The Obo Parser is build on Scala and Spark

Make sure to import all external libraries by running

`sbt update`. 

To build the application, run the following from the command line in the root directory of the project

sbt ";clean;assembly"

Then get the application jar file from

${root of the project}/target/scala-2.12/obo-parser-assembly-0.1.0-SNAPSHOT.jar

• Spark 3.0.0

Two arguments is required to executing a build with Obo Parser : obo_file_input_url json_output_local_path . obo_file_input_url is the URL or local path of the input file. json_output_local_path is the local path where the json output will be saved

${SPARK_HOME}/bin/spark-submit --master ${spark_master} --class ${full_main_class_name} ./obo-parser/target/scala-2.12/obo-parser-assembly-0.1.0-SNAPSHOT.jar ${obo_file_input_url} ${json_output_local_path}

1st argument: Path to fetch input obo file

• https://purl.obolibrary.org/obo/hp.obo
• https://purl.obolibrary.org/obo/mondo.obo
• https://purl.obolibrary.org/obo/ncit.obo
• S3 path for ICD, we fetch the XML file here: https://www.cdc.gov/nchs/icd/icd-10-cm/files.html, and add it to S3 bucket.

2nd argument: Type of ontological terms, values can be one of those: hpo or mondo or ncit or icd.

3rd argument (optional): ex. MONDO:0700096.

For MONDO terms, a desired to node should be provided. MONDO has many top nodes, so we need to specify which one we want to use. the desired top node for MONDO, it should be MONDO:0700096 (human disease). Using that as a desired top node we remove the same level branch MONDO:0005583 (non-human animal disease). We should get: MONDO:0000001 (disease) -> MONDO:0700096 (human disease) -> {REST of Mondo tree}