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Covid-19-Community

This project is a community effort to build a Neo4j Knowledge Graph (KG) that integrates heterogeneous biomedical and environmental datasets to help researchers analyze the interplay between host, pathogen, the environment, and COVID-19.

Knowledge Graph Schema

Location Subgraph: This subgraph represents the geographic hierarchy from the world to the city level (population > 1000), as well as PostalCode (US ZIP) and US Census Tract level. Each geographic node has a Location label (not shown), to simplify finding locations without specifying a specific level in the geographic hierarchy.

Epidemiology Subgraph: This subgraph represents COVID-19 cases including information about viral strains, and the pathogen and host organism. Cases and Strains are linked to the locations where they were reported and found, respectively.

Biology Subgraph: This subgraph represents organism, genome, chromosome, gene, variant, protein, protein structure, protein domain, protein family, pathogen-host protein-protein interactions, and links to publications.

Population Characteristics Subgraph: This subgraph represents data from the American Community Survey 2018 5-year estimates. Selected population characteristics that may be risk factors for COVID-19 infections have been included. These data are currently available at three geographic levels: US Counties (Admin2), US ZIP Codes (PostalCode), and US Census Tract (Tract).

Note, this KG is work in progress and changes frequently.

Browse the Knowledge Graph with the Neo4j Browser

The Knowledge Graph is updated daily approximately between 07:00 and 09:00 UTC.

View of Neo4j Browser showing the result of a query about interactions of the Spike glycoprotein with human host proteins and related publications in PubMedCentral.

You can browse the Knowledge Graph here (click the launch button and follow the instructions below)

Neo4j Browser

Run a Full-text Query

Full-text queries enable a wide range of search options including exact phrase queries, fuzzy and wildcard queries, range queries, regular expression queries, and use of boolean expressions (see tutorial on FulltextQuery).

The KG can be searched by the following full-text indices:

bioentities Organism, Genome, Chromosome, Gene, GeneName, Protein, ProteinName, ProteinDomain, ProteinFamily, Structure, Chain, Outbreak, Strain, Variant, Publication

bioids keyword (exact) query for bioentity identifiers (e.g., id, taxonomyId, accession, proId, genomeAccession, doi, variantType, variantConsequence)

sequences full-text and regular expression query for protein sequences

locations UNRegion, UNSubRegion, UNIntermediateRegion, Country, Admin1, Admin2, USRegion, USDivision, City, PostalCode, Tract, CruiseShip

geoids keyword (exact) query for geographic identifiers (e.g., zip codes, fips codes, country iso codes)

Full-text queries have the following format:

CALL db.index.fulltext.queryNodes('<type of entity>', '<text query>') YIELD node, score

The queries return the node and score for each match (higher scores indicate closer matches).

Example full-text query for bioentities for proteins that contain the word spike in the name

Query: (copy and paste into Neo4j browser)

CALL db.index.fulltext.queryNodes("bioentities", "spike") YIELD node
WHERE 'Protein' IN labels(node) // only return nodes with the label Protein
RETURN node

Result:

The full-text query matches several Spike proteins from several coronaviruses. The SARS-CoV-2 Spike glycoprotein (uniprot:P0DTC2) is highlighted in the center with its four cleavage products: Spike glycoprotein without signal peptide (uniprot.chain:PRO_0000449646), Spike protein S1 (uniprot.chain:PRO_0000449647), Spike protein S2 (uniprot.chain:PRO_0000449648), and Spike protein S2' (uniprot.chain:PRO_0000449649) linked by a CLEAVED_BY relationship.

Example full-text query: find spike proteins - tabular results

The following query returns the names of the matched bioentities and the labels of the nodes (e.g., Protein, ProteinName) sorted by the match score in descending order.

Query:

CALL db.index.fulltext.queryNodes("bioentities", "spike") YIELD node, score
RETURN node.name, labels(node), score

Result:

Run a Cypher Query

Specific Nodes and Relationships in the KG can be searched using the Cypher query language.

Example Cypher query: find viral strains collected in Houston

Query: (limited to 10 hits)

MATCH (s:Strain)-[:FOUND_IN]->(l:Location{name: 'Houston'}) RETURN s, l LIMIT 10

Result:

This subgraph shows viral strains (green) of the SARS-CoV-2 virus carried by human hosts in Houston (organisms in gray). The strains have several variants (e.g., mutations)(red) in common. Details of the high-lighted variant is shown at the bottom. This variant is a missense mutation in the S gene (S:c.1841gAt>gGt): the base "A" (Adenosine) found in the Wuhan-Hu-1 reference genome NC_45512 was mutated to a "G" (Guanine) at position 23403, resulting in the encoded Spike glycoprotein (QHD43416) to be changed from a "D" (Aspartic acid) to a "G" (Glycine) amino acid at position 614 (QHD43416.1:p.614D>G).

Example Cypher query: aggregate cummulative COVID-19 case numbers at the US state (Admin1) level

Query:

MATCH (o:Outbreak{id: "COVID-19"})<-[:RELATED_TO]-(c:Cases{date: date("2020-08-31"), source: 'JHU'})-[:REPORTED_IN]->(a:Admin2)-[:IN]->(a1:Admin1)
RETURN a1.name as state, sum(c.cases) as cases, sum(c.deaths) as deaths
ORDER BY cases DESC;

Result:

Note, some cases in the COVID-19 Data Repository by Johns Hopkins University cannot be mapped to a county or state location (e.g., correctional facilities, missing location data). Therefore, the results of this query will underreport the actual number of cases.

Query the Knowledge Graph in Jupyter Notebook

Cypher queries can be run in Jupyter Notebooks to enable reproducible data analyses and visualizations.

You can run the following Jupyter Notebooks in your web browser:

NOTE: Authentication is now required to launch binder! Sign into GitHub from your browser, then click on the launch binder badge below to launch Jupyter Lab.

Binder

Once Jupyter Lab launches, navigate to the notebooks/queries and notebooks/analysesdirectory and run the following notebooks:

Notebook Description
FulltextQuery Runs example fulltext queries
CaseCounts Runs example queries for case counts
Locations Runs example queries for locations
Demographics Runs example queries for demographics data from the American Community Survey
SocialCharacteristics Runs example queries for social characteristics from the American Community Survey
EconomicCharacteristics Runs example queries for economic characteristics from the American Community Survey
Housing Runs example queries for housing characteristics from the American Community Survey
Bioentities Runs example queries for bioentities
EmergingStrains Analyze emerging SARS-CoV-2 Strains
EmergingStrainsInLiterature Analyze emerging SARS-CoV-2 Strains based on mentioning in the Literature
StrainB.1.1.7 Analyze B.1.1.7 Strain
AnalyzeVariantsSpikeGlycoprotein Analyze SARS-CoV-2 Spike Glycoprotein Variants
Coronavirus3DStructures Inventory of coronavirus 3D protein structures
GraphVisualization Demo of graph visualization with Cytoscape
MapMutationsTo3D Map mutations from SARS-CoV-2 strains to 3D Structures
RiskFactorsByStateCounty Explore Risk Factors for COVID-19 for Counties in US States
RiskFactorsSanDiegoCounty Explore Risk Factors for COVID-19 for San Diego County
CovidRatesByStates Explore COVID-19 confirmed cases and death rates for states in a selected country
... add examples here ...

Data Download, Preparation, and Integration

COVID-19-Net Knowledge Graph is created from publically available resources, including databases, files, and web services. A reproducible workflow, defined in this repository, is used to run a daily update of the knowledge graph. The Jupyter notebooks listed in the table below download, clean, standardize, and integrate data in the form of .csv files for ingestion into the Knowledge Graph. The prepared data files are saved in the NEO4J_HOME/import directory and cached intermediate files are saved in the NEO4J_HOME/import/cache directory. These notebooks are run daily at 07:00 UTC in batch using Papermill with the update script to download the latest data and update the Knowlege Graph.

Notebook Description
00b-NCBITaxonomy Downloads the NCBI taxonomy for a subset of organisms
00b-PANGOLineage Downloads the PANGO lineage designations for SARS-CoV-2
00e-GeoNamesCountry Downloads country information from GeoNames.org
00f-GeoNamesAdmin1 Downloads first administrative divisions (State, Province, Municipality) information from GeoNames.org
00g-GeoNamesAdmin2 Downloads second administrative divisions (Counties in the US) information from GeoNames.org
00h-GeoNamesCity Downloads city information (population > 1000) from GeoNames.org
00i-USCensusRegionDivisionState2017 Downloads US regions, divisions, and assigns state FIPS codes from the US Census Bureau
00j-USCensusCountyCity2017 Downloads US County FIPS codes from the US Census Bureau
00k-UNRegion Downloads UN geographic regions, subregions, and intermediate region information from United Nations
00m-USHUDCrosswalk Downloads mappings of US Census tracts to US Postal Service ZIP codes and US Counties
00n-GeoNamesData Downloads longitude, latitude, elevation, and population data from GeoNames.org
00o-GeoNamesPostalCode Downloads US zip code, place name, latitude, longitude data from GeoNames.org
01a-UniProtGene Downloads chromosome and gene information from UniProt
01a-UniProtProtein Downloads protein information from UniProt
01b-NCBIGeneProtein Downloads gene and protein information from NCBI
01c-CNCBStrain Downloads SARS-CoV-2 viral strain metadata from CNCB (China National Center for Bioinformation)
01c-CNCBVariation Downloads variant data from CNCB (China National Center for Bioinformation)
01d-Nextstrain Downloads the SARS-CoV-2 strain metadata from Nextstrain
01e-ProteinProteinInteraction Downloads SARS-CoV-2 - human protein interaction data from IntAct
01f-PDBStructure Downloads 3D protein structures from the Protein Data Bank
01g-PfamDomain Downloads mappings between PDB protein chains and Pfam domains
01h-CORDLineages Maps publications and preprints in the CORD-19 data set to PANGO lineages
01h-PublicationLink Downloads mappings between datasets and publications indexed by PubMed Central (PMC) and Preprints (PPR) and PubMed (PM)
02a-JHUCases Downloads cummulative confimed cases and deaths from the COVID-19 Data Repository by Johns Hopkins University
02a-JHUCasesLocation Standardizes location data for the COVID-19 Data Repository by Johns Hopkins University
02c-SDHHSACases Downloads cummulative confirmed COVID-19 cases from the County of San Diego, Health and Human Services Agency
03a-USCensusDP02Education Downloads social characteristics (DP02) from the American Community Survey 5-Year Data 2018
03a-USCensusDP02Computers Downloads social characteristics (DP02) from the American Community Survey 5-Year Data 2018
03a-USCensusDP03Commuting Downloads economic characteristics (DP03) from the American Community Survey 5-Year Data 2018
03a-USCensusDP03Employment Downloads economic characteristics (DP03) from the American Community Survey 5-Year Data 2018
03a-USCensusDP03HealthInsurance Downloads economic characteristics (DP03) from the American Community Survey 5-Year Data 2018
03a-USCensusDP03Income Downloads economic characteristics (DP03) from the American Community Survey 5-Year Data 2018
03a-USCensusDP03Income Downloads economic characteristics (DP03) from the American Community Survey 5-Year Data 2018
03a-USCensusDP03Occupation Downloads economic characteristics (DP03) from the American Community Survey 5-Year Data 2018
03a-USCensusDP03Poverty Downloads economic characteristics (DP03) from the American Community Survey 5-Year Data 2018
03a-USCensusDP04 Downloads housing (DP04) from the American Community Survey 5-Year Data 2018
03a-USCensusDP05 Downloads demographic data estimates (DP05) from the American Community Survey 5-Year Data 2018
... Future notebooks that add new data to the knowledge graph

How to run Jupyter Notebook Examples locally

1. Fork this project

A fork is a copy of a repository in your GitHub account. Forking a repository allows you to freely experiment with changes without affecting the original project.

In the top-right corner of this GitHub page, click Fork.

Then, download all materials to your laptop by cloning your copy of the repository, where your-user-name is your GitHub user name. To clone the repository from a Terminal window or the Anaconda prompt (Windows), run:

git clone https://github.com/your-user-name/covid-19-community.git
cd covid-19-community

2. Create a conda environment

The file environment.yml specifies the Python version and all packages required by the tutorial.

conda env create -f environment.yml

Activate the conda environment

conda activate covid-19-community

Install Jupyter Lab extensions

jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyterlab-plotly@4.14.3

3. Launch Jupyter Lab

jupyter lab

Navigate to the notebooks/queries directory to run the example Jupyter Notebooks.

How to run the Data Download and Preparation steps locally

Note, the following steps have been implemented for MacOS and Linux only.

Some steps will take a very long time, e.g., notebook 01d-CNCBStrain may take more than 12 hours to run the first time.

Follow steps 1. - 3. from above.

4. Install Neo4j Desktop

Download Neo4j

Then, launch the Neo4j Browser, create an empty database, set the password to "neo4jbinder", and close the database.

5. Set Environment Variable

Add the environment variable NEO4J_HOME with the path to the Neo4j database installation to your .bash_profile file, e.g.

export NEO4J_HOME="/Users/username/Library/Application Support/Neo4j Desktop/Application/neo4jDatabases/database-.../installation-4.0.3"

Add the environment variable NEO4J_IMPORT with the path to the Neo4j database import directory to your .bash_profile file, e.g.

export NEO4J_IMPORT="/Users/username/Library/Application Support/Neo4j Desktop/Application/neo4jDatabases/database-.../installation-4.0.3/import"

6. Run Data Download Notebooks

Start Jupyter Lab.

jupyter lab

Navigate to the (notebooks/dataprep/) directory and run all notebooks in alphabetical order to download, clean, standardize and save the data in the NEO4J_HOME/import directory for ingestion into the Neo4j database.

7. Upload Data into a Local Neo4j Database

Afer all data files have been created in step 6, run (notebooks/local/2-CreateKGLocal.ipynb to import the data into your local Neo4j database. Make sure the Neo4j Browser is closed before running the database import!

8. Browse local KG in Neo4j Browser

After step 7 has completed, start the database in the Neo4j Browser to interactively explore the KG or run local queries.

How can you contribute?

  • File an issue to discuss your idea so we can coordinate efforts
  • Help with specific issues
  • Suggest publically accessible data sets
  • Add Jupyter Notebooks with data analyses, maps, and visualizations
  • Report bugs or issues

Citation

Peter W. Rose, David Valentine, Ilya Zaslavsky, COVID-19-Net: Integrating Health, Pathogen and Environmental Data into a Knowledge Graph for Case Tracking, Analysis, and Forecasting. Available online: https://github.com/covid-19-net/covid-19-community (2020).

Please also cite the data providers.

Data Providers

The schema below shows how data sources are integrated into the nodes of the Knowledge Graph.

Acknowledgements

Neo4j provided technical support and organized the community development: "GraphHackers, Let’s Unite to Help Save the World — Graphs4Good 2020".

Students of the UCSD Spatial Data Science course DSC-198: EXPLORING COVID-19 PANDEMIC WITH DATA SCIENCE

Contributors: Kaushik Ganapathy, Braden Riggs, Eric Yu

Alexander Din, U.S. Department of Housing and Urban Development, for help with HUD Crosswalk Files.

Project KONQUER team members at UC San Diego and UTHealth at Houston.

Project Pangeo hosts a Binder instance used to launch Jupyter Notebooks on the web. Pangeo is supported, in part, by the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA). Google provided compute credits on Google Compute Engine.

Funding

Development of this prototype is in part supported by the National Science Foundation under Award Numbers:

NSF Convergence Accelerator Phase I (RAISE): Knowledge Open Network Queries for Research (KONQUER) (1937136)

NSF RAPID: COVID-19-Net: Integrating Health, Pathogen and Environmental Data into a Knowledge Graph for Case Tracking, Analysis, and Forecasting (2028411)