Viguno

Viguno (Versatile Interface for Genetics Utilization of Nice Ontologies) is the component of a VarFish installation that provides information on HPO phenotypes, diseases, and their relation to genes.

Viguno provides a REST API.

Running the Docker Image

The commands used below assume that you have a viguno executable on your machine (e.g., via cargo install). However, we also provide Docker images. You can run version v0.1.1 as follows. We assume that the current working directory is a check of viguno so we have a copy of the HPO and HGNC xlink table in tests/data. We bind-mount this into the container with -v $PWD/tests/data:/data.

# docker run \
    -v $PWD/tests/data:/data \
    -it ghcr.io/varfish-org/viguno:0.1.1

Preparing Data

The initial step is to download the official HPO data to a local directory. We fix ourselves to the release from 2023-06-06.

# RELEASE=2023-06-06
# URL=https://github.com/obophenotype/human-phenotype-ontology/releases/download
# NAMES="hp.obo phenotype.hpoa phenotype_to_genes.txt genes_to_phenotype.txt"

# mkdir -p /tmp/data/hpo
# for name in $NAMES; do \
    wget \
        -O /tmp/data/hpo/$name \
        $URL/v$RELEASE/$name;
  done

You can now conver the downloaded text HPO files to a binary format which will improve performance of loading data.

# viguno convert \
    --path-hpo-dir /tmp/data/hpo \
    --path-out-bin /tmp/data/hpo/hpo.bin

To use the similarity computations, you will need to run some simulation as precomputation. You should fix the seed for reproducibility. The number of simulations should be high for production (the default is 100k) but you can reduce this for a local setup.

# viguno simulate \
    --num-simulations 10 \
    --seed 42 \
    --path-hpo-dir /tmp/data/hpo/hpo \
    --path-out-rocksdb /tmp/data/hpo/hpo/scores-fun-sim-avg-resnik-gene \
    --combiner fun-sim-avg \
    --similarity resnik \
    --ic-base gene

Running the Server

After having the precomputed data, you can startup the server as follows:

# viguno run-server \
    --path-hpo-dir tests/data/hpo
INFO args_common = Args { verbose: Verbosity { verbose: 0, quiet: 0, phantom: PhantomData<clap_verbosity_flag::InfoLevel> } }
INFO args = Args { path_hpo_dir: "tests/data/hpo", suppress_hints: false, listen_host: "127.0.0.1", listen_port: 8080 }
INFO Loading HPO...
INFO ...done loading HPO in 8.180012599s
INFO Opening RocksDB for reading...
INFO ...done opening RocksDB in 19.027133ms
INFO Launching server main on http://127.0.0.1:8080 ...
INFO   try: http://127.0.0.1:8080/hpo/genes?gene_symbol=TGDS
INFO   try: http://127.0.0.1:8080/hpo/genes?gene_id=23483&hpo_terms=true
INFO   try: http://127.0.0.1:8080/hpo/omims?omim_id=616145&hpo_terms=true
INFO   try: http://127.0.0.1:8080/hpo/terms?term_id=HP:0000023&genes=true
INFO   try: http://127.0.0.1:8080/hpo/sim/term-term?lhs=HP:0001166,HP:0040069&rhs=HP:0005918,HP:0004188
INFO   try: http://127.0.0.1:8080/hpo/sim/term-gene?terms=HP:0001166,HP:0000098&gene_symbols=FBN1,TGDS,TTN
INFO starting 4 workers
INFO Actix runtime found; starting in Actix runtime

Now the server is running and you could stop it with Ctrl-C.

In another terminal, you then now do as suggested above. Note that we truncate the output JSON.

# curl 'http://127.0.0.1:8080/hpo/genes?gene_symbol=TGDS'
[{"gene_ncbi_id":23483,"gene_symbol":"TGDS"}]

# curl 'http://127.0.0.1:8080/hpo/genes?gene_id=23483&hpo_terms=true'
[{"gene_ncbi_id":23483,"gene_symbol":"TGDS","hpo_terms":[{"term_...

# curl 'http://127.0.0.1:8080/hpo/omims?omim_id=616145&hpo_terms=true'
[{"omim_id":"OMIM:616145","name":"Catel-Manzke syndrome","hpo_te...

# curl 'http://127.0.0.1:8080/hpo/terms?term_id=HP:0000023&genes=true'
[{"term_id":"HP:0000023","name":"Inguinal hernia","genes":[{"gen...

# curl 'http://127.0.0.1:8080/hpo/sim/term-term?lhs=HP:0001166,HP:0040069&rhs=HP:0005918,HP:0004188'
[{"lhs":"HP:0001166","rhs":"HP:0005918","score":1.4280319,"sim":...

Developer Documentation

The following is for developers of Viguno itself.

Creating Docker Builds

We automatically build Docker images using GitHub actions. To do this locally, you can do:

# bash utils/docker/build-docker.sh

You can set the following environment variables

• GIT_TAG a git "treeish" (can be a tag or version) to build (inferred via git describe --tags by default)
• DOCKER_VERSION the version to use for the Docker label (by default it uses $GIT_TAG and the v prefix will be stripped)