Ontology Cross-References API

The API provides the methods to find mappings (or cross-references) between terms from ontologies and coding standards. The API uses data extracted from a variety of biomedical ontologies that contain cross-references information.

Data collection pipeline

Prerequisite

The pipeline requires some third-party software programs that you will need to install them first:

ROBOT tool (http://robot.obolibrary.org/)
CSVJSON (https://csvjson.com/)
JQ (https://stedolan.github.io/jq/)

Running the pipeline

Clone the repository:

$ git clone https://github.com/johardi/xref-extractor.git
$ cd xref-extractor

Type the command below:

$ make xref_all

Client API

Prerequisite

The client module requires Python 3.x

Example code

from backend import ConnectionManager

con_mngr = ConnectionManager.init("/path/to/xref-all.json")
con = con_mngr.get_connection()
service = con.get_service("XrefService")

# Find ICD10CM code for 'EFO:0000095'"
service.find_xref("EFO:0000095", "ICD10CM")

# Find DOID code for 'MONDO:0004948'"
service.find_xref("MONDO:0004948", "DOID")