Discover clingen-data-model/common-user-experience Open Source project

SEARCH V4 :: The aim of the project is to integrate ClinGen's internal data services and public external data services around a common user experience to ensure clinically relevant knowledge about genes and variants is available for use in precision medicine and research.

website-clinicalgenome-search

Allele (variant) interpretation model and API for ClinGen

clingen-interpretation

HTML

community-curation

Web based gene curation workflow tracking application

clingen-gene-tracker

Python library for creating JSON documents conforming to the DMWG interpretation model.

architecture

HCL

interpretation_json

Software for working with the ClinVar web API

clinvar-api

Description and support material for a global allele registry

allele-registry-use-cases

genegraph-ui

User interface for Genegraph

Performs filtering against gnomAD and ClinVar datasets. Uses Hail to report records with a population FAF above certain thresholds by gene.

clingen-hail-reports

Jupyter Notebook

gene-lookup

serveur

Configuration and documentation of Kafka for data exchange

expediter

HTML

data-exchange-shared-json

JSON schema utilized to share data from the curation interfaces into the Data Exchange. CONTAINS GENE EXPRESS JSON DATA

cg-kb-init

Code for initializing Neo4j database backing cg-knowledgebase

Python script to generate gene prioritization Excel report for ClinGen curation

gene-prioritization

Umbrella project for housing all of the various modeling work by the Data Modeling WG in ClinGen

data-model-docs

JavaScript

gpm

ClinGen Expert Panel Management System

OWL Ontology enumerating ClinGen application specific terms

clingen-terms

hypothesis-funcexp-reformatting

Example code for processing Allele Functional Experimental evidence from annotations in hypothes.is

Jupyter Notebook

clinvar-streams

Generator for JSON-LD Context files given OWL ontologies (plus some metadata)

ld-context

Website for data model documentation

clingen-data-model.github.io

HTML

garde-manger

Application for feeding data from various sources into the ClinGen Data Exchange

clojure-utility

Clojure Utility

Pilot streaming service to share clinvar SCV data with VCI

clinvar-raw-producer

Application for transforming messages formatted according to the data model for ClinVar submission

clinvar-submitter

The persister project is an adaptable kafka topic consumer that persists all topic messages to a file system. The goal is to provide a means of auditing, troubleshooting, possible data sharing and a rough semblance of backup to the ClinGen data exchanges.

persister

ep-management

Scripts for transforming VCI JSON-LD into DMWG Interpretation JSON-LD

VCI-transformation

clinvar-ingest

Repositories holding schemas for data model entities within ClinGen

clingen-schemas

clinvar-ftp-watcher

Cloud Function for detecting new files on the clinvar ftp site