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.

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 phenotypetogenes.txt genestophenotype.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'

[{"genencbiid":23483,"gene_symbol":"TGDS"}]

curl 'http://127.0.0.1:8080/hpo/genes?geneid=23483&hpoterms=true'

[{"genencbiid":23483,"genesymbol":"TGDS","hpoterms":[{"term_...

curl 'http://127.0.0.1:8080/hpo/omims?omimid=616145&hpoterms=true'

[{"omimid":"OMIM:616145","name":"Catel-Manzke syndrome","hpote...

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.

Managing Project with Terraform

```

export GITHUB_OWNER=bihealth

export GITHUBTOKEN=ghpTOKEN

cd utils/terraform

terraform init

terraform import github_repository.viguno viguno

terraform validate

terraform fmt

terraform plan

terraform apply

```