cross-talk

Prereqs

• Neo4j
• Docker

Docker

To shell into and debug the container:

$ docker run -i -v $PWD:/app --workdir /app -t cross-talk /bin/bash

to build the container

docker build -f Dockerfile -t cross-talk .

Neo4J

See neo4j-install instructions

1. Create new project
2. Under that project create or connect to a new DBMS
3. Start DBMS (version 5.7 because at the time of writing this the plugins weren't available in later versionss)
4. Install plugins: n10s, Graph Data Science, and APOC.

Post install Neo4J

CREATE CONSTRAINT n10s_unique_uri FOR (r:Resource) REQUIRE r.uri IS UNIQUE;
CALL n10s.graphconfig.init({handleVocabUris: "MAP"});

Importing ontologies

MESH

WITH "https://data.bioontology.org/ontologies/MESH/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=rdf"
AS uri
CALL n10s.rdf.import.fetch(uri, 'RDF/XML',{ classLabel : 'MESH_Class'})
YIELD terminationStatus, triplesLoaded, triplesParsed, namespaces, callParams, extraInfo
RETURN terminationStatus, triplesLoaded, triplesParsed, namespaces, callParams, extraInfo;

NCIT

WITH "https://data.bioontology.org/ontologies/NCIT/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb&download_format=rdf"
AS uri
CALL n10s.rdf.import.fetch(uri, 'RDF/XML',{ classLabel : 'NCIT_Class'})
YIELD terminationStatus, triplesLoaded, triplesParsed, namespaces, callParams, extraInfo
RETURN terminationStatus, triplesLoaded, triplesParsed, namespaces, callParams, extraInfo;

Local file access

In order to access local files, we need to change some configuration of Neo4J. In the settings, you must add the following with modifications depending on your system (also covered in the neo4j-install.md instructions):

dbms.security.allow_csv_import_from_file_urls=true
server.directories.import=/home/paul/
apoc.import.file.enabled=true

You should replace the import directory to match your system, but all imports will be relative to this directory.

Executing things at the command line

In order to execute things at the command line, you must set some environment variables.

export APPDIR=path to this repo
export DATADIR=path to data directory # e.g. parent of pdfs.biomechanics
export OPENAI_API_KEY=foobar

Next steps

The next steps are described in:

Step 1 - Convert PDFs

Step 2 - Annotate texts

Step 3 - Populate KG

Example queries are shown in NEO4J_COMMANDS.