FORGEdb is an online tool designed to aid interpretation of genetic variants associated with diseases, for example variants analyzed in genome-wide association studies (GWAS). Its purpose is to annotate individual variants to identify relevant alleles and target genes.
The platform provides integrated data on individual genetic variants, including associated regulatory elements, transcription factor binding sites, and target genes. This information, derived from a wide range of biological samples, presents a thorough examination of the regulatory context for each variant at the tissue and cell type level. Data sources include Combined Annotation Dependent Depletion (CADD) scores, expression quantitative trait loci (eQTLs), activity-by-contact (ABC) interactions, and transcription factor (TF) motifs.
Notably, FORGEdb introduces a unique scoring system, the FORGEdb score. This score evaluates the functional importance of genetic variants, helping researchers prioritize variants for functional validation. It uses extensive datasets, including those from ENCODE, Roadmap Epigenomics, and BLUEPRINT consortia. With FORGEdb, researchers can quickly analyze different genomic variants and accelerate their research on disease-associated mechanisms.
- FORGEdb: https://forgedb.cancer.gov
- FORGEdb Paper: https://doi.org/10.1101/2022.11.14.516365
- FORGE2: https://forge2.altiusinstitute.org
Building
- git
- node.js
Hosting
- Any static file server. The example instructions use Apache.
Each dataset is available for download at the following urls:
- Clone the repository:
git clone https://github.com/CBIIT/nci-webtools-dceg-forgedb.git
- Under your static file server's document root, create an
api
folder under which you wish to host the FORGEdb api. - Copy the contents of the
client/public/api
folder to theapi
folder you created in step 2. - Download source datasets from the table above to the appropriate folder. For example, place
abc.forgedb.csv.gz
underapi/abc/v1.0/
. - Navigate to the repository's
database
folder - Run
npm install
to install dependencies - For each dataset, execute the
import.js
script. For example:node import.js $DOCUMENT_ROOT/api/abc/v1.0/abc.forgedb.csv.gz
- Clone the repositrory:
git clone https://github.com/CBIIT/nci-webtools-dceg-forgedb.git
- Navigate to the
client
folder and runnpm install && npm run build
to generate theout
folder. If your api is served under a subpath (eg:https://your_hostname/your_subpath/api/
), specify the subpath as theNEXT_PUBLIC_BASE_PATH
environment variable before building (eg:export NEXT_PUBLIC_BASE_PATH=/your_subpath
). - Upload the
out
folder to your static file server's document root, ensuring that you do not overwrite the contents of theapi
folder.
AWS S3/Cloudfront is a cost-effective, high-performance method of hosting FORGEdb. The recommended approach is to split the API and website code across two S3 Buckets so they can be managed independently.
- Create or log in to an AWS Account
- Create two S3 buckets (eg:
${org-name}-forgedb-api
,${org-name}-forgedb-website
) - Create a Cloudfront distribution with an
/api
origin and adefault
origin. The/api
origin should be served from${$org-name}-forgedb-api
, and thedefault
origin should be served from${org-name}-forgedb-website
- Build the website code and push it to the
$org-name-forgedb-website
bucket - Copy the
client/public/api
folder to anapi
folder under the$org-name-forgedb-api
bucket - Download the forgedb source files above
- Upload each source file to the appropriate folder. For example, place
abc.forgedb.csv.gz
underapi/abc/v1.0/
. - Navigate to the repository's
database
folder - Run
npm install
to install dependencies - For each dataset, execute the
import.js
script. For example:node import.js s3://$org-name-forgedb-api/api/abc/v1.0/abc.forgedb.csv.gz
. Ensure your environment has s3 credentials configured.