ClinicalTrialAnnotator

Build Instruction

1. Import as maven project.
2. Download the MetaMap Web API and add to the build path.
3. Download the Stanford CoreNLP models and add to the build path. Note: a UMLS Terminlogy Service (UTS) account is required to use MetaMap and OntologyBuilder.

Usage

MetaMap

This program takes 4 command line arguments: UTS account name, password, email, and file name (the file must be in plain text format).

OntologyBuilder

This program takes 5 command line arguments: UTS account name, password, email, input xml file (from clinical trials), and output json file name.

GraphBuilder

1. Modify main method of GraphBuilder, provide required neo4j authentication information.
2. Create a directory named xml and place all xml files that need to be annotated there.
3. Run the program, converted json files are going to be created under the build path.

Typical Issues

Since MetaMap does not support non-ASCII characters, you will get an error if the input file contains any non-ASCII characters that are not yet handled by the program (see Issues tab for details). GraphBuilder will not crash in this case, but you will get a untokenizable warning from Stanford NLP.