This repositry contains scripts and data files for manuscript "COVID-19 Trial Graph: A Linked Graph for COVID-19 Clinical Trials".
Please download and install Neo4j Desktop from https://neo4j.com/download/ . All the data files (in csv format) for COVID-19 Trial Graph are provided in the neo4j_data folder. To import the data to Neo4j database, please do the following steps:
- Create a local database in Neo4j desktop and create your own user and password, which will be used to connect the database and load your data
- Activate the database by clicking “Start” button.
- Click three-dot button in your database and choose “manage”. Once the new page shows up, click “Open Folder” button, where you are going to put the csv data files
- Copy neo4j_data folder into database’s import directory
- Replace the user and password in csv_to_neo4j.py and run the script
Neo4j Python Driver is required:
pip install neo4j
Screenshot of COVID-19 Trial Graph
Case query 1
Retrieve all COVID-19 clinical trials that target “remdesivir” as the intervention
match (c:Clinicaltrial)-[r:HAS_INTERVENTION]->(t:Intervention)
where toLower(t.name) CONTAINS "remdesivir"
return distinct c
Case query 2
Retrieve all COVID-19 clinical trials that target “remdesivir” as the intervention but exclude pregnant women [OMOP ID: 4299535] from participating
match (c:Clinicaltrial)-[r:HAS_INTERVENTION]->(t:Intervention)
where toLower(t.name) CONTAINS "remdesivir"
AND EXISTS {match (c)-[ic:EXCLUDE_CONDITION]->(condi:Condition)
where condi.id = "4299535"}
return distinct c
OR
match (c:Clinicaltrial)-[r:HAS_INTERVENTION]->(t:Intervention)
where toLower(t.name) CONTAINS "remdesivir"
AND EXISTS {match (c)-[ic:EXCLUDE_CONDITION]->(condi:Condition)
where condi.name = "Pregnant"}
return distinct c
Case query 3
Retrieve all COVID-19 clinical trials that target “hydroxychloroquine” as the intervention and allow patients with shortness of breath [OMOP ID: 312437] to participate
match (c:Clinicaltrial)-[r:HAS_INTERVENTION]->(t:Intervention)
where toLower(t.name) CONTAINS "hydroxychloroquine"
AND EXISTS {match (c)-[ic:INCLUDE_CONDITION]->(condi:Condition)
where condi.id = "312437"}
return distinct c
OR
match (c:Clinicaltrial)-[r:HAS_INTERVENTION]->(t:Intervention)
where toLower(t.name) CONTAINS "hydroxychloroquine"
AND EXISTS {match (c)-[ic:INCLUDE_CONDITION]->(condi:Condition)
where condi.name = "Dyspnea"}
return distinct c
Case query 4
Retrieve all COVID-19 clinical trials in the United States that target “hydroxychloroquine” as the intervention and allow patients with diabetes to participate
match (c:Clinicaltrial)-[r:HAS_INTERVENTION]->(t:Intervention)
where toLower(t.name) CONTAINS "hydroxychloroquine"
AND EXISTS {match (c)-[rloc:HAS_LOCATION]->(loc:Location)
where toLower(loc.name) = "united states"}
AND EXISTS {match (c)-[ic:INCLUDE_CONDITION]->(condi:Condition)
where toLower(condi.name) CONTAINS "diabetes"}
return distinct c
We also provide eligibility criteria terms mapping file for the reference. Users can use this file ec_terms_mapping.tsv to look up clinical concepts and their OMOP IDs.
Please contact Jingcheng Du: [email protected], if you have any questions