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Accepts list of human HGNC gene symbols, finds annotations from selected databases, and displays the results as a browser-based interactive graph visualization.
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Current annotation sources include Gene Ontology, Reactome pathway database, and BioGRID protein-protein interaction database.
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Results can be downloaded as a JSON file viewable in cytoscape, a set of plain text tables, and an opencog atomese scheme file.
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Download the datasets from https://mozi.ai/datasets
Note: The datasets are compressed and you have to extract the files before using them.
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Create
datasetsfolder in your home directory and move the extracted datasets to that directory -
Create
resultsfolder in your home directory and define aRESULT_DIRenvironment variable that points to the directory. This is where the scheme results will be stored.cd $HOME mkdir results export RESULT_DIR=$HOME/results -
Define the following Environment variables.
$ export SERVICE_ADDR=localhost $ export GRPC_ADDR=http://localhost:3001 $ export RESULT_ADDR=http://localhost:3002 $ export DATASET=$HOME/datasets -
Clone the Project and checkout to the development branch.
git clone --recursive https://github.com/MOZI-AI/annotation-service.git -
Build & Run the atomspace-rpc server. You can get the instructions on the githup repo here.
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--host 0.0.0.0option while starting the server - If you use a custom port (other than 50051), make sure to update the port in the
ATOM_SERVERenv variable indocker-compose-dev.yml
- Make sure you use
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Go the project directory and Start the services
docker-compose -f docker-compose-dev.yml up --build -
You should be able to access the annotation service UI at
http://localhost:3003