE6004 ',
    'estDepartureAirportHorizDistance': 5036,
    'estDepartureAirportVertDistance': 493,
    'estArrivalAirportHorizDistance': None,
    'estArrivalAirportVertDistance': None,
    'departureAirportCandidatesCount': 1,
    'arrivalAirportCandidatesCount': 0
    }]

Data restrictions on pulling arrival and departure data is a two hour window. We will need to write a script to pull all the historical data in 2 hour chunks.

Case Data

The most reliable case data is from John Hopkis whom is pulling World Health Organization data and publishing to their github repository: https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data

Case data includes: Province/State, Country/Region ,Last Update, Confirmed, Deaths, Recovered, Latitude, Longitude

Genomic Drug Effectiveness:

Currently there are 113 submitted ARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences in the GenBank database. https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/

Meta Data on COVID-19 GenBank

https://github.com/nextstrain/ncov/blob/master/data/metadata.tsv

Economic Impact:

Pull Social Media Data?

Pull New Sources Data? (Some listed below)

Trading Data

http://docs.tradingeconomics.com/#snapshots

Additional Data

https://www.moh.gov.sg/covid-19/

https://www.cdc.gov/coronavirus/2019-ncov/

https://2019ncov.nosugartech.com/data.json

https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/

https://drive.google.com/file/d/1y3lf7-fiEW_jtoNg_V3rTLn-Ub8yXRcY/view

https://bnonews.com/index.php/2020/01/the-latest-coronavirus-cases/

https://experience.arcgis.com/experience/685d0ace521648f8a5beeeee1b9125cd

TigerGraph Resources

https://github.com/tigergraph/ecosys

https://docs.tigergraph.com/

Education Materials:

https://www.tigergraph.com/certification-graph-fundamentals/

https://www.tigergraph.com/certification-gsql-101/

COVID19 Repository

https://github.com/futuristacademy/COVID19

COVID Free Server:

https://covid19.i.tgcloud.io:14240/#/schema-designer

Where to Help

Get Started

• Join the Discord Group so we can communicate

• Short read on “Why it’s important to connect data”

• If you would like to learn about TigerGraph look at education materials

  • https://www.tigergraph.com/certification-graph-fundamentals/

  • https://www.tigergraph.com/certification-gsql-101/

• Get access to COVID19 Repository (send email to [email protected])

• Get access to this document (send email to [email protected])

Data Pipelines:

• Setup Data Pipeline for Flight data (Pull from source,Normalization, Push to TG)

• Setup Data Pipeline for Case data (Pull from source,Normalization, Push to TG)

• Determine other data sources

• Setup pipes to other data sources

Database:

• Sample datasets to build database model (schema)

• Once we have data pipeline create loading job to ingest data

Intelligent Layer on top of DB:

• Determine what that would look like

Additional Notes: