I’m trying to use the medcat.neo, im getting module not found error for medcat.neo.
Does medcat.neo comes with medcat? I have medcat installed.
Hi.
We removed that module along with the py2neo dependency back in release 1.8.2. That was because py2neo had (at least at that time) been removed from PyPI which made it impossible to install medcat.
The change was made in this PR:
With that said, you can access the code that was there in here:
Seems like pip py2neo is working now. So i can install the medcat version 1.8.1 to try out it.
One more thing what is the structure of the document.csv and patients.csv files that is needed for the neo4j? I need to create the two files for the processing. From the tutorail it seems the document.csv file has a column documentId and text. How does the patient.csv looks like?
You’re right, py2neo was restored some time later. I’m guessing it was because its removal bricked a lot more installs than just ours.
But the neo4j parts weren’t really a core part of the MedCAT library so they were not added back subsequently.
With that said, I don’t think any of the MedCAT tutorials mention a documents.csv or patient.csv nor do they use neo4j as far as I can tell.
So I don’t know what tutorial you’re following exactly. Thus, I don’t know what the format of the files would have to be.
I’m talking about the blog and its corresponding jupyter notebook : Exploring Electronic Health Records with MedCAT and Neo4j | by Zeljko | Towards Data Science the link to this blog is given in the news part of medcat website.