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Repository Details

Repositories holding schemas for data model entities within ClinGen

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1

allele

Documentation for data model of ClinGen
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2

genegraph

Presents an RDF triplestore of gene information using GraphQL APIs
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3

website-clinicalgenome-search

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.
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4

clingen-interpretation

Allele (variant) interpretation model and API for ClinGen
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5

community-curation

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6

clingen-gene-tracker

Web based gene curation workflow tracking application
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7

architecture

HCL
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8

interpretation_json

Python library for creating JSON documents conforming to the DMWG interpretation model.
Python
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9

clinvar-api

Software for working with the ClinVar web API
Python
2
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10

allele-registry-use-cases

Description and support material for a global allele registry
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11

genegraph-ui

User interface for Genegraph
Clojure
1
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12

clingen-hail-reports

Performs filtering against gnomAD and ClinVar datasets. Uses Hail to report records with a population FAF above certain thresholds by gene.
Jupyter Notebook
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13

gene-lookup

PHP
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14

serveur

Clojure
1
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15

expediter

Configuration and documentation of Kafka for data exchange
HTML
1
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16

data-exchange-shared-json

JSON schema utilized to share data from the curation interfaces into the Data Exchange. CONTAINS GENE EXPRESS JSON DATA
1
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17

cg-kb-init

Code for initializing Neo4j database backing cg-knowledgebase
Clojure
1
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18

gene-prioritization

Python script to generate gene prioritization Excel report for ClinGen curation
Python
1
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19

data-model-docs

Umbrella project for housing all of the various modeling work by the Data Modeling WG in ClinGen
JavaScript
1
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20

gpm

ClinGen Expert Panel Management System
PHP
1
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21

clingen-terms

OWL Ontology enumerating ClinGen application specific terms
1
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22

hypothesis-funcexp-reformatting

Example code for processing Allele Functional Experimental evidence from annotations in hypothes.is
Jupyter Notebook
1
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23

clinvar-streams

Clojure
1
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24

ld-context

Generator for JSON-LD Context files given OWL ontologies (plus some metadata)
Clojure
1
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25

clingen-data-model.github.io

Website for data model documentation
HTML
1
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26

garde-manger

Application for feeding data from various sources into the ClinGen Data Exchange
Clojure
1
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27

clojure-utility

Clojure Utility
Clojure
1
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28

clinvar-raw-producer

Pilot streaming service to share clinvar SCV data with VCI
Clojure
1
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29

clinvar-submitter

Application for transforming messages formatted according to the data model for ClinVar submission
Clojure
1
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30

persister

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.
Clojure
1
star
31

ep-management

Python
1
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32

VCI-transformation

Scripts for transforming VCI JSON-LD into DMWG Interpretation JSON-LD
Python
1
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33

common-user-experience

Capture documentation, artifacts, and code assets of the Common User Experience for ClinGen resources.
1
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34

clinvar-ingest

Python
1
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35

clinvar-ftp-watcher

Cloud Function for detecting new files on the clinvar ftp site
Clojure
1
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