The DeepPhe system extracts information from the patient cancer reports and stores the data in Neo4j graph database. The DeepPhe-Viz tool represents the extracted information in an organized workflow to end users, enabling exploration and discovery of patient data. This deepphe-viz-neo4j module creates extended Neo4j functions as plugin jars that are being used by the DeepPhe-Viz to query the Neo4j database.
NOTE - this plugin works with Neo4j 3.5 - preferably 3.5.12. Don't try with 4.0 or newer versions.
To build the plugin jars, you'll just do mvn clean package in the root directory of the DeepPhe system. You'll have a file named deepphe-viz-0.4.0-plugin.zip in the directory deepphe-viz-neo4j/target after building. This compressed file contains a directory named plugins. All the jar files of the plugins directory must be copied to <NEO4J_HOME>/plugins directory. Then the DeepPhe-Viz uses these libraries to interact with the customized DeepPhe system database.
The following DeepPhe-specific neo4j functions can be called directly within a Cypher query. In Neo4j browser, you can use CALL dbms.functions() to list all the functions including the following ones. Calling a function in Cypher looks like return deepphe.getCohortData().
This function returns a list of all patients (patient properties and stages).
This function returns a list of diagnoses per patient for a given list of patient IDs.
This function returns biomarkers information for a given list of patient IDs.
This function returns patient properties as a map for a given pateint ID.
This function returns patient cancer and tumor information for a given patient ID.
This function returns the patient information and all the reports/notes for a given patient ID.
This function returns report text and all text mentions for a given report ID.
This function returns fact information as json for a given fact ID.