From 63d143ed94387cb68c3c1a86c13255ae571f1b30 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Thu, 11 Jul 2024 09:25:50 +0200 Subject: [PATCH 1/6] feat: hgnc_xlink.tsv is expected now in hpo folder (#170) --- Cargo.toml | 1 + README.md | 60 +++++------ build.rs | 25 ++++- openapi.yaml | 101 +++++++++++++++++- .../viguno/v1/simulation.proto | 0 src/query/mod.rs | 6 +- src/server/run/hpo_genes.rs | 1 + src/server/run/hpo_omims.rs | 1 + src/server/run/hpo_sim/term_gene.rs | 1 + src/server/run/hpo_sim/term_term.rs | 1 + src/server/run/hpo_terms.rs | 1 + src/server/run/mod.rs | 58 ++-------- tests/data/hgnc_xlink.tsv | 3 - tests/data/hpo/bootstraph.sh | 4 +- tests/data/hpo/genes_to_phenotype.txt | 3 + tests/data/hpo/hgnc_xlink.tsv | 3 + tests/data/hpo/hp.obo | 4 +- tests/data/hpo/hpo.bin | 4 +- tests/data/hpo/phenotype.hpoa | 4 +- tests/data/hpo/phenotype_to_genes.txt | 4 +- utils/docker/entrypoint.sh | 3 +- 21 files changed, 182 insertions(+), 106 deletions(-) rename {src/proto => protos}/viguno/v1/simulation.proto (100%) delete mode 100644 tests/data/hgnc_xlink.tsv create mode 100644 tests/data/hpo/genes_to_phenotype.txt create mode 100644 tests/data/hpo/hgnc_xlink.tsv diff --git a/Cargo.toml b/Cargo.toml index 4b54948..81b4ed2 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -45,6 +45,7 @@ utoipa-swagger-ui = { version = "7.1.0", features = ["actix-web"] } utoipa = { version = "4.2", features = ["actix_extras", "chrono", "indexmap", "preserve_order", "yaml"] } [build-dependencies] +anyhow = "1.0" prost-build = "0.12" [dev-dependencies] diff --git a/README.md b/README.md index 187d4f4..399038e 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ 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" +# NAMES="hp-base.obo phenotype.hpoa phenotype_to_genes.txt genes_to_phenotype.txt" # mkdir -p /tmp/data/hpo # for name in $NAMES; do \ @@ -42,6 +42,21 @@ We fix ourselves to the release from 2023-06-06. -O /tmp/data/hpo/$name \ $URL/v$RELEASE/$name; done +# mv /tmp/data/hpo/hp-base.obo /tmp/data/hpo/hp.obo +# sed -i -e 's|/hp-base.owl||' /tmp/data/hpo/hp.obo +``` + +Next, generate the cross-link file between different gene identifiers. + +``` +# wget -O /tmp/hgnc_complete_set.json \ + https://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json +# echo -e "hgnc_id\tensembl_gene_id\tentrez_id\tgene_symbol" \ + > /tmp/data/hpo/hgnc_xlink.tsv +# jq -r '.response.docs[] | select(.entrez_id != null) | [.hgnc_id, .ensembl_gene_id, .entrez_id, .symbol] | @tsv' \ + /tmp/hgnc_complete_set.json \ + | LC_ALL=C sort -t $'\t' -k3,3n \ + >> /tmp/data/hpo/hgnc_xlink.tsv ``` You can now conver the downloaded text HPO files to a binary format which will improve performance of loading data. @@ -57,46 +72,29 @@ You can now conver the downloaded text HPO files to a binary format which will i After having the precomputed data, you can startup the server as follows: ``` -# viguno run-server \ +# viguno server run \ --path-hpo-dir tests/data/hpo INFO args_common = Args { verbose: Verbosity { verbose: 0, quiet: 0, phantom: PhantomData } } 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 attempting to load binary HPO file from tests/data/hpo +INFO ...done loading HPO in 4.788750172s +INFO Loading HGNC xlink... +INFO ... done loading HGNC xlink in 156.362034ms +INFO Loading HPO OBO... +INFO ... done loading HPO OBO in 1.90213703s +INFO Indexing OBO... +INFO ... done indexing OBO in 835.558794ms 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 SEE SWAGGER UI FOR INTERACTIVE DOCS: http://127.0.0.1:8080/swagger-ui/ +INFO starting 8 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":... -``` +You can go to http://127.0.0.1/swagger-ui to see the automatically generated interactive API documentation. +You can find the OpenAPI YAML file for the `main` branch [here on GitHub](https://raw.githubusercontent.com/varfish-org/viguno/main/openapi.yaml) and e.g., open it [here in the public Swagger editor](https://editor.swagger.io?url=https://raw.githubusercontent.com/varfish-org/viguno/main/openapi.yaml). # Developer Documentation diff --git a/build.rs b/build.rs index 32f41de..c5bc7cc 100644 --- a/build.rs +++ b/build.rs @@ -1,13 +1,28 @@ -// The custom build script, needed as we use protocolbuffers. +use std::{env, path::PathBuf}; + +fn main() -> Result<(), anyhow::Error> { + let root = PathBuf::from(env!("CARGO_MANIFEST_DIR")).join("protos"); + let proto_files = vec!["viguno/v1/simulation.proto"] + .iter() + .map(|f| root.join(f)) + .collect::>(); + + // Tell cargo to recompile if any of these proto files are changed + for proto_file in &proto_files { + println!("cargo:rerun-if-changed={}", proto_file.display()); + } + + let descriptor_path = PathBuf::from(env::var("OUT_DIR").unwrap()).join("proto_descriptor.bin"); -fn main() { prost_build::Config::new() - .protoc_arg("-Isrc/proto") + // Save descriptors to file + .file_descriptor_set_path(&descriptor_path) // Add serde serialization and deserialization to the generated code. .type_attribute(".", "#[derive(serde::Serialize, serde::Deserialize)]") // Skip serializing `None` values. .type_attribute(".", "#[serde_with::skip_serializing_none]") // Define the protobuf files to compile. - .compile_protos(&["viguno/v1/simulation.proto"], &["src/"]) - .unwrap(); + .compile_protos(&proto_files, &[root])?; + + Ok(()) } diff --git a/openapi.yaml b/openapi.yaml index 7b2d53d..a7aa3e8 100644 --- a/openapi.yaml +++ b/openapi.yaml @@ -14,7 +14,7 @@ paths: tags: - hpo_genes summary: Query for genes in the HPO database. - operationId: handle + operationId: hpo_genes parameters: - name: gene_id in: query @@ -63,7 +63,7 @@ paths: tags: - hpo_omims summary: Query for OMIM diseases in the HPO database. - operationId: handle + operationId: hpo_omims parameters: - name: omim_id in: query @@ -107,6 +107,101 @@ paths: application/json: schema: $ref: '#/components/schemas/Result' + /hpo/sim/term-gene: + get: + tags: + - hpo_sim::term_gene + summary: Query for similarity between a set of terms to each entry in a + description: list of genes. + operationId: hpo_sim_term_gene + parameters: + - name: terms + in: query + description: Set of terms to use as query. + required: true + schema: + type: array + items: + type: string + - name: gene_ids + in: query + description: The set of ids for genes to use as "database". + required: false + schema: + type: array + items: + type: string + nullable: true + - name: gene_symbols + in: query + description: The set of symbols for genes to use as "database". + required: false + schema: + type: array + items: + type: string + nullable: true + responses: + '200': + description: The query was successful. + content: + application/json: + schema: + $ref: '#/components/schemas/Result' + /hpo/sim/term-term: + get: + tags: + - hpo_sim::term_term + summary: Query for pairwise term similarity. + description: |- + In the case of Resnik, this corresponds to `IC(MICA(t_1, t_2))`. + + # Errors + + In the case that there is an error running the server. + operationId: hpo_sim_term_term + parameters: + - name: lhs + in: query + description: The one set of HPO terms to compute similarity for. + required: true + schema: + type: array + items: + type: string + - name: rhs + in: query + description: The second set of HPO terms to compute similarity for. + required: true + schema: + type: array + items: + type: string + - name: ic_base + in: query + description: What should information content be based on. + required: false + schema: + $ref: '#/components/schemas/IcBasedOn' + - name: similarity + in: query + description: The similarity method to use. + required: false + schema: + $ref: '#/components/schemas/SimilarityMethod' + - name: combiner + in: query + description: The score combiner. + required: false + schema: + $ref: '#/components/schemas/ScoreCombiner' + responses: + '200': + description: The query was successful. + content: + application/json: + schema: + $ref: '#/components/schemas/Result' /hpo/terms: get: tags: @@ -116,7 +211,7 @@ paths: # Errors In the case that there is an error running the server. - operationId: handle + operationId: hpo_terms parameters: - name: term_id in: query diff --git a/src/proto/viguno/v1/simulation.proto b/protos/viguno/v1/simulation.proto similarity index 100% rename from src/proto/viguno/v1/simulation.proto rename to protos/viguno/v1/simulation.proto diff --git a/src/query/mod.rs b/src/query/mod.rs index ad043b3..f7bab3e 100644 --- a/src/query/mod.rs +++ b/src/query/mod.rs @@ -18,9 +18,6 @@ pub struct Args { /// Path to the directory with the HPO files. #[arg(long, required = true)] pub path_hpo_dir: String, - /// Path to the TSV file with the HGNC xlink data. - #[arg(long, required = true)] - pub path_hgnc_xlink: String, /// Path to JSON file with the genes to rank. #[arg(long)] @@ -318,7 +315,8 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: tracing::info!("Loading HGNC xlink..."); let before_load_xlink = Instant::now(); - let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(&args.path_hgnc_xlink)?; + let path_hgnc_xlink = format!("{}/hgnc_xlink.tsv", args.path_hpo_dir); + let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(&path_hgnc_xlink)?; tracing::info!( "... done loading HGNC xlink in {:?}", before_load_xlink.elapsed() diff --git a/src/server/run/hpo_genes.rs b/src/server/run/hpo_genes.rs index 63b2c91..8c2f4eb 100644 --- a/src/server/run/hpo_genes.rs +++ b/src/server/run/hpo_genes.rs @@ -132,6 +132,7 @@ pub struct Result { /// Query for genes in the HPO database. #[allow(clippy::unused_async)] #[utoipa::path( + operation_id = "hpo_genes", params(Query), responses( (status = 200, description = "The query was successful.", body = Result), diff --git a/src/server/run/hpo_omims.rs b/src/server/run/hpo_omims.rs index c294d03..6efc642 100644 --- a/src/server/run/hpo_omims.rs +++ b/src/server/run/hpo_omims.rs @@ -145,6 +145,7 @@ pub struct Result { /// Query for OMIM diseases in the HPO database. #[allow(clippy::unused_async)] #[utoipa::path( + operation_id = "hpo_omims", params(Query), responses( (status = 200, description = "The query was successful.", body = Result), diff --git a/src/server/run/hpo_sim/term_gene.rs b/src/server/run/hpo_sim/term_gene.rs index 4e3b34f..f523d2b 100644 --- a/src/server/run/hpo_sim/term_gene.rs +++ b/src/server/run/hpo_sim/term_gene.rs @@ -49,6 +49,7 @@ pub struct Query { /// list of genes. #[allow(clippy::unused_async)] #[utoipa::path( + operation_id = "hpo_sim_term_gene", params(Query), responses( (status = 200, description = "The query was successful.", body = Result), diff --git a/src/server/run/hpo_sim/term_term.rs b/src/server/run/hpo_sim/term_term.rs index 1535394..39e0d5a 100644 --- a/src/server/run/hpo_sim/term_term.rs +++ b/src/server/run/hpo_sim/term_term.rs @@ -105,6 +105,7 @@ pub struct ResultEntry { /// In the case that there is an error running the server. #[allow(clippy::unused_async)] #[utoipa::path( + operation_id = "hpo_sim_term_term", params(RequestQuery), responses( (status = 200, description = "The query was successful.", body = Result), diff --git a/src/server/run/hpo_terms.rs b/src/server/run/hpo_terms.rs index 06ada38..dd7857c 100644 --- a/src/server/run/hpo_terms.rs +++ b/src/server/run/hpo_terms.rs @@ -208,6 +208,7 @@ pub struct Result { #[allow(clippy::unused_async)] #[allow(clippy::too_many_lines)] #[utoipa::path( + operation_id = "hpo_terms", params(Query), responses( (status = 200, description = "The query was successful.", body = Result), diff --git a/src/server/run/mod.rs b/src/server/run/mod.rs index f46994e..2e67223 100644 --- a/src/server/run/mod.rs +++ b/src/server/run/mod.rs @@ -32,9 +32,6 @@ pub struct Args { /// Path to the directory with the HPO files. #[arg(long, required = true)] pub path_hpo_dir: String, - /// Path to the TSV file with the HGNC xlink data. - #[arg(long, required = true)] - pub path_hgnc_xlink: String, /// Whether to suppress printing hints. #[arg(long, default_value_t = false)] @@ -158,7 +155,13 @@ where /// Utoipa-based `OpenAPI` generation helper. #[derive(utoipa::OpenApi)] #[openapi( - paths(hpo_genes::handle, hpo_terms::handle, hpo_omims::handle,), + paths( + hpo_genes::handle, + hpo_terms::handle, + hpo_omims::handle, + hpo_sim::term_term::handle, + hpo_sim::term_gene::handle, + ), components(schemas( hpo_genes::Query, hpo_genes::Result, @@ -227,49 +230,7 @@ pub fn print_hints(args: &Args) { } tracing::info!( - " ==> for Swagger UI, see: http://{}:{}/swagger-ui/", - args.listen_host.as_str(), - args.listen_port - ); - - // The endpoint `/hpo/genes` provides information related to genes by symbol. - tracing::info!( - " try: http://{}:{}/hpo/genes?gene_symbol=TGDS", - args.listen_host.as_str(), - args.listen_port - ); - // Also, you can query `/hpo/genes` by NCBI gene ID and return the HPO terms of the gene. - tracing::info!( - " try: http://{}:{}/hpo/genes?gene_id=23483&hpo_terms=true", - args.listen_host.as_str(), - args.listen_port - ); - // The `/hpo/omims` term provides information on OMIM terms and can include HPO terms for - // the disease. - tracing::info!( - " try: http://{}:{}/hpo/omims?omim_id=616145&hpo_terms=true", - args.listen_host.as_str(), - args.listen_port - ); - // The `/hpo/terms` endpoint allows to query by HPO term ID and optionally return a list of - // genes that are linked to the term. - tracing::info!( - " try: http://{}:{}/hpo/terms?term_id=HP:0000023&genes=true", - args.listen_host.as_str(), - args.listen_port - ); - // We can use `/hpo/sim/term-term` to compute similarity between two HPO term sets `lhs` - // and `rhs` using a similarity metric. - tracing::info!( - " try: http://{}:{}/hpo/sim/term-term?lhs=HP:0001166,HP:0040069&rhs=HP:0005918,\ - HP:0004188", - args.listen_host.as_str(), - args.listen_port - ); - // The endpoint `/hpo/sim/term-gene` allows to compute the same for a list of `terms` and - // `gene_symbols`. - tracing::info!( - " try: http://{}:{}/hpo/sim/term-gene?terms=HP:0001166,HP:0000098&gene_symbols=FBN1,TGDS,TTN", + " SEE SWAGGER UI FOR INTERACTIVE DOCS: http://{}:{}/swagger-ui/", args.listen_host.as_str(), args.listen_port ); @@ -302,7 +263,8 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: tracing::info!("Loading HGNC xlink..."); let before_load_xlink = std::time::Instant::now(); - let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(&args.path_hgnc_xlink)?; + let path_hgnc_xlink = format!("{}/hgnc_xlink.tsv", args.path_hpo_dir); + let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(&path_hgnc_xlink)?; let hgnc_to_ncbi = crate::common::hgnc_xlink::inverse_hashmap(&ncbi_to_hgnc); tracing::info!( "... done loading HGNC xlink in {:?}", diff --git a/tests/data/hgnc_xlink.tsv b/tests/data/hgnc_xlink.tsv deleted file mode 100644 index 17eae3a..0000000 --- a/tests/data/hgnc_xlink.tsv +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:4c01161ffc88a348ad813c45df51e0d387ceabbb331ceb37ccb67e39fcf9af12 -size 1804332 diff --git a/tests/data/hpo/bootstraph.sh b/tests/data/hpo/bootstraph.sh index 0ef0327..6a6a1c3 100644 --- a/tests/data/hpo/bootstraph.sh +++ b/tests/data/hpo/bootstraph.sh @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:d2615ded1da39a3ca105fe4d7222271fc343a6190c0068e7abeb25c5d922072b -size 257 +oid sha256:c2ef6b0d0269733875abab3c86ee6d467b57f133983c9bb2cd358d7b633868cb +size 1207 diff --git a/tests/data/hpo/genes_to_phenotype.txt b/tests/data/hpo/genes_to_phenotype.txt new file mode 100644 index 0000000..d6fe5f1 --- /dev/null +++ b/tests/data/hpo/genes_to_phenotype.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:133a29cb2019c06ab25d8f52be872801c68f8700d135b1e7c9ef5215288b5d8d +size 19400620 diff --git a/tests/data/hpo/hgnc_xlink.tsv b/tests/data/hpo/hgnc_xlink.tsv new file mode 100644 index 0000000..66d35e0 --- /dev/null +++ b/tests/data/hpo/hgnc_xlink.tsv @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7a74d0ee645b511a60eadbf6b69060b5d55fe026fe09bde04d57bbdb01798c30 +size 1811039 diff --git a/tests/data/hpo/hp.obo b/tests/data/hpo/hp.obo index 3bd3fdb..24d7d2f 100644 --- a/tests/data/hpo/hp.obo +++ b/tests/data/hpo/hp.obo @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:ca48543eff79fb92a8fab867165bc4cd812663297bdd018aa6803ccfb0b43d15 -size 9174481 +oid sha256:7053cb3e230e1d672bbe7d7aee33a27ab23b72f610053ffd93c3283c2c6f00b4 +size 10348342 diff --git a/tests/data/hpo/hpo.bin b/tests/data/hpo/hpo.bin index abf702b..49e1e24 100644 --- a/tests/data/hpo/hpo.bin +++ b/tests/data/hpo/hpo.bin @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:eab47e3e3652be9010184efcf6c3d9a7a5d50077828b596c156d286b256ae5e9 -size 4801046 +oid sha256:edb3bcb193ff061b99ea02b5f1ba1bbf2357883afed4b4a093e2e7cebb694556 +size 5688605 diff --git a/tests/data/hpo/phenotype.hpoa b/tests/data/hpo/phenotype.hpoa index 8e1178c..f805214 100644 --- a/tests/data/hpo/phenotype.hpoa +++ b/tests/data/hpo/phenotype.hpoa @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:e0b9dc1401ee7416a1e58ae7e759b5dedf4f2ee53a96fd402d32e8d59648970a -size 31274991 +oid sha256:3d8a7bbb484b302b59cd6df29571211f371ecb0db36ea5559af93e8bcba59f2f +size 32813915 diff --git a/tests/data/hpo/phenotype_to_genes.txt b/tests/data/hpo/phenotype_to_genes.txt index 223506a..06e78f5 100644 --- a/tests/data/hpo/phenotype_to_genes.txt +++ b/tests/data/hpo/phenotype_to_genes.txt @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:7540c4385048ffbe2cd417e42a4d4d3d549c641ea82c74cf7a8d736f1ec21b4e -size 32975064 +oid sha256:34ce08f504f421eb6499b41995a80d9f3a66a9920a4c62a225efa839a6670568 +size 62039342 diff --git a/utils/docker/entrypoint.sh b/utils/docker/entrypoint.sh index cf3858b..c29ae8c 100644 --- a/utils/docker/entrypoint.sh +++ b/utils/docker/entrypoint.sh @@ -26,8 +26,7 @@ if [ "$first" == exec ]; then exec "$@" else exec \ - viguno \ - run-server \ + viguno server run \ --path-hpo-dir "$PATH_HPO_DIR" \ --path-hgnc-xlink "$PATH_HGNC_XLINK" \ --listen-host "$HTTP_HOST" \ From 9b638a8e4eec571dc32e37238351b11d89177ac0 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Thu, 11 Jul 2024 09:43:21 +0200 Subject: [PATCH 2/6] wip --- src/algos/phenomizer.rs | 2 +- src/server/run/hpo_genes.rs | 2 +- ...hpo_sim_term_gene_terms_hgnc_gene_ids.snap | 666 +++++++++++------- ...hpo_sim_term_gene_terms_ncbi_gene_ids.snap | 666 +++++++++++------- ...test__hpo_sim_term_gene_terms_symbols.snap | 666 +++++++++++------- ...term__test__hpo_sim_term_term_one_one.snap | 6 +- ...term__test__hpo_sim_term_term_two_two.snap | 12 +- ...nes_gene_symbol_contains_no_hpo_terms.snap | 13 +- ...s_gene_symbol_contains_with_hpo_terms.snap | 216 +++++- ..._genes_gene_symbol_exact_no_hpo_terms.snap | 4 +- ...enes_gene_symbol_exact_with_hpo_terms.snap | 10 +- ...genes_gene_symbol_prefix_no_hpo_terms.snap | 4 +- ...nes_gene_symbol_prefix_with_hpo_terms.snap | 10 +- ...genes_gene_symbol_suffix_no_hpo_terms.snap | 4 +- ...nes_gene_symbol_suffix_with_hpo_terms.snap | 10 +- ...genes_hgnc_gene_id_exact_no_hpo_terms.snap | 4 +- ...nes_hgnc_gene_id_exact_with_hpo_terms.snap | 4 +- ...genes_ncbi_gene_id_exact_no_hpo_terms.snap | 4 +- ...nes_ncbi_gene_id_exact_with_hpo_terms.snap | 4 +- ..._hpo_omims_name_contains_no_hpo_terms.snap | 4 +- ...po_omims_name_contains_with_hpo_terms.snap | 8 +- ...st__hpo_omims_name_exact_no_hpo_terms.snap | 4 +- ...__hpo_omims_name_exact_with_hpo_terms.snap | 8 +- ...t__hpo_omims_name_prefix_no_hpo_terms.snap | 4 +- ..._hpo_omims_name_prefix_with_hpo_terms.snap | 8 +- ...t__hpo_omims_name_suffix_no_hpo_terms.snap | 4 +- ..._hpo_omims_name_suffix_with_hpo_terms.snap | 8 +- ..._hpo_omims_omim_id_exact_no_hpo_terms.snap | 4 +- ...po_omims_omim_id_exact_with_hpo_terms.snap | 8 +- ...__test__hpo_terms_name_exact_no_genes.snap | 6 +- ...test__hpo_terms_name_exact_with_genes.snap | 78 +- ...__test__hpo_terms_name_fuzzy_no_genes.snap | 6 +- ...test__hpo_terms_name_fuzzy_with_genes.snap | 78 +- ...est__hpo_terms_term_id_exact_no_genes.snap | 5 +- ...t__hpo_terms_term_id_exact_with_genes.snap | 71 +- 35 files changed, 1736 insertions(+), 875 deletions(-) diff --git a/src/algos/phenomizer.rs b/src/algos/phenomizer.rs index 1a91761..cd49f04 100644 --- a/src/algos/phenomizer.rs +++ b/src/algos/phenomizer.rs @@ -84,7 +84,7 @@ mod test { let score = score(&prepare(query), &hpo_marfan, &hpo); - assert!((score - 1.770_859_7).abs() < 0.00001, "score = {score}"); + assert!((score - 1.757_194).abs() < 0.00001, "score = {score}"); Ok(()) } diff --git a/src/server/run/hpo_genes.rs b/src/server/run/hpo_genes.rs index 8c2f4eb..40ac46f 100644 --- a/src/server/run/hpo_genes.rs +++ b/src/server/run/hpo_genes.rs @@ -216,7 +216,7 @@ pub(crate) mod test { pub fn web_server_data() -> Arc { let ontology = crate::common::load_hpo("tests/data/hpo").expect("could not load HPO"); let ncbi_to_hgnc = - crate::common::hgnc_xlink::load_ncbi_to_hgnc("tests/data/hgnc_xlink.tsv") + crate::common::hgnc_xlink::load_ncbi_to_hgnc("tests/data/hpo/hgnc_xlink.tsv") .expect("could not HGNC xlink"); let hgnc_to_ncbi = crate::common::hgnc_xlink::inverse_hashmap(&ncbi_to_hgnc); let hpo_doc = fastobo::from_file("tests/data/hpo/hp.obo").expect("could not load HPO OBO"); diff --git a/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_hgnc_gene_ids.snap b/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_hgnc_gene_ids.snap index c9b90ee..6028685 100644 --- a/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_hgnc_gene_ids.snap +++ b/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_hgnc_gene_ids.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_sim/term_gene.rs -expression: "&run_query(\"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_ids=HGNC:20324,HGNC:12403\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_ids=HGNC:20324,HGNC:12403\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: terms: @@ -20,7 +20,7 @@ query: hgnc_id: "HGNC:20324" result: - gene_symbol: TGDS - raw_score: 1.028543 + raw_score: 1.0164213 terms: - term_query: term_id: "HP:0000347" @@ -28,395 +28,422 @@ result: term_gene: term_id: "HP:0000347" term_name: Micrognathia - score: 1.8309557 + score: 1.8036361 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0001831" term_name: Short toe - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0003097" term_name: Short femur - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0005792" term_name: Short humerus - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0010049" term_name: Short metacarpal - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000272" term_name: Malar flattening - score: 1.341162 + score: 1.3065242 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001181" term_name: Adducted thumb - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0004209" term_name: Clinodactyly of the 5th finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009464" term_name: Ulnar deviation of the 2nd finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009467" term_name: Radial deviation of the 2nd finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0030368" term_name: Hyperphalangy of the 2nd finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100490" term_name: Camptodactyly of finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002857" term_name: Genu valgum - score: 1.0733097 + score: 1.0609595 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0010508" term_name: Metatarsus valgus - score: 1.0733097 + score: 1.0609595 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0005930" term_name: Abnormal epiphysis morphology - score: 1.002138 + score: 0.99177706 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0000954" term_name: Single transverse palmar crease - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001762" term_name: Talipes equinovarus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000470" term_name: Short neck - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000767" term_name: Pectus excavatum - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000768" term_name: Pectus carinatum - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0002650" term_name: Scoliosis - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001373" term_name: Joint dislocation - score: 0.48051217 + score: 0.46725264 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: - term_id: "HP:0001387" - term_name: Joint stiffness - score: 0.44339323 - - term_query: - term_id: "HP:0010442" - term_name: Polydactyly - term_gene: - term_id: "HP:0001388" - term_name: Joint laxity - score: 0.44339323 + term_id: "HP:0001382" + term_name: Joint hypermobility + score: 0.42905885 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: - term_id: "HP:0005692" - term_name: Joint hyperflexibility - score: 0.44339323 + term_id: "HP:0001387" + term_name: Joint stiffness + score: 0.42905885 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000160" term_name: Narrow mouth - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000162" term_name: Glossoptosis - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000175" term_name: Cleft palate - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000193" term_name: Bifid uvula - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000201" term_name: Pierre-Robin sequence - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000204" term_name: Cleft upper lip - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000218" term_name: High palate - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000293" term_name: Full cheeks - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000460" term_name: Narrow nose - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000579" term_name: Nasolacrimal duct obstruction - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000582" term_name: Upslanted palpebral fissure - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0002553" term_name: Highly arched eyebrow - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0009933" term_name: Narrow naris - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0010285" term_name: Oral synechia - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0010763" term_name: Low insertion of columella - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0045074" term_name: Thin eyebrow - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000476" term_name: Cystic hygroma - score: 0.4094388 + score: 0.4090133 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0000023" term_name: Inguinal hernia - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001537" term_name: Umbilical hernia - score: 0.28058913 - - term_query: ~ + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000028" term_name: Cryptorchidism - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000316" term_name: Hypertelorism - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000368" term_name: "Low-set, posteriorly rotated ears" - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000389" term_name: Chronic otitis media - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000520" term_name: Proptosis - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001250" term_name: Seizure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001263" term_name: Global developmental delay - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001508" term_name: Failure to thrive - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001511" term_name: Intrauterine growth retardation - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001629" term_name: Ventricular septal defect - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001631" term_name: Atrial septal defect - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001651" term_name: Dextrocardia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001680" term_name: Coarctation of aorta - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002119" term_name: Ventriculomegaly - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002623" term_name: Overriding aorta - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0004322" term_name: Short stature - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0008897" term_name: Postnatal growth retardation - score: 0 + score: 0.00039364694 - gene_symbol: TTN - raw_score: 0.91585016 + raw_score: 0.89086473 terms: - term_query: term_id: "HP:0000347" @@ -424,647 +451,788 @@ result: term_gene: term_id: "HP:0000308" term_name: Microretrognathia - score: 1.8309557 + score: 1.8036361 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000303" term_name: Mandibular prognathia - score: 1.5641111 + score: 1.5222461 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100807" term_name: Long fingers - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001385" term_name: Hip dysplasia - score: 1.002138 + score: 0.99177706 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003273" term_name: Hip contracture - score: 1.002138 - - term_query: - term_id: "HP:0010442" - term_name: Polydactyly - term_gene: - term_id: "HP:0000982" - term_name: Palmoplantar keratoderma - score: 0.73446083 + score: 0.99177706 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001761" term_name: Pes cavus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001762" term_name: Talipes equinovarus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001763" term_name: Pes planus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001771" term_name: Achilles tendon contracture - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003547" term_name: Shoulder girdle muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003691" term_name: Scapular winging - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003731" term_name: Quadriceps muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003749" term_name: Pelvic girdle muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008959" term_name: Distal upper limb muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008963" term_name: Tibialis muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008981" term_name: Calf muscle hypertrophy - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009027" term_name: Foot dorsiflexor weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009049" term_name: Peroneal muscle atrophy - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009077" term_name: Weakness of long finger extensor muscles - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0002650" term_name: Scoliosis - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0003306" term_name: Spinal rigidity - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0003307" term_name: Hyperlordosis - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002828" term_name: Multiple joint contractures - score: 0.48051217 + score: 0.46725264 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008800" term_name: Limited hip movement - score: 0.44339323 + score: 0.42905885 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000160" term_name: Narrow mouth - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000193" term_name: Bifid uvula - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000218" term_name: High palate - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000276" term_name: Long face - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0001349" term_name: Facial diplegia - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0005991" term_name: Limited neck flexion - score: 0.4094388 + score: 0.4090133 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001290" term_name: Generalized hypotonia - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002355" term_name: Difficulty walking - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002359" term_name: Frequent falls - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002421" term_name: Poor head control - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003323" term_name: Progressive muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003324" term_name: Generalized muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003327" term_name: Axial muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003391" term_name: Gowers sign - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003403" term_name: "EMG: decremental response of compound muscle action potential to repetitive nerve stimulation" - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003458" term_name: "EMG: myopathic abnormalities" - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003551" term_name: Difficulty climbing stairs - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003555" term_name: Muscle fiber splitting - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003557" term_name: Increased variability in muscle fiber diameter - score: 0.28058913 + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0003560" + term_name: Muscular dystrophy + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003687" term_name: Centrally nucleated skeletal muscle fibers - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003700" term_name: Generalized amyotrophy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003715" term_name: Myofibrillar myopathy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003722" term_name: Neck flexor weakness - score: 0.28058913 - - term_query: - term_id: "HP:0010442" - term_name: Polydactyly - term_gene: - term_id: "HP:0003741" - term_name: Congenital muscular dystrophy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003789" term_name: Minicore myopathy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003803" term_name: Type 1 muscle fiber predominance - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003805" term_name: Rimmed vacuoles - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0004889" term_name: Intermittent episodes of respiratory insufficiency due to muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008978" term_name: Necrotizing myopathy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009046" term_name: Difficulty running - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009058" term_name: Increased muscle lipid content - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009113" term_name: Diaphragmatic weakness - score: 0.28058913 + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0011399" + term_name: Tibialis anterior muscle atrophy + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0012548" term_name: Fatty replacement of skeletal muscle - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0030091" term_name: Absent muscle fiber merosin - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0031237" term_name: Internally nucleated skeletal muscle fibers - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0031374" term_name: Ankle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100293" term_name: Hypertrophied muscle fibers - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100295" term_name: Muscle fiber atrophy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100297" term_name: Increased endomysial connective tissue - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100578" term_name: Lipoatrophy - score: 0.28058913 - - term_query: ~ + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000407" term_name: Sensorineural hearing impairment - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000411" term_name: Protruding ear - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000508" term_name: Ptosis - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000602" term_name: Ophthalmoplegia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000750" term_name: Delayed speech and language development - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0000969" + term_name: Edema + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001256" term_name: "Intellectual disability, mild" - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001260" term_name: Dysarthria - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0001279" + term_name: Syncope + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001284" term_name: Areflexia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001508" term_name: Failure to thrive - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001618" term_name: Dysphonia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001620" term_name: High pitched voice - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001634" term_name: Mitral valve prolapse - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001635" term_name: Congestive heart failure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001639" term_name: Hypertrophic cardiomyopathy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001644" term_name: Dilated cardiomyopathy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001645" term_name: Sudden cardiac death - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0001658" + term_name: Myocardial infarction + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001667" term_name: Right ventricular hypertrophy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001678" term_name: Atrioventricular block - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001708" term_name: Right ventricular failure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001712" term_name: Left ventricular hypertrophy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: - term_id: "HP:0001874" - term_name: Abnormality of neutrophils - score: 0 - - term_query: ~ + term_id: "HP:0001727" + term_name: Thromboembolic stroke + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0001962" + term_name: Palpitations + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002091" term_name: Restrictive ventilatory defect - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002194" term_name: Delayed gross motor development - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002312" term_name: Clumsiness - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0002321" + term_name: Vertigo + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002515" term_name: Waddling gait - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002527" term_name: Falls - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002792" term_name: Reduced vital capacity - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0002875" + term_name: Exertional dyspnea + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002877" term_name: Nocturnal hypoventilation - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002878" term_name: Respiratory failure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0003376" term_name: Steppage gait - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0003546" + term_name: Exercise intolerance + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0004322" term_name: Short stature - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0004756" term_name: Ventricular tachycardia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0005110" term_name: Atrial fibrillation - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0006699" term_name: Premature atrial contractions - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0008180" term_name: Mildly elevated creatine kinase - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0011717" term_name: Atrioventricular reentrant tachycardia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0012378" + term_name: Fatigue + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0012666" term_name: Severely reduced left ventricular ejection fraction - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0012764" term_name: Orthopnea - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0030059" term_name: Mitochondrial depletion - score: 0 + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0100749" + term_name: Chest pain + score: 0.00039364694 diff --git a/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_ncbi_gene_ids.snap b/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_ncbi_gene_ids.snap index 037fb40..693dd98 100644 --- a/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_ncbi_gene_ids.snap +++ b/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_ncbi_gene_ids.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_sim/term_gene.rs -expression: "&run_query(\"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_ids=23483,7273\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_ids=23483,7273\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: terms: @@ -20,7 +20,7 @@ query: hgnc_id: "HGNC:20324" result: - gene_symbol: TGDS - raw_score: 1.028543 + raw_score: 1.0164213 terms: - term_query: term_id: "HP:0000347" @@ -28,395 +28,422 @@ result: term_gene: term_id: "HP:0000347" term_name: Micrognathia - score: 1.8309557 + score: 1.8036361 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0001831" term_name: Short toe - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0003097" term_name: Short femur - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0005792" term_name: Short humerus - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0010049" term_name: Short metacarpal - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000272" term_name: Malar flattening - score: 1.341162 + score: 1.3065242 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001181" term_name: Adducted thumb - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0004209" term_name: Clinodactyly of the 5th finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009464" term_name: Ulnar deviation of the 2nd finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009467" term_name: Radial deviation of the 2nd finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0030368" term_name: Hyperphalangy of the 2nd finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100490" term_name: Camptodactyly of finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002857" term_name: Genu valgum - score: 1.0733097 + score: 1.0609595 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0010508" term_name: Metatarsus valgus - score: 1.0733097 + score: 1.0609595 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0005930" term_name: Abnormal epiphysis morphology - score: 1.002138 + score: 0.99177706 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0000954" term_name: Single transverse palmar crease - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001762" term_name: Talipes equinovarus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000470" term_name: Short neck - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000767" term_name: Pectus excavatum - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000768" term_name: Pectus carinatum - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0002650" term_name: Scoliosis - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001373" term_name: Joint dislocation - score: 0.48051217 + score: 0.46725264 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: - term_id: "HP:0001387" - term_name: Joint stiffness - score: 0.44339323 - - term_query: - term_id: "HP:0010442" - term_name: Polydactyly - term_gene: - term_id: "HP:0001388" - term_name: Joint laxity - score: 0.44339323 + term_id: "HP:0001382" + term_name: Joint hypermobility + score: 0.42905885 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: - term_id: "HP:0005692" - term_name: Joint hyperflexibility - score: 0.44339323 + term_id: "HP:0001387" + term_name: Joint stiffness + score: 0.42905885 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000160" term_name: Narrow mouth - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000162" term_name: Glossoptosis - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000175" term_name: Cleft palate - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000193" term_name: Bifid uvula - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000201" term_name: Pierre-Robin sequence - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000204" term_name: Cleft upper lip - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000218" term_name: High palate - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000293" term_name: Full cheeks - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000460" term_name: Narrow nose - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000579" term_name: Nasolacrimal duct obstruction - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000582" term_name: Upslanted palpebral fissure - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0002553" term_name: Highly arched eyebrow - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0009933" term_name: Narrow naris - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0010285" term_name: Oral synechia - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0010763" term_name: Low insertion of columella - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0045074" term_name: Thin eyebrow - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000476" term_name: Cystic hygroma - score: 0.4094388 + score: 0.4090133 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0000023" term_name: Inguinal hernia - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001537" term_name: Umbilical hernia - score: 0.28058913 - - term_query: ~ + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000028" term_name: Cryptorchidism - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000316" term_name: Hypertelorism - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000368" term_name: "Low-set, posteriorly rotated ears" - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000389" term_name: Chronic otitis media - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000520" term_name: Proptosis - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001250" term_name: Seizure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001263" term_name: Global developmental delay - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001508" term_name: Failure to thrive - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001511" term_name: Intrauterine growth retardation - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001629" term_name: Ventricular septal defect - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001631" term_name: Atrial septal defect - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001651" term_name: Dextrocardia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001680" term_name: Coarctation of aorta - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002119" term_name: Ventriculomegaly - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002623" term_name: Overriding aorta - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0004322" term_name: Short stature - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0008897" term_name: Postnatal growth retardation - score: 0 + score: 0.00039364694 - gene_symbol: TTN - raw_score: 0.91585016 + raw_score: 0.89086473 terms: - term_query: term_id: "HP:0000347" @@ -424,647 +451,788 @@ result: term_gene: term_id: "HP:0000308" term_name: Microretrognathia - score: 1.8309557 + score: 1.8036361 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000303" term_name: Mandibular prognathia - score: 1.5641111 + score: 1.5222461 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100807" term_name: Long fingers - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001385" term_name: Hip dysplasia - score: 1.002138 + score: 0.99177706 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003273" term_name: Hip contracture - score: 1.002138 - - term_query: - term_id: "HP:0010442" - term_name: Polydactyly - term_gene: - term_id: "HP:0000982" - term_name: Palmoplantar keratoderma - score: 0.73446083 + score: 0.99177706 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001761" term_name: Pes cavus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001762" term_name: Talipes equinovarus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001763" term_name: Pes planus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001771" term_name: Achilles tendon contracture - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003547" term_name: Shoulder girdle muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003691" term_name: Scapular winging - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003731" term_name: Quadriceps muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003749" term_name: Pelvic girdle muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008959" term_name: Distal upper limb muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008963" term_name: Tibialis muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008981" term_name: Calf muscle hypertrophy - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009027" term_name: Foot dorsiflexor weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009049" term_name: Peroneal muscle atrophy - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009077" term_name: Weakness of long finger extensor muscles - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0002650" term_name: Scoliosis - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0003306" term_name: Spinal rigidity - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0003307" term_name: Hyperlordosis - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002828" term_name: Multiple joint contractures - score: 0.48051217 + score: 0.46725264 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008800" term_name: Limited hip movement - score: 0.44339323 + score: 0.42905885 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000160" term_name: Narrow mouth - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000193" term_name: Bifid uvula - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000218" term_name: High palate - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000276" term_name: Long face - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0001349" term_name: Facial diplegia - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0005991" term_name: Limited neck flexion - score: 0.4094388 + score: 0.4090133 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001290" term_name: Generalized hypotonia - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002355" term_name: Difficulty walking - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002359" term_name: Frequent falls - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002421" term_name: Poor head control - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003323" term_name: Progressive muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003324" term_name: Generalized muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003327" term_name: Axial muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003391" term_name: Gowers sign - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003403" term_name: "EMG: decremental response of compound muscle action potential to repetitive nerve stimulation" - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003458" term_name: "EMG: myopathic abnormalities" - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003551" term_name: Difficulty climbing stairs - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003555" term_name: Muscle fiber splitting - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003557" term_name: Increased variability in muscle fiber diameter - score: 0.28058913 + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0003560" + term_name: Muscular dystrophy + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003687" term_name: Centrally nucleated skeletal muscle fibers - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003700" term_name: Generalized amyotrophy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003715" term_name: Myofibrillar myopathy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003722" term_name: Neck flexor weakness - score: 0.28058913 - - term_query: - term_id: "HP:0010442" - term_name: Polydactyly - term_gene: - term_id: "HP:0003741" - term_name: Congenital muscular dystrophy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003789" term_name: Minicore myopathy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003803" term_name: Type 1 muscle fiber predominance - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003805" term_name: Rimmed vacuoles - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0004889" term_name: Intermittent episodes of respiratory insufficiency due to muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008978" term_name: Necrotizing myopathy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009046" term_name: Difficulty running - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009058" term_name: Increased muscle lipid content - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009113" term_name: Diaphragmatic weakness - score: 0.28058913 + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0011399" + term_name: Tibialis anterior muscle atrophy + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0012548" term_name: Fatty replacement of skeletal muscle - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0030091" term_name: Absent muscle fiber merosin - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0031237" term_name: Internally nucleated skeletal muscle fibers - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0031374" term_name: Ankle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100293" term_name: Hypertrophied muscle fibers - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100295" term_name: Muscle fiber atrophy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100297" term_name: Increased endomysial connective tissue - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100578" term_name: Lipoatrophy - score: 0.28058913 - - term_query: ~ + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000407" term_name: Sensorineural hearing impairment - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000411" term_name: Protruding ear - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000508" term_name: Ptosis - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000602" term_name: Ophthalmoplegia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000750" term_name: Delayed speech and language development - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0000969" + term_name: Edema + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001256" term_name: "Intellectual disability, mild" - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001260" term_name: Dysarthria - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0001279" + term_name: Syncope + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001284" term_name: Areflexia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001508" term_name: Failure to thrive - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001618" term_name: Dysphonia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001620" term_name: High pitched voice - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001634" term_name: Mitral valve prolapse - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001635" term_name: Congestive heart failure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001639" term_name: Hypertrophic cardiomyopathy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001644" term_name: Dilated cardiomyopathy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001645" term_name: Sudden cardiac death - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0001658" + term_name: Myocardial infarction + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001667" term_name: Right ventricular hypertrophy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001678" term_name: Atrioventricular block - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001708" term_name: Right ventricular failure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001712" term_name: Left ventricular hypertrophy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: - term_id: "HP:0001874" - term_name: Abnormality of neutrophils - score: 0 - - term_query: ~ + term_id: "HP:0001727" + term_name: Thromboembolic stroke + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0001962" + term_name: Palpitations + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002091" term_name: Restrictive ventilatory defect - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002194" term_name: Delayed gross motor development - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002312" term_name: Clumsiness - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0002321" + term_name: Vertigo + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002515" term_name: Waddling gait - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002527" term_name: Falls - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002792" term_name: Reduced vital capacity - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0002875" + term_name: Exertional dyspnea + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002877" term_name: Nocturnal hypoventilation - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002878" term_name: Respiratory failure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0003376" term_name: Steppage gait - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0003546" + term_name: Exercise intolerance + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0004322" term_name: Short stature - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0004756" term_name: Ventricular tachycardia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0005110" term_name: Atrial fibrillation - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0006699" term_name: Premature atrial contractions - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0008180" term_name: Mildly elevated creatine kinase - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0011717" term_name: Atrioventricular reentrant tachycardia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0012378" + term_name: Fatigue + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0012666" term_name: Severely reduced left ventricular ejection fraction - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0012764" term_name: Orthopnea - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0030059" term_name: Mitochondrial depletion - score: 0 + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0100749" + term_name: Chest pain + score: 0.00039364694 diff --git a/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_symbols.snap b/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_symbols.snap index 4a7fbb4..dabfcb2 100644 --- a/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_symbols.snap +++ b/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_gene__test__hpo_sim_term_gene_terms_symbols.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_sim/term_gene.rs -expression: "&run_query(\"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_symbols=TGDS,TTN\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/sim/term-gene?terms=HP:0010442,HP:0000347&gene_symbols=TGDS,TTN\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: terms: @@ -20,7 +20,7 @@ query: hgnc_id: "HGNC:20324" result: - gene_symbol: TGDS - raw_score: 1.028543 + raw_score: 1.0164213 terms: - term_query: term_id: "HP:0000347" @@ -28,395 +28,422 @@ result: term_gene: term_id: "HP:0000347" term_name: Micrognathia - score: 1.8309557 + score: 1.8036361 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0001831" term_name: Short toe - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0003097" term_name: Short femur - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0005792" term_name: Short humerus - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0010049" term_name: Short metacarpal - score: 1.4382622 + score: 1.4235806 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000272" term_name: Malar flattening - score: 1.341162 + score: 1.3065242 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001181" term_name: Adducted thumb - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0004209" term_name: Clinodactyly of the 5th finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009464" term_name: Ulnar deviation of the 2nd finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009467" term_name: Radial deviation of the 2nd finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0030368" term_name: Hyperphalangy of the 2nd finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100490" term_name: Camptodactyly of finger - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002857" term_name: Genu valgum - score: 1.0733097 + score: 1.0609595 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0010508" term_name: Metatarsus valgus - score: 1.0733097 + score: 1.0609595 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0005930" term_name: Abnormal epiphysis morphology - score: 1.002138 + score: 0.99177706 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0000954" term_name: Single transverse palmar crease - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001762" term_name: Talipes equinovarus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000470" term_name: Short neck - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000767" term_name: Pectus excavatum - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000768" term_name: Pectus carinatum - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0002650" term_name: Scoliosis - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001373" term_name: Joint dislocation - score: 0.48051217 + score: 0.46725264 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: - term_id: "HP:0001387" - term_name: Joint stiffness - score: 0.44339323 - - term_query: - term_id: "HP:0010442" - term_name: Polydactyly - term_gene: - term_id: "HP:0001388" - term_name: Joint laxity - score: 0.44339323 + term_id: "HP:0001382" + term_name: Joint hypermobility + score: 0.42905885 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: - term_id: "HP:0005692" - term_name: Joint hyperflexibility - score: 0.44339323 + term_id: "HP:0001387" + term_name: Joint stiffness + score: 0.42905885 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000160" term_name: Narrow mouth - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000162" term_name: Glossoptosis - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000175" term_name: Cleft palate - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000193" term_name: Bifid uvula - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000201" term_name: Pierre-Robin sequence - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000204" term_name: Cleft upper lip - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000218" term_name: High palate - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000293" term_name: Full cheeks - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000460" term_name: Narrow nose - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000579" term_name: Nasolacrimal duct obstruction - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000582" term_name: Upslanted palpebral fissure - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0002553" term_name: Highly arched eyebrow - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0009933" term_name: Narrow naris - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0010285" term_name: Oral synechia - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0010763" term_name: Low insertion of columella - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0045074" term_name: Thin eyebrow - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000476" term_name: Cystic hygroma - score: 0.4094388 + score: 0.4090133 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0000023" term_name: Inguinal hernia - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001537" term_name: Umbilical hernia - score: 0.28058913 - - term_query: ~ + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000028" term_name: Cryptorchidism - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000316" term_name: Hypertelorism - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000368" term_name: "Low-set, posteriorly rotated ears" - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000389" term_name: Chronic otitis media - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000520" term_name: Proptosis - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001250" term_name: Seizure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001263" term_name: Global developmental delay - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001508" term_name: Failure to thrive - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001511" term_name: Intrauterine growth retardation - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001629" term_name: Ventricular septal defect - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001631" term_name: Atrial septal defect - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001651" term_name: Dextrocardia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001680" term_name: Coarctation of aorta - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002119" term_name: Ventriculomegaly - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002623" term_name: Overriding aorta - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0004322" term_name: Short stature - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0008897" term_name: Postnatal growth retardation - score: 0 + score: 0.00039364694 - gene_symbol: TTN - raw_score: 0.91585016 + raw_score: 0.89086473 terms: - term_query: term_id: "HP:0000347" @@ -424,647 +451,788 @@ result: term_gene: term_id: "HP:0000308" term_name: Microretrognathia - score: 1.8309557 + score: 1.8036361 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000303" term_name: Mandibular prognathia - score: 1.5641111 + score: 1.5222461 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100807" term_name: Long fingers - score: 1.2074362 + score: 1.1945721 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001385" term_name: Hip dysplasia - score: 1.002138 + score: 0.99177706 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003273" term_name: Hip contracture - score: 1.002138 - - term_query: - term_id: "HP:0010442" - term_name: Polydactyly - term_gene: - term_id: "HP:0000982" - term_name: Palmoplantar keratoderma - score: 0.73446083 + score: 0.99177706 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001761" term_name: Pes cavus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001762" term_name: Talipes equinovarus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001763" term_name: Pes planus - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001771" term_name: Achilles tendon contracture - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003547" term_name: Shoulder girdle muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003691" term_name: Scapular winging - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003731" term_name: Quadriceps muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003749" term_name: Pelvic girdle muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008959" term_name: Distal upper limb muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008963" term_name: Tibialis muscle weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008981" term_name: Calf muscle hypertrophy - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009027" term_name: Foot dorsiflexor weakness - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009049" term_name: Peroneal muscle atrophy - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009077" term_name: Weakness of long finger extensor muscles - score: 0.73446083 + score: 0.7227021 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0002650" term_name: Scoliosis - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0003306" term_name: Spinal rigidity - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0003307" term_name: Hyperlordosis - score: 0.6371871 + score: 0.6254407 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002828" term_name: Multiple joint contractures - score: 0.48051217 + score: 0.46725264 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008800" term_name: Limited hip movement - score: 0.44339323 + score: 0.42905885 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000160" term_name: Narrow mouth - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000193" term_name: Bifid uvula - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000218" term_name: High palate - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0000276" term_name: Long face - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0001349" term_name: Facial diplegia - score: 0.4183606 + score: 0.4173417 - term_query: term_id: "HP:0000347" term_name: Micrognathia term_gene: term_id: "HP:0005991" term_name: Limited neck flexion - score: 0.4094388 + score: 0.4090133 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0001290" term_name: Generalized hypotonia - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002355" term_name: Difficulty walking - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002359" term_name: Frequent falls - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0002421" term_name: Poor head control - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003323" term_name: Progressive muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003324" term_name: Generalized muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003327" term_name: Axial muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003391" term_name: Gowers sign - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003403" term_name: "EMG: decremental response of compound muscle action potential to repetitive nerve stimulation" - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003458" term_name: "EMG: myopathic abnormalities" - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003551" term_name: Difficulty climbing stairs - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003555" term_name: Muscle fiber splitting - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003557" term_name: Increased variability in muscle fiber diameter - score: 0.28058913 + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0003560" + term_name: Muscular dystrophy + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003687" term_name: Centrally nucleated skeletal muscle fibers - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003700" term_name: Generalized amyotrophy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003715" term_name: Myofibrillar myopathy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003722" term_name: Neck flexor weakness - score: 0.28058913 - - term_query: - term_id: "HP:0010442" - term_name: Polydactyly - term_gene: - term_id: "HP:0003741" - term_name: Congenital muscular dystrophy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003789" term_name: Minicore myopathy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003803" term_name: Type 1 muscle fiber predominance - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0003805" term_name: Rimmed vacuoles - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0004889" term_name: Intermittent episodes of respiratory insufficiency due to muscle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0008978" term_name: Necrotizing myopathy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009046" term_name: Difficulty running - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009058" term_name: Increased muscle lipid content - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0009113" term_name: Diaphragmatic weakness - score: 0.28058913 + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0011399" + term_name: Tibialis anterior muscle atrophy + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0012548" term_name: Fatty replacement of skeletal muscle - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0030091" term_name: Absent muscle fiber merosin - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0031237" term_name: Internally nucleated skeletal muscle fibers - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0031374" term_name: Ankle weakness - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100293" term_name: Hypertrophied muscle fibers - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100295" term_name: Muscle fiber atrophy - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100297" term_name: Increased endomysial connective tissue - score: 0.28058913 + score: 0.28650212 - term_query: term_id: "HP:0010442" term_name: Polydactyly term_gene: term_id: "HP:0100578" term_name: Lipoatrophy - score: 0.28058913 - - term_query: ~ + score: 0.28650212 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000407" term_name: Sensorineural hearing impairment - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000411" term_name: Protruding ear - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000508" term_name: Ptosis - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000602" term_name: Ophthalmoplegia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0000750" term_name: Delayed speech and language development - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0000969" + term_name: Edema + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001256" term_name: "Intellectual disability, mild" - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001260" term_name: Dysarthria - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0001279" + term_name: Syncope + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001284" term_name: Areflexia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001508" term_name: Failure to thrive - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001618" term_name: Dysphonia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001620" term_name: High pitched voice - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001634" term_name: Mitral valve prolapse - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001635" term_name: Congestive heart failure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001639" term_name: Hypertrophic cardiomyopathy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001644" term_name: Dilated cardiomyopathy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001645" term_name: Sudden cardiac death - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0001658" + term_name: Myocardial infarction + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001667" term_name: Right ventricular hypertrophy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001678" term_name: Atrioventricular block - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001708" term_name: Right ventricular failure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0001712" term_name: Left ventricular hypertrophy - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: - term_id: "HP:0001874" - term_name: Abnormality of neutrophils - score: 0 - - term_query: ~ + term_id: "HP:0001727" + term_name: Thromboembolic stroke + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0001962" + term_name: Palpitations + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002091" term_name: Restrictive ventilatory defect - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002194" term_name: Delayed gross motor development - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002312" term_name: Clumsiness - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0002321" + term_name: Vertigo + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002515" term_name: Waddling gait - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002527" term_name: Falls - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002792" term_name: Reduced vital capacity - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0002875" + term_name: Exertional dyspnea + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002877" term_name: Nocturnal hypoventilation - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0002878" term_name: Respiratory failure - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0003376" term_name: Steppage gait - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0003546" + term_name: Exercise intolerance + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0004322" term_name: Short stature - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0004756" term_name: Ventricular tachycardia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0005110" term_name: Atrial fibrillation - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0006699" term_name: Premature atrial contractions - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0008180" term_name: Mildly elevated creatine kinase - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0011717" term_name: Atrioventricular reentrant tachycardia - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0012378" + term_name: Fatigue + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0012666" term_name: Severely reduced left ventricular ejection fraction - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0012764" term_name: Orthopnea - score: 0 - - term_query: ~ + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly term_gene: term_id: "HP:0030059" term_name: Mitochondrial depletion - score: 0 + score: 0.00039364694 + - term_query: + term_id: "HP:0010442" + term_name: Polydactyly + term_gene: + term_id: "HP:0100749" + term_name: Chest pain + score: 0.00039364694 diff --git a/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_term__test__hpo_sim_term_term_one_one.snap b/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_term__test__hpo_sim_term_term_one_one.snap index c3a92b8..23029fa 100644 --- a/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_term__test__hpo_sim_term_term_one_one.snap +++ b/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_term__test__hpo_sim_term_term_one_one.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_sim/term_term.rs -expression: "&run_query(\"/hpo/sim/term-term?lhs=HP:0010442&rhs=HP:0001780\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/sim/term-term?lhs=HP:0010442&rhs=HP:0001780\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: lhs: @@ -16,4 +16,4 @@ query: result: - lhs: "HP:0010442" rhs: "HP:0001780" - score: 1.2074362 + score: 1.1945721 diff --git a/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_term__test__hpo_sim_term_term_two_two.snap b/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_term__test__hpo_sim_term_term_two_two.snap index ac39b28..c8c3f4a 100644 --- a/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_term__test__hpo_sim_term_term_two_two.snap +++ b/src/server/run/hpo_sim/snapshots/viguno__server__run__hpo_sim__term_term__test__hpo_sim_term_term_two_two.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_sim/term_term.rs -expression: "&run_query(\"/hpo/sim/term-term?lhs=HP:0010442,HP:0000347&rhs=HP:0001780,HP:0000252\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/sim/term-term?lhs=HP:0010442,HP:0000347&rhs=HP:0001780,HP:0000252\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: lhs: @@ -18,13 +18,13 @@ query: result: - lhs: "HP:0010442" rhs: "HP:0001780" - score: 1.2074362 + score: 1.1945721 - lhs: "HP:0000347" rhs: "HP:0000252" - score: 0.7606594 + score: 0.7402858 - lhs: "HP:0010442" rhs: "HP:0000252" - score: 0.48051217 + score: 0.46725264 - lhs: "HP:0000347" rhs: "HP:0001780" - score: 0.48051217 + score: 0.46725264 diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_contains_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_contains_no_hpo_terms.snap index b5e2a33..21da3ee 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_contains_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_contains_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_symbol=GD&match=contains\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/genes?gene_symbol=GD&match=contains\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: ~ @@ -45,12 +45,18 @@ result: - gene_ncbi_id: 4967 gene_symbol: OGDH hgnc_id: "HGNC:8124" + - gene_ncbi_id: 5910 + gene_symbol: RAP1GDS1 + hgnc_id: "HGNC:9859" - gene_ncbi_id: 7358 gene_symbol: UGDH hgnc_id: "HGNC:12525" - gene_ncbi_id: 8200 gene_symbol: GDF5 hgnc_id: "HGNC:4220" + - gene_ncbi_id: 9518 + gene_symbol: GDF15 + hgnc_id: "HGNC:30142" - gene_ncbi_id: 9573 gene_symbol: GDF3 hgnc_id: "HGNC:4218" @@ -75,6 +81,9 @@ result: - gene_ncbi_id: 55753 gene_symbol: OGDHL hgnc_id: "HGNC:25590" + - gene_ncbi_id: 58528 + gene_symbol: RRAGD + hgnc_id: "HGNC:19903" - gene_ncbi_id: 79641 gene_symbol: ROGDI hgnc_id: "HGNC:29478" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_contains_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_contains_with_hpo_terms.snap index 412fd0d..4dd9905 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_contains_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_contains_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_symbol=GD&match=contains&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/genes?gene_symbol=GD&match=contains&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: ~ @@ -94,8 +94,6 @@ result: name: Testicular atrophy - term_id: "HP:0000049" name: Shawl scrotum - - term_id: "HP:0000144" - name: Decreased fertility - term_id: "HP:0000175" name: Cleft palate - term_id: "HP:0000204" @@ -158,8 +156,6 @@ result: name: "Intellectual disability, mild" - term_id: "HP:0001263" name: Global developmental delay - - term_id: "HP:0001388" - name: Joint laxity - term_id: "HP:0001419" name: X-linked recessive inheritance - term_id: "HP:0001508" @@ -176,12 +172,16 @@ result: name: Broad foot - term_id: "HP:0001773" name: Short foot + - term_id: "HP:0001840" + name: Metatarsus adductus - term_id: "HP:0001883" name: Talipes - term_id: "HP:0002055" name: Curved linear dimple below the lower lip - term_id: "HP:0002650" name: Scoliosis + - term_id: "HP:0002750" + name: Delayed skeletal maturation - term_id: "HP:0002816" name: Genu recurvatum - term_id: "HP:0003196" @@ -198,16 +198,12 @@ result: name: Short palm - term_id: "HP:0005640" name: Abnormal vertebral segmentation and fusion - - term_id: "HP:0005692" - name: Joint hyperflexibility - term_id: "HP:0006101" name: Finger syndactyly - term_id: "HP:0007018" name: Attention deficit hyperactivity disorder - term_id: "HP:0008232" name: Elevated circulating follicle stimulating hormone level - - term_id: "HP:0008572" - name: External ear malformation - term_id: "HP:0008689" name: Bilateral cryptorchidism - term_id: "HP:0009237" @@ -221,15 +217,13 @@ result: - term_id: "HP:0012774" name: Increased upper to lower segment ratio - term_id: "HP:0030680" - name: Abnormality of cardiovascular system morphology + name: Abnormal cardiovascular system morphology - term_id: "HP:0032277" name: Lozenge-shaped umbilicus - term_id: "HP:0040171" name: Decreased serum testosterone concentration - term_id: "HP:0100490" name: Camptodactyly of finger - - term_id: "HP:0100543" - name: Cognitive impairment - term_id: "HP:0200055" name: Small hand - gene_ncbi_id: 2657 @@ -316,6 +310,12 @@ result: hpo_terms: - term_id: "HP:0000006" name: Autosomal dominant inheritance + - term_id: "HP:0000214" + name: Lip telangiectasia + - term_id: "HP:0000227" + name: Tongue telangiectasia + - term_id: "HP:0000434" + name: Nasal mucosa telangiectasia - term_id: "HP:0000524" name: Conjunctival telangiectasia - term_id: "HP:0000646" @@ -342,8 +342,8 @@ result: name: Portal hypertension - term_id: "HP:0001635" name: Congestive heart failure - - term_id: "HP:0001935" - name: Microcytic anemia + - term_id: "HP:0001903" + name: Anemia - term_id: "HP:0002040" name: Esophageal varix - term_id: "HP:0002076" @@ -360,12 +360,20 @@ result: name: Gastrointestinal hemorrhage - term_id: "HP:0002326" name: Transient ischemic attack + - term_id: "HP:0002408" + name: Cerebral arteriovenous malformation + - term_id: "HP:0002629" + name: Gastrointestinal arteriovenous malformation - term_id: "HP:0002910" - name: Elevated hepatic transaminase + name: Elevated circulating hepatic transaminase concentration - term_id: "HP:0004406" name: "Spontaneous, recurrent epistaxis" - term_id: "HP:0004936" name: Venous thrombosis + - term_id: "HP:0006548" + name: Pulmonary arteriovenous malformation + - term_id: "HP:0006574" + name: Hepatic arteriovenous malformation - term_id: "HP:0007420" name: Spontaneous hematomas - term_id: "HP:0007763" @@ -476,12 +484,14 @@ result: name: Hearing abnormality - term_id: "HP:0000366" name: Abnormality of the nose + - term_id: "HP:0000501" + name: Glaucoma - term_id: "HP:0000504" name: Abnormality of vision - - term_id: "HP:0000592" - name: Blue sclerae - term_id: "HP:0000787" name: Nephrolithiasis + - term_id: "HP:0000821" + name: Hypothyroidism - term_id: "HP:0000822" name: Hypertension - term_id: "HP:0001373" @@ -494,12 +504,24 @@ result: name: Growth abnormality - term_id: "HP:0001597" name: Abnormality of the nail + - term_id: "HP:0001650" + name: Aortic valve stenosis + - term_id: "HP:0001653" + name: Mitral regurgitation - term_id: "HP:0001658" name: Myocardial infarction - term_id: "HP:0001717" name: Coronary artery calcification + - term_id: "HP:0001718" + name: Mitral stenosis + - term_id: "HP:0001878" + name: Hemolytic anemia - term_id: "HP:0002621" name: Atherosclerosis + - term_id: "HP:0002650" + name: Scoliosis + - term_id: "HP:0002659" + name: Increased susceptibility to fractures - term_id: "HP:0002758" name: Osteoarthritis - term_id: "HP:0002808" @@ -536,26 +558,42 @@ result: name: Irregular hyperpigmentation - term_id: "HP:0007832" name: Pigmentation of the sclera + - term_id: "HP:0007906" + name: Ocular hypertension - term_id: "HP:0008419" - name: Intervertebral disc degeneration + name: Intervertebral disk degeneration - term_id: "HP:0008800" name: Limited hip movement - term_id: "HP:0010501" name: Limitation of knee mobility + - term_id: "HP:0011034" + name: Amyloidosis + - term_id: "HP:0011982" + name: Black pigment gallstones + - term_id: "HP:0012119" + name: Methemoglobinemia - term_id: "HP:0012213" name: Decreased glomerular filtration rate + - term_id: "HP:0025612" + name: Corneal astigmatism - term_id: "HP:0030764" name: Ochronosis - term_id: "HP:0033666" name: Diminished physical functioning - term_id: "HP:0033704" name: Elevated urinary homogentisic acid + - term_id: "HP:0040319" + name: Dark urine - term_id: "HP:0100550" name: Tendon rupture - term_id: "HP:0100593" name: Calcification of cartilage - term_id: "HP:0100773" name: Cartilage destruction + - term_id: "HP:6000025" + name: Dark cerumen + - term_id: "HP:6000365" + name: Brown pigmentation of the conjunctiva - gene_ncbi_id: 3248 gene_symbol: HPGD hgnc_id: "HGNC:5154" @@ -584,8 +622,6 @@ result: name: Osteoporosis - term_id: "HP:0000975" name: Hyperhidrosis - - term_id: "HP:0000976" - name: Eczematoid dermatitis - term_id: "HP:0000982" name: Palmoplantar keratoderma - term_id: "HP:0001051" @@ -639,7 +675,7 @@ result: - term_id: "HP:0002970" name: Genu varum - term_id: "HP:0002992" - name: Abnormality of tibia morphology + name: Abnormal tibia morphology - term_id: "HP:0003040" name: Arthropathy - term_id: "HP:0003103" @@ -653,7 +689,7 @@ result: - term_id: "HP:0004398" name: Peptic ulcer - term_id: "HP:0005561" - name: Abnormality of bone marrow cell morphology + name: Abnormal bone marrow cell morphology - term_id: "HP:0005930" name: Abnormal epiphysis morphology - term_id: "HP:0008069" @@ -723,7 +759,7 @@ result: - term_id: "HP:0002119" name: Ventriculomegaly - term_id: "HP:0002151" - name: Increased serum lactate + name: Increased circulating lactate concentration - term_id: "HP:0002194" name: Delayed gross motor development - term_id: "HP:0002317" @@ -744,6 +780,70 @@ result: name: Abnormal salivary gland morphology - term_id: "HP:0012401" name: Abnormal urine alpha-ketoglutarate concentration + - gene_ncbi_id: 5910 + gene_symbol: RAP1GDS1 + hgnc_id: "HGNC:9859" + hpo_terms: + - term_id: "HP:0000007" + name: Autosomal recessive inheritance + - term_id: "HP:0000085" + name: Horseshoe kidney + - term_id: "HP:0000233" + name: Thin vermilion border + - term_id: "HP:0000252" + name: Microcephaly + - term_id: "HP:0000278" + name: Retrognathia + - term_id: "HP:0000316" + name: Hypertelorism + - term_id: "HP:0000319" + name: Smooth philtrum + - term_id: "HP:0000322" + name: Short philtrum + - term_id: "HP:0000325" + name: Triangular face + - term_id: "HP:0000348" + name: High forehead + - term_id: "HP:0000369" + name: Low-set ears + - term_id: "HP:0000414" + name: Bulbous nose + - term_id: "HP:0000718" + name: Aggressive behavior + - term_id: "HP:0001249" + name: Intellectual disability + - term_id: "HP:0001258" + name: Spastic paraplegia + - term_id: "HP:0001263" + name: Global developmental delay + - term_id: "HP:0001265" + name: Hyporeflexia + - term_id: "HP:0001270" + name: Motor delay + - term_id: "HP:0001382" + name: Joint hypermobility + - term_id: "HP:0001762" + name: Talipes equinovarus + - term_id: "HP:0002069" + name: Bilateral tonic-clonic seizure + - term_id: "HP:0002188" + name: Delayed CNS myelination + - term_id: "HP:0002474" + name: Expressive language delay + - term_id: "HP:0002553" + name: Highly arched eyebrow + - term_id: "HP:0003593" + name: Infantile onset + - term_id: "HP:0003623" + name: Neonatal onset + - term_id: "HP:0004322" + name: Short stature + - term_id: "HP:0008936" + name: Axial hypotonia + - term_id: "HP:0010863" + name: Receptive language delay + - term_id: "HP:0030863" + name: Nasal flaring - gene_ncbi_id: 7358 gene_symbol: UGDH hgnc_id: "HGNC:12525" @@ -842,6 +942,8 @@ result: name: Abnormal fingernail morphology - term_id: "HP:0001249" name: Intellectual disability + - term_id: "HP:0001382" + name: Joint hypermobility - term_id: "HP:0001385" name: Hip dysplasia - term_id: "HP:0001387" @@ -916,8 +1018,6 @@ result: name: Synostosis of carpal bones - term_id: "HP:0005096" name: Distal femoral bowing - - term_id: "HP:0005692" - name: Joint hyperflexibility - term_id: "HP:0005736" name: Short tibia - term_id: "HP:0005792" @@ -1044,6 +1144,16 @@ result: name: Camptodactyly of finger - term_id: "HP:0100543" name: Cognitive impairment + - term_id: "HP:6000650" + name: Distal tibiofibular synostosis + - gene_ncbi_id: 9518 + gene_symbol: GDF15 + hgnc_id: "HGNC:30142" + hpo_terms: + - term_id: "HP:0000006" + name: Autosomal dominant inheritance + - term_id: "HP:0012188" + name: Hyperemesis gravidarum - gene_ncbi_id: 9573 gene_symbol: GDF3 hgnc_id: "HGNC:4218" @@ -1228,10 +1338,10 @@ result: name: Global developmental delay - term_id: "HP:0001373" name: Joint dislocation + - term_id: "HP:0001382" + name: Joint hypermobility - term_id: "HP:0001387" name: Joint stiffness - - term_id: "HP:0001388" - name: Joint laxity - term_id: "HP:0001508" name: Failure to thrive - term_id: "HP:0001511" @@ -1268,8 +1378,6 @@ result: name: Clinodactyly of the 5th finger - term_id: "HP:0004322" name: Short stature - - term_id: "HP:0005692" - name: Joint hyperflexibility - term_id: "HP:0005792" name: Short humerus - term_id: "HP:0005930" @@ -1584,6 +1692,8 @@ result: name: Rapidly progressive - term_id: "HP:0003731" name: Quadriceps muscle weakness + - term_id: "HP:0003803" + name: Type 1 muscle fiber predominance - term_id: "HP:0006064" name: Limited interphalangeal movement - term_id: "HP:0006248" @@ -1650,6 +1760,10 @@ result: name: Weakness of facial musculature - term_id: "HP:0031629" name: Impaired tandem gait + - term_id: "HP:0033685" + name: Fiber type grouping + - term_id: "HP:0034045" + name: Angulated muscle fibers - term_id: "HP:0040078" name: Axonal degeneration - gene_ncbi_id: 54834 @@ -1768,6 +1882,44 @@ result: name: Infantile spasms - term_id: "HP:0030799" name: Scaphocephaly + - gene_ncbi_id: 58528 + gene_symbol: RRAGD + hgnc_id: "HGNC:19903" + hpo_terms: + - term_id: "HP:0000006" + name: Autosomal dominant inheritance + - term_id: "HP:0000103" + name: Polyuria + - term_id: "HP:0000121" + name: Nephrocalcinosis + - term_id: "HP:0001250" + name: Seizure + - term_id: "HP:0001281" + name: Tetany + - term_id: "HP:0001644" + name: Dilated cardiomyopathy + - term_id: "HP:0001942" + name: Metabolic acidosis + - term_id: "HP:0002900" + name: Hypokalemia + - term_id: "HP:0002901" + name: Hypocalcemia + - term_id: "HP:0002902" + name: Hyponatremia + - term_id: "HP:0002917" + name: Hypomagnesemia + - term_id: "HP:0003593" + name: Infantile onset + - term_id: "HP:0003621" + name: Juvenile onset + - term_id: "HP:0011463" + name: Childhood onset + - term_id: "HP:0012664" + name: Reduced left ventricular ejection fraction + - term_id: "HP:0025708" + name: Early young adult onset + - term_id: "HP:0034307" + name: Elevated left ventricular end-diastolic diameter - gene_ncbi_id: 79641 gene_symbol: ROGDI hgnc_id: "HGNC:29478" @@ -1849,7 +2001,7 @@ result: - term_id: "HP:0001285" name: Spastic tetraparesis - term_id: "HP:0002062" - name: Morphological abnormality of the pyramidal tract + name: Abnormal pyramidal tract morphology - term_id: "HP:0002071" name: Abnormality of extrapyramidal motor function - term_id: "HP:0002171" @@ -2108,3 +2260,5 @@ result: name: Myoclonic seizure - term_id: "HP:0100704" name: Cerebral visual impairment + - term_id: "HP:6000246" + name: Elevated CSF D-2-hydroxyglutaric acid concentration diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_exact_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_exact_no_hpo_terms.snap index feaeb0e..b6f82f3 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_exact_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_exact_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_symbol=TGDS\").await?" +expression: "&run_query(web_server_data.clone(), \"/hpo/genes?gene_symbol=TGDS\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: ~ diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_exact_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_exact_with_hpo_terms.snap index 43d40f0..1ab9e7a 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_exact_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_exact_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_symbol=TGDS&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/genes?gene_symbol=TGDS&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: ~ @@ -74,10 +74,10 @@ result: name: Global developmental delay - term_id: "HP:0001373" name: Joint dislocation + - term_id: "HP:0001382" + name: Joint hypermobility - term_id: "HP:0001387" name: Joint stiffness - - term_id: "HP:0001388" - name: Joint laxity - term_id: "HP:0001508" name: Failure to thrive - term_id: "HP:0001511" @@ -114,8 +114,6 @@ result: name: Clinodactyly of the 5th finger - term_id: "HP:0004322" name: Short stature - - term_id: "HP:0005692" - name: Joint hyperflexibility - term_id: "HP:0005792" name: Short humerus - term_id: "HP:0005930" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_prefix_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_prefix_no_hpo_terms.snap index d8a9f2b..81798c3 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_prefix_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_prefix_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_symbol=TGD&match=prefix\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/genes?gene_symbol=TGD&match=prefix\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: ~ diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_prefix_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_prefix_with_hpo_terms.snap index d26f565..034eb64 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_prefix_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_prefix_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_symbol=TGD&match=prefix&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/genes?gene_symbol=TGD&match=prefix&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: ~ @@ -74,10 +74,10 @@ result: name: Global developmental delay - term_id: "HP:0001373" name: Joint dislocation + - term_id: "HP:0001382" + name: Joint hypermobility - term_id: "HP:0001387" name: Joint stiffness - - term_id: "HP:0001388" - name: Joint laxity - term_id: "HP:0001508" name: Failure to thrive - term_id: "HP:0001511" @@ -114,8 +114,6 @@ result: name: Clinodactyly of the 5th finger - term_id: "HP:0004322" name: Short stature - - term_id: "HP:0005692" - name: Joint hyperflexibility - term_id: "HP:0005792" name: Short humerus - term_id: "HP:0005930" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_suffix_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_suffix_no_hpo_terms.snap index f05816e..ca3649c 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_suffix_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_suffix_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_symbol=GDS&match=suffix\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/genes?gene_symbol=GDS&match=suffix\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: ~ diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_suffix_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_suffix_with_hpo_terms.snap index 5c30b6e..a3a115d 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_suffix_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_gene_symbol_suffix_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_symbol=GDS&match=suffix&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/genes?gene_symbol=GDS&match=suffix&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: ~ @@ -74,10 +74,10 @@ result: name: Global developmental delay - term_id: "HP:0001373" name: Joint dislocation + - term_id: "HP:0001382" + name: Joint hypermobility - term_id: "HP:0001387" name: Joint stiffness - - term_id: "HP:0001388" - name: Joint laxity - term_id: "HP:0001508" name: Failure to thrive - term_id: "HP:0001511" @@ -114,8 +114,6 @@ result: name: Clinodactyly of the 5th finger - term_id: "HP:0004322" name: Short stature - - term_id: "HP:0005692" - name: Joint hyperflexibility - term_id: "HP:0005792" name: Short humerus - term_id: "HP:0005930" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_hgnc_gene_id_exact_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_hgnc_gene_id_exact_no_hpo_terms.snap index e074ea0..59d0988 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_hgnc_gene_id_exact_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_hgnc_gene_id_exact_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_id=HGNC:3791\").await?" +expression: "&run_query(web_server_data.clone(), \"/hpo/genes?gene_id=HGNC:3791\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: "HGNC:3791" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_hgnc_gene_id_exact_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_hgnc_gene_id_exact_with_hpo_terms.snap index a02ed94..8a7a70b 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_hgnc_gene_id_exact_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_hgnc_gene_id_exact_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_id=HGNC:3791&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/genes?gene_id=HGNC:3791&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: "HGNC:3791" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_ncbi_gene_id_exact_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_ncbi_gene_id_exact_no_hpo_terms.snap index 8c8a419..064e405 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_ncbi_gene_id_exact_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_ncbi_gene_id_exact_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_id=2348\").await?" +expression: "&run_query(web_server_data.clone(), \"/hpo/genes?gene_id=2348\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: "2348" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_ncbi_gene_id_exact_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_ncbi_gene_id_exact_with_hpo_terms.snap index 6744808..9710a35 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_ncbi_gene_id_exact_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_genes__test__hpo_genes_ncbi_gene_id_exact_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_genes.rs -expression: "&run_query(\"/hpo/genes?gene_id=2348&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/genes?gene_id=2348&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: gene_id: "2348" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_no_hpo_terms.snap index 5273993..bf6fad2 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_omims.rs -expression: "&run_query(\"/hpo/omims?name=tel-Manzke+syndro&match=contains\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/omims?name=tel-Manzke+syndro&match=contains\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: omim_id: ~ diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_with_hpo_terms.snap index fe84f8c..a99d788 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_omims.rs -expression: "&run_query(\"/hpo/omims?name=tel-Manzke+syndro&match=contains&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/omims?name=tel-Manzke+syndro&match=contains&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: omim_id: ~ @@ -69,8 +69,8 @@ result: name: Global developmental delay - term_id: "HP:0001373" name: Joint dislocation - - term_id: "HP:0001388" - name: Joint laxity + - term_id: "HP:0001382" + name: Joint hypermobility - term_id: "HP:0001511" name: Intrauterine growth retardation - term_id: "HP:0001537" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_no_hpo_terms.snap index 9d4f627..33a14ad 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_omims.rs -expression: "&run_query(\"/hpo/omims?name=Catel-Manzke+syndrome\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/omims?name=Catel-Manzke+syndrome\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: omim_id: ~ diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_with_hpo_terms.snap index bffb04c..f78af79 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_omims.rs -expression: "&run_query(\"/hpo/omims?name=Catel-Manzke+syndrome&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/omims?name=Catel-Manzke+syndrome&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: omim_id: ~ @@ -69,8 +69,8 @@ result: name: Global developmental delay - term_id: "HP:0001373" name: Joint dislocation - - term_id: "HP:0001388" - name: Joint laxity + - term_id: "HP:0001382" + name: Joint hypermobility - term_id: "HP:0001511" name: Intrauterine growth retardation - term_id: "HP:0001537" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_no_hpo_terms.snap index 281fdd5..42dae91 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_omims.rs -expression: "&run_query(\"/hpo/omims?name=Catel-Manzke+syndro&match=prefix\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/omims?name=Catel-Manzke+syndro&match=prefix\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: omim_id: ~ diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_with_hpo_terms.snap index 3341d7c..9022e08 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_omims.rs -expression: "&run_query(\"/hpo/omims?name=Catel-Manzke+syndro&match=prefix&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/omims?name=Catel-Manzke+syndro&match=prefix&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: omim_id: ~ @@ -69,8 +69,8 @@ result: name: Global developmental delay - term_id: "HP:0001373" name: Joint dislocation - - term_id: "HP:0001388" - name: Joint laxity + - term_id: "HP:0001382" + name: Joint hypermobility - term_id: "HP:0001511" name: Intrauterine growth retardation - term_id: "HP:0001537" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_no_hpo_terms.snap index 0410ae3..223d861 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_omims.rs -expression: "&run_query(\"/hpo/omims?name=tel-Manzke+syndrome&match=suffix\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/omims?name=tel-Manzke+syndrome&match=suffix\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: omim_id: ~ diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_with_hpo_terms.snap index e9b2bcb..d2564bb 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_omims.rs -expression: "&run_query(\"/hpo/omims?name=tel-Manzke+syndrome&match=suffix&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/omims?name=tel-Manzke+syndrome&match=suffix&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: omim_id: ~ @@ -69,8 +69,8 @@ result: name: Global developmental delay - term_id: "HP:0001373" name: Joint dislocation - - term_id: "HP:0001388" - name: Joint laxity + - term_id: "HP:0001382" + name: Joint hypermobility - term_id: "HP:0001511" name: Intrauterine growth retardation - term_id: "HP:0001537" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_no_hpo_terms.snap index 07efe5d..e4852d9 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_no_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_omims.rs -expression: "&run_query(\"/hpo/omims?omim_id=616145\").await?" +expression: "&run_query(web_server_data.clone(), \"/hpo/omims?omim_id=616145\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: omim_id: "616145" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_with_hpo_terms.snap index 361cfd1..e57a71f 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_with_hpo_terms.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_omims.rs -expression: "&run_query(\"/hpo/omims?omim_id=616145&hpo_terms=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/omims?omim_id=616145&hpo_terms=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: omim_id: "616145" @@ -69,8 +69,8 @@ result: name: Global developmental delay - term_id: "HP:0001373" name: Joint dislocation - - term_id: "HP:0001388" - name: Joint laxity + - term_id: "HP:0001382" + name: Joint hypermobility - term_id: "HP:0001511" name: Intrauterine growth retardation - term_id: "HP:0001537" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_exact_no_genes.snap b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_exact_no_genes.snap index e27673f..3182604 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_exact_no_genes.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_exact_no_genes.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_terms.rs -expression: "&run_query(\"/hpo/terms?name=Inguinal+hernia\").await?" +expression: "&run_query(web_server_data.clone(), \"/hpo/terms?name=Inguinal+hernia\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: term_id: ~ @@ -17,7 +17,6 @@ result: synonyms: ~ xrefs: - "MEDDRA:10022016" - - "MSH:D006552" - "SNOMEDCT_US:396232000" - "UMLS:C0019294" - term_id: "HP:0100541" @@ -27,6 +26,5 @@ result: - Crural hernia xrefs: - "MEDDRA:10016434" - - "MSH:D006550" - "SNOMEDCT_US:50063009" - "UMLS:C0019288" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_exact_with_genes.snap b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_exact_with_genes.snap index 85aba17..ed863a2 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_exact_with_genes.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_exact_with_genes.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_terms.rs -expression: "&run_query(\"/hpo/terms?name=Inguinal+hernia&genes=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/terms?name=Inguinal+hernia&genes=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: term_id: ~ @@ -17,7 +17,6 @@ result: synonyms: ~ xrefs: - "MEDDRA:10022016" - - "MSH:D006552" - "SNOMEDCT_US:396232000" - "UMLS:C0019294" genes: @@ -111,6 +110,9 @@ result: - ncbi_gene_id: 1312 gene_symbol: COMT hgnc_id: "HGNC:2228" + - ncbi_gene_id: 1353 + gene_symbol: COX11 + hgnc_id: "HGNC:2261" - ncbi_gene_id: 1387 gene_symbol: CREBBP hgnc_id: "HGNC:2348" @@ -126,9 +128,15 @@ result: - ncbi_gene_id: 1656 gene_symbol: DDX6 hgnc_id: "HGNC:2747" + - ncbi_gene_id: 1748 + gene_symbol: DLX4 + hgnc_id: "HGNC:2917" - ncbi_gene_id: 1801 gene_symbol: DPH1 hgnc_id: "HGNC:3003" + - ncbi_gene_id: 1802 + gene_symbol: DPH2 + hgnc_id: "HGNC:3004" - ncbi_gene_id: 1836 gene_symbol: SLC26A2 hgnc_id: "HGNC:10994" @@ -156,6 +164,9 @@ result: - ncbi_gene_id: 2200 gene_symbol: FBN1 hgnc_id: "HGNC:3603" + - ncbi_gene_id: 2202 + gene_symbol: EFEMP1 + hgnc_id: "HGNC:3218" - ncbi_gene_id: 2239 gene_symbol: GPC4 hgnc_id: "HGNC:4452" @@ -228,6 +239,9 @@ result: - ncbi_gene_id: 2990 gene_symbol: GUSB hgnc_id: "HGNC:4696" + - ncbi_gene_id: 3229 + gene_symbol: HOXC13 + hgnc_id: "HGNC:5125" - ncbi_gene_id: 3339 gene_symbol: HSPG2 hgnc_id: "HGNC:5273" @@ -357,6 +371,9 @@ result: - ncbi_gene_id: 5832 gene_symbol: ALDH18A1 hgnc_id: "HGNC:9722" + - ncbi_gene_id: 5908 + gene_symbol: RAP1B + hgnc_id: "HGNC:9857" - ncbi_gene_id: 5982 gene_symbol: RFC2 hgnc_id: "HGNC:9970" @@ -396,6 +413,9 @@ result: - ncbi_gene_id: 6804 gene_symbol: STX1A hgnc_id: "HGNC:11433" + - ncbi_gene_id: 6874 + gene_symbol: TAF4 + hgnc_id: "HGNC:11537" - ncbi_gene_id: 6899 gene_symbol: TBX1 hgnc_id: "HGNC:11592" @@ -426,6 +446,9 @@ result: - ncbi_gene_id: 7353 gene_symbol: UFD1 hgnc_id: "HGNC:12520" + - ncbi_gene_id: 7403 + gene_symbol: KDM6A + hgnc_id: "HGNC:12637" - ncbi_gene_id: 7458 gene_symbol: EIF4H hgnc_id: "HGNC:12741" @@ -447,6 +470,9 @@ result: - ncbi_gene_id: 8076 gene_symbol: MFAP5 hgnc_id: "HGNC:29673" + - ncbi_gene_id: 8085 + gene_symbol: KMT2D + hgnc_id: "HGNC:7133" - ncbi_gene_id: 8091 gene_symbol: HMGA2 hgnc_id: "HGNC:5009" @@ -516,6 +542,9 @@ result: - ncbi_gene_id: 9469 gene_symbol: CHST3 hgnc_id: "HGNC:1971" + - ncbi_gene_id: 9487 + gene_symbol: PIGL + hgnc_id: "HGNC:8966" - ncbi_gene_id: 9509 gene_symbol: ADAMTS2 hgnc_id: "HGNC:218" @@ -528,6 +557,9 @@ result: - ncbi_gene_id: 9652 gene_symbol: SKIC3 hgnc_id: "HGNC:23639" + - ncbi_gene_id: 9681 + gene_symbol: DEPDC5 + hgnc_id: "HGNC:18423" - ncbi_gene_id: 9719 gene_symbol: ADAMTSL2 hgnc_id: "HGNC:14631" @@ -597,6 +629,9 @@ result: - ncbi_gene_id: 10984 gene_symbol: KCNQ1OT1 hgnc_id: "HGNC:6295" + - ncbi_gene_id: 11080 + gene_symbol: DNAJB4 + hgnc_id: "HGNC:14886" - ncbi_gene_id: 11107 gene_symbol: PRDM5 hgnc_id: "HGNC:9349" @@ -633,6 +668,9 @@ result: - ncbi_gene_id: 23405 gene_symbol: DICER1 hgnc_id: "HGNC:17098" + - ncbi_gene_id: 23476 + gene_symbol: BRD4 + hgnc_id: "HGNC:13575" - ncbi_gene_id: 23483 gene_symbol: TGDS hgnc_id: "HGNC:20324" @@ -654,6 +692,9 @@ result: - ncbi_gene_id: 25836 gene_symbol: NIPBL hgnc_id: "HGNC:28862" + - ncbi_gene_id: 25885 + gene_symbol: POLR1A + hgnc_id: "HGNC:17264" - ncbi_gene_id: 25942 gene_symbol: SIN3A hgnc_id: "HGNC:19353" @@ -735,6 +776,12 @@ result: - ncbi_gene_id: 56623 gene_symbol: INPP5E hgnc_id: "HGNC:21474" + - ncbi_gene_id: 56896 + gene_symbol: DPYSL5 + hgnc_id: "HGNC:20637" + - ncbi_gene_id: 57020 + gene_symbol: VPS35L + hgnc_id: "HGNC:24641" - ncbi_gene_id: 57492 gene_symbol: ARID1B hgnc_id: "HGNC:18040" @@ -774,6 +821,9 @@ result: - ncbi_gene_id: 64840 gene_symbol: PORCN hgnc_id: "HGNC:17652" + - ncbi_gene_id: 65267 + gene_symbol: WNK3 + hgnc_id: "HGNC:14543" - ncbi_gene_id: 79158 gene_symbol: GNPTAB hgnc_id: "HGNC:29670" @@ -783,6 +833,9 @@ result: - ncbi_gene_id: 79813 gene_symbol: EHMT1 hgnc_id: "HGNC:24650" + - ncbi_gene_id: 79875 + gene_symbol: THSD4 + hgnc_id: "HGNC:25835" - ncbi_gene_id: 79989 gene_symbol: IFT56 hgnc_id: "HGNC:21882" @@ -798,6 +851,9 @@ result: - ncbi_gene_id: 84163 gene_symbol: GTF2IRD2 hgnc_id: "HGNC:30775" + - ncbi_gene_id: 84231 + gene_symbol: TRAF7 + hgnc_id: "HGNC:20456" - ncbi_gene_id: 84277 gene_symbol: DNAJC30 hgnc_id: "HGNC:16410" @@ -813,6 +869,12 @@ result: - ncbi_gene_id: 84992 gene_symbol: PIGY hgnc_id: "HGNC:28213" + - ncbi_gene_id: 90459 + gene_symbol: ERI1 + hgnc_id: "HGNC:23994" + - ncbi_gene_id: 91039 + gene_symbol: DPP9 + hgnc_id: "HGNC:18648" - ncbi_gene_id: 91147 gene_symbol: TMEM67 hgnc_id: "HGNC:28396" @@ -861,6 +923,9 @@ result: - ncbi_gene_id: 170302 gene_symbol: ARX hgnc_id: "HGNC:18060" + - ncbi_gene_id: 170689 + gene_symbol: ADAMTS15 + hgnc_id: "HGNC:16305" - ncbi_gene_id: 197257 gene_symbol: LDHD hgnc_id: "HGNC:19708" @@ -904,7 +969,6 @@ result: - Crural hernia xrefs: - "MEDDRA:10016434" - - "MSH:D006550" - "SNOMEDCT_US:50063009" - "UMLS:C0019288" genes: @@ -929,6 +993,9 @@ result: - ncbi_gene_id: 2187 gene_symbol: FANCB hgnc_id: "HGNC:3583" + - ncbi_gene_id: 2202 + gene_symbol: EFEMP1 + hgnc_id: "HGNC:3218" - ncbi_gene_id: 2535 gene_symbol: FZD2 hgnc_id: "HGNC:4040" @@ -962,3 +1029,6 @@ result: - ncbi_gene_id: 129563 gene_symbol: DIS3L2 hgnc_id: "HGNC:28648" + - ncbi_gene_id: 157922 + gene_symbol: CAMSAP1 + hgnc_id: "HGNC:19946" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_fuzzy_no_genes.snap b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_fuzzy_no_genes.snap index 737d89e..5c67cf1 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_fuzzy_no_genes.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_fuzzy_no_genes.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_terms.rs -expression: "&run_query(\"/hpo/terms?name=Inguinal+hern\").await?" +expression: "&run_query(web_server_data.clone(), \"/hpo/terms?name=Inguinal+hern\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: term_id: ~ @@ -17,7 +17,6 @@ result: synonyms: ~ xrefs: - "MEDDRA:10022016" - - "MSH:D006552" - "SNOMEDCT_US:396232000" - "UMLS:C0019294" - term_id: "HP:0100541" @@ -27,6 +26,5 @@ result: - Crural hernia xrefs: - "MEDDRA:10016434" - - "MSH:D006550" - "SNOMEDCT_US:50063009" - "UMLS:C0019288" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_fuzzy_with_genes.snap b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_fuzzy_with_genes.snap index 12d5f8a..36cf012 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_fuzzy_with_genes.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_name_fuzzy_with_genes.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_terms.rs -expression: "&run_query(\"/hpo/terms?name=Inguinal+hern&genes=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/terms?name=Inguinal+hern&genes=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: term_id: ~ @@ -17,7 +17,6 @@ result: synonyms: ~ xrefs: - "MEDDRA:10022016" - - "MSH:D006552" - "SNOMEDCT_US:396232000" - "UMLS:C0019294" genes: @@ -111,6 +110,9 @@ result: - ncbi_gene_id: 1312 gene_symbol: COMT hgnc_id: "HGNC:2228" + - ncbi_gene_id: 1353 + gene_symbol: COX11 + hgnc_id: "HGNC:2261" - ncbi_gene_id: 1387 gene_symbol: CREBBP hgnc_id: "HGNC:2348" @@ -126,9 +128,15 @@ result: - ncbi_gene_id: 1656 gene_symbol: DDX6 hgnc_id: "HGNC:2747" + - ncbi_gene_id: 1748 + gene_symbol: DLX4 + hgnc_id: "HGNC:2917" - ncbi_gene_id: 1801 gene_symbol: DPH1 hgnc_id: "HGNC:3003" + - ncbi_gene_id: 1802 + gene_symbol: DPH2 + hgnc_id: "HGNC:3004" - ncbi_gene_id: 1836 gene_symbol: SLC26A2 hgnc_id: "HGNC:10994" @@ -156,6 +164,9 @@ result: - ncbi_gene_id: 2200 gene_symbol: FBN1 hgnc_id: "HGNC:3603" + - ncbi_gene_id: 2202 + gene_symbol: EFEMP1 + hgnc_id: "HGNC:3218" - ncbi_gene_id: 2239 gene_symbol: GPC4 hgnc_id: "HGNC:4452" @@ -228,6 +239,9 @@ result: - ncbi_gene_id: 2990 gene_symbol: GUSB hgnc_id: "HGNC:4696" + - ncbi_gene_id: 3229 + gene_symbol: HOXC13 + hgnc_id: "HGNC:5125" - ncbi_gene_id: 3339 gene_symbol: HSPG2 hgnc_id: "HGNC:5273" @@ -357,6 +371,9 @@ result: - ncbi_gene_id: 5832 gene_symbol: ALDH18A1 hgnc_id: "HGNC:9722" + - ncbi_gene_id: 5908 + gene_symbol: RAP1B + hgnc_id: "HGNC:9857" - ncbi_gene_id: 5982 gene_symbol: RFC2 hgnc_id: "HGNC:9970" @@ -396,6 +413,9 @@ result: - ncbi_gene_id: 6804 gene_symbol: STX1A hgnc_id: "HGNC:11433" + - ncbi_gene_id: 6874 + gene_symbol: TAF4 + hgnc_id: "HGNC:11537" - ncbi_gene_id: 6899 gene_symbol: TBX1 hgnc_id: "HGNC:11592" @@ -426,6 +446,9 @@ result: - ncbi_gene_id: 7353 gene_symbol: UFD1 hgnc_id: "HGNC:12520" + - ncbi_gene_id: 7403 + gene_symbol: KDM6A + hgnc_id: "HGNC:12637" - ncbi_gene_id: 7458 gene_symbol: EIF4H hgnc_id: "HGNC:12741" @@ -447,6 +470,9 @@ result: - ncbi_gene_id: 8076 gene_symbol: MFAP5 hgnc_id: "HGNC:29673" + - ncbi_gene_id: 8085 + gene_symbol: KMT2D + hgnc_id: "HGNC:7133" - ncbi_gene_id: 8091 gene_symbol: HMGA2 hgnc_id: "HGNC:5009" @@ -516,6 +542,9 @@ result: - ncbi_gene_id: 9469 gene_symbol: CHST3 hgnc_id: "HGNC:1971" + - ncbi_gene_id: 9487 + gene_symbol: PIGL + hgnc_id: "HGNC:8966" - ncbi_gene_id: 9509 gene_symbol: ADAMTS2 hgnc_id: "HGNC:218" @@ -528,6 +557,9 @@ result: - ncbi_gene_id: 9652 gene_symbol: SKIC3 hgnc_id: "HGNC:23639" + - ncbi_gene_id: 9681 + gene_symbol: DEPDC5 + hgnc_id: "HGNC:18423" - ncbi_gene_id: 9719 gene_symbol: ADAMTSL2 hgnc_id: "HGNC:14631" @@ -597,6 +629,9 @@ result: - ncbi_gene_id: 10984 gene_symbol: KCNQ1OT1 hgnc_id: "HGNC:6295" + - ncbi_gene_id: 11080 + gene_symbol: DNAJB4 + hgnc_id: "HGNC:14886" - ncbi_gene_id: 11107 gene_symbol: PRDM5 hgnc_id: "HGNC:9349" @@ -633,6 +668,9 @@ result: - ncbi_gene_id: 23405 gene_symbol: DICER1 hgnc_id: "HGNC:17098" + - ncbi_gene_id: 23476 + gene_symbol: BRD4 + hgnc_id: "HGNC:13575" - ncbi_gene_id: 23483 gene_symbol: TGDS hgnc_id: "HGNC:20324" @@ -654,6 +692,9 @@ result: - ncbi_gene_id: 25836 gene_symbol: NIPBL hgnc_id: "HGNC:28862" + - ncbi_gene_id: 25885 + gene_symbol: POLR1A + hgnc_id: "HGNC:17264" - ncbi_gene_id: 25942 gene_symbol: SIN3A hgnc_id: "HGNC:19353" @@ -735,6 +776,12 @@ result: - ncbi_gene_id: 56623 gene_symbol: INPP5E hgnc_id: "HGNC:21474" + - ncbi_gene_id: 56896 + gene_symbol: DPYSL5 + hgnc_id: "HGNC:20637" + - ncbi_gene_id: 57020 + gene_symbol: VPS35L + hgnc_id: "HGNC:24641" - ncbi_gene_id: 57492 gene_symbol: ARID1B hgnc_id: "HGNC:18040" @@ -774,6 +821,9 @@ result: - ncbi_gene_id: 64840 gene_symbol: PORCN hgnc_id: "HGNC:17652" + - ncbi_gene_id: 65267 + gene_symbol: WNK3 + hgnc_id: "HGNC:14543" - ncbi_gene_id: 79158 gene_symbol: GNPTAB hgnc_id: "HGNC:29670" @@ -783,6 +833,9 @@ result: - ncbi_gene_id: 79813 gene_symbol: EHMT1 hgnc_id: "HGNC:24650" + - ncbi_gene_id: 79875 + gene_symbol: THSD4 + hgnc_id: "HGNC:25835" - ncbi_gene_id: 79989 gene_symbol: IFT56 hgnc_id: "HGNC:21882" @@ -798,6 +851,9 @@ result: - ncbi_gene_id: 84163 gene_symbol: GTF2IRD2 hgnc_id: "HGNC:30775" + - ncbi_gene_id: 84231 + gene_symbol: TRAF7 + hgnc_id: "HGNC:20456" - ncbi_gene_id: 84277 gene_symbol: DNAJC30 hgnc_id: "HGNC:16410" @@ -813,6 +869,12 @@ result: - ncbi_gene_id: 84992 gene_symbol: PIGY hgnc_id: "HGNC:28213" + - ncbi_gene_id: 90459 + gene_symbol: ERI1 + hgnc_id: "HGNC:23994" + - ncbi_gene_id: 91039 + gene_symbol: DPP9 + hgnc_id: "HGNC:18648" - ncbi_gene_id: 91147 gene_symbol: TMEM67 hgnc_id: "HGNC:28396" @@ -861,6 +923,9 @@ result: - ncbi_gene_id: 170302 gene_symbol: ARX hgnc_id: "HGNC:18060" + - ncbi_gene_id: 170689 + gene_symbol: ADAMTS15 + hgnc_id: "HGNC:16305" - ncbi_gene_id: 197257 gene_symbol: LDHD hgnc_id: "HGNC:19708" @@ -904,7 +969,6 @@ result: - Crural hernia xrefs: - "MEDDRA:10016434" - - "MSH:D006550" - "SNOMEDCT_US:50063009" - "UMLS:C0019288" genes: @@ -929,6 +993,9 @@ result: - ncbi_gene_id: 2187 gene_symbol: FANCB hgnc_id: "HGNC:3583" + - ncbi_gene_id: 2202 + gene_symbol: EFEMP1 + hgnc_id: "HGNC:3218" - ncbi_gene_id: 2535 gene_symbol: FZD2 hgnc_id: "HGNC:4040" @@ -962,3 +1029,6 @@ result: - ncbi_gene_id: 129563 gene_symbol: DIS3L2 hgnc_id: "HGNC:28648" + - ncbi_gene_id: 157922 + gene_symbol: CAMSAP1 + hgnc_id: "HGNC:19946" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_term_id_exact_no_genes.snap b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_term_id_exact_no_genes.snap index 4d3d479..1325122 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_term_id_exact_no_genes.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_term_id_exact_no_genes.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_terms.rs -expression: "&run_query(\"/hpo/terms?term_id=HP:0000023\").await?" +expression: "&run_query(web_server_data.clone(), \"/hpo/terms?term_id=HP:0000023\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: term_id: "HP:0000023" @@ -17,6 +17,5 @@ result: synonyms: ~ xrefs: - "MEDDRA:10022016" - - "MSH:D006552" - "SNOMEDCT_US:396232000" - "UMLS:C0019294" diff --git a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_term_id_exact_with_genes.snap b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_term_id_exact_with_genes.snap index 5548ee4..cb7a665 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_term_id_exact_with_genes.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_terms__test__hpo_terms_term_id_exact_with_genes.snap @@ -1,9 +1,9 @@ --- source: src/server/run/hpo_terms.rs -expression: "&run_query(\"/hpo/terms?term_id=HP:0000023&genes=true\").await?" +expression: "&run_query(web_server_data.clone(),\n \"/hpo/terms?term_id=HP:0000023&genes=true\").await?" --- version: - hpo: 2023-04-05 + hpo: 2024-07-01 viguno: 0.0.0 query: term_id: "HP:0000023" @@ -17,7 +17,6 @@ result: synonyms: ~ xrefs: - "MEDDRA:10022016" - - "MSH:D006552" - "SNOMEDCT_US:396232000" - "UMLS:C0019294" genes: @@ -111,6 +110,9 @@ result: - ncbi_gene_id: 1312 gene_symbol: COMT hgnc_id: "HGNC:2228" + - ncbi_gene_id: 1353 + gene_symbol: COX11 + hgnc_id: "HGNC:2261" - ncbi_gene_id: 1387 gene_symbol: CREBBP hgnc_id: "HGNC:2348" @@ -126,9 +128,15 @@ result: - ncbi_gene_id: 1656 gene_symbol: DDX6 hgnc_id: "HGNC:2747" + - ncbi_gene_id: 1748 + gene_symbol: DLX4 + hgnc_id: "HGNC:2917" - ncbi_gene_id: 1801 gene_symbol: DPH1 hgnc_id: "HGNC:3003" + - ncbi_gene_id: 1802 + gene_symbol: DPH2 + hgnc_id: "HGNC:3004" - ncbi_gene_id: 1836 gene_symbol: SLC26A2 hgnc_id: "HGNC:10994" @@ -156,6 +164,9 @@ result: - ncbi_gene_id: 2200 gene_symbol: FBN1 hgnc_id: "HGNC:3603" + - ncbi_gene_id: 2202 + gene_symbol: EFEMP1 + hgnc_id: "HGNC:3218" - ncbi_gene_id: 2239 gene_symbol: GPC4 hgnc_id: "HGNC:4452" @@ -228,6 +239,9 @@ result: - ncbi_gene_id: 2990 gene_symbol: GUSB hgnc_id: "HGNC:4696" + - ncbi_gene_id: 3229 + gene_symbol: HOXC13 + hgnc_id: "HGNC:5125" - ncbi_gene_id: 3339 gene_symbol: HSPG2 hgnc_id: "HGNC:5273" @@ -357,6 +371,9 @@ result: - ncbi_gene_id: 5832 gene_symbol: ALDH18A1 hgnc_id: "HGNC:9722" + - ncbi_gene_id: 5908 + gene_symbol: RAP1B + hgnc_id: "HGNC:9857" - ncbi_gene_id: 5982 gene_symbol: RFC2 hgnc_id: "HGNC:9970" @@ -396,6 +413,9 @@ result: - ncbi_gene_id: 6804 gene_symbol: STX1A hgnc_id: "HGNC:11433" + - ncbi_gene_id: 6874 + gene_symbol: TAF4 + hgnc_id: "HGNC:11537" - ncbi_gene_id: 6899 gene_symbol: TBX1 hgnc_id: "HGNC:11592" @@ -426,6 +446,9 @@ result: - ncbi_gene_id: 7353 gene_symbol: UFD1 hgnc_id: "HGNC:12520" + - ncbi_gene_id: 7403 + gene_symbol: KDM6A + hgnc_id: "HGNC:12637" - ncbi_gene_id: 7458 gene_symbol: EIF4H hgnc_id: "HGNC:12741" @@ -447,6 +470,9 @@ result: - ncbi_gene_id: 8076 gene_symbol: MFAP5 hgnc_id: "HGNC:29673" + - ncbi_gene_id: 8085 + gene_symbol: KMT2D + hgnc_id: "HGNC:7133" - ncbi_gene_id: 8091 gene_symbol: HMGA2 hgnc_id: "HGNC:5009" @@ -516,6 +542,9 @@ result: - ncbi_gene_id: 9469 gene_symbol: CHST3 hgnc_id: "HGNC:1971" + - ncbi_gene_id: 9487 + gene_symbol: PIGL + hgnc_id: "HGNC:8966" - ncbi_gene_id: 9509 gene_symbol: ADAMTS2 hgnc_id: "HGNC:218" @@ -528,6 +557,9 @@ result: - ncbi_gene_id: 9652 gene_symbol: SKIC3 hgnc_id: "HGNC:23639" + - ncbi_gene_id: 9681 + gene_symbol: DEPDC5 + hgnc_id: "HGNC:18423" - ncbi_gene_id: 9719 gene_symbol: ADAMTSL2 hgnc_id: "HGNC:14631" @@ -597,6 +629,9 @@ result: - ncbi_gene_id: 10984 gene_symbol: KCNQ1OT1 hgnc_id: "HGNC:6295" + - ncbi_gene_id: 11080 + gene_symbol: DNAJB4 + hgnc_id: "HGNC:14886" - ncbi_gene_id: 11107 gene_symbol: PRDM5 hgnc_id: "HGNC:9349" @@ -633,6 +668,9 @@ result: - ncbi_gene_id: 23405 gene_symbol: DICER1 hgnc_id: "HGNC:17098" + - ncbi_gene_id: 23476 + gene_symbol: BRD4 + hgnc_id: "HGNC:13575" - ncbi_gene_id: 23483 gene_symbol: TGDS hgnc_id: "HGNC:20324" @@ -654,6 +692,9 @@ result: - ncbi_gene_id: 25836 gene_symbol: NIPBL hgnc_id: "HGNC:28862" + - ncbi_gene_id: 25885 + gene_symbol: POLR1A + hgnc_id: "HGNC:17264" - ncbi_gene_id: 25942 gene_symbol: SIN3A hgnc_id: "HGNC:19353" @@ -735,6 +776,12 @@ result: - ncbi_gene_id: 56623 gene_symbol: INPP5E hgnc_id: "HGNC:21474" + - ncbi_gene_id: 56896 + gene_symbol: DPYSL5 + hgnc_id: "HGNC:20637" + - ncbi_gene_id: 57020 + gene_symbol: VPS35L + hgnc_id: "HGNC:24641" - ncbi_gene_id: 57492 gene_symbol: ARID1B hgnc_id: "HGNC:18040" @@ -774,6 +821,9 @@ result: - ncbi_gene_id: 64840 gene_symbol: PORCN hgnc_id: "HGNC:17652" + - ncbi_gene_id: 65267 + gene_symbol: WNK3 + hgnc_id: "HGNC:14543" - ncbi_gene_id: 79158 gene_symbol: GNPTAB hgnc_id: "HGNC:29670" @@ -783,6 +833,9 @@ result: - ncbi_gene_id: 79813 gene_symbol: EHMT1 hgnc_id: "HGNC:24650" + - ncbi_gene_id: 79875 + gene_symbol: THSD4 + hgnc_id: "HGNC:25835" - ncbi_gene_id: 79989 gene_symbol: IFT56 hgnc_id: "HGNC:21882" @@ -798,6 +851,9 @@ result: - ncbi_gene_id: 84163 gene_symbol: GTF2IRD2 hgnc_id: "HGNC:30775" + - ncbi_gene_id: 84231 + gene_symbol: TRAF7 + hgnc_id: "HGNC:20456" - ncbi_gene_id: 84277 gene_symbol: DNAJC30 hgnc_id: "HGNC:16410" @@ -813,6 +869,12 @@ result: - ncbi_gene_id: 84992 gene_symbol: PIGY hgnc_id: "HGNC:28213" + - ncbi_gene_id: 90459 + gene_symbol: ERI1 + hgnc_id: "HGNC:23994" + - ncbi_gene_id: 91039 + gene_symbol: DPP9 + hgnc_id: "HGNC:18648" - ncbi_gene_id: 91147 gene_symbol: TMEM67 hgnc_id: "HGNC:28396" @@ -861,6 +923,9 @@ result: - ncbi_gene_id: 170302 gene_symbol: ARX hgnc_id: "HGNC:18060" + - ncbi_gene_id: 170689 + gene_symbol: ADAMTS15 + hgnc_id: "HGNC:16305" - ncbi_gene_id: 197257 gene_symbol: LDHD hgnc_id: "HGNC:19708" From 722195baa836473819d0be2576d004ca845df31d Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Thu, 11 Jul 2024 10:08:55 +0200 Subject: [PATCH 3/6] wip --- utils/docker/Dockerfile | 3 ++- utils/install-protoc.sh | 22 ++++++++-------------- 2 files changed, 10 insertions(+), 15 deletions(-) diff --git a/utils/docker/Dockerfile b/utils/docker/Dockerfile index 97609a0..ed4ad4f 100644 --- a/utils/docker/Dockerfile +++ b/utils/docker/Dockerfile @@ -25,7 +25,7 @@ RUN apt-get update && \ RUN rustup component add rustfmt # Install build dependency `protoc`. COPY utils/install-protoc.sh /tmp -RUN CMAKE_INSTALL_PREFIX=/usr/local bash /tmp/install-protoc.sh +RUN PREFIX=/usr/local bash /tmp/install-protoc.sh # Now for the two-step building. # @@ -43,6 +43,7 @@ RUN cargo build --release # Now copy in the rest of the sources. COPY build.rs /usr/src/viguno/ COPY src /usr/src/viguno/src/ +COPY protos /usr/src/viguno/protos/ COPY utils/alpine-linker-script.sh /usr/src/viguno/utils/ RUN chmod a+rx /usr/src/viguno/utils/alpine-linker-script.sh COPY .cargo /usr/src/viguno/.cargo/ diff --git a/utils/install-protoc.sh b/utils/install-protoc.sh index ed51c73..41df102 100644 --- a/utils/install-protoc.sh +++ b/utils/install-protoc.sh @@ -8,19 +8,13 @@ set -x set -euo pipefail -CMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX-$HOME/.local/share/protoc} +RELEASE=${RELEASE-27.2} +ARCH=${ARCH-linux-x86_64} +PREFIX=${PREFIX-$HOME/.local/share/protoc} -mkdir -p utils/var -cd utils/var +wget -O /tmp/protoc-${RELEASE}-${ARCH}.zip \ + https://github.com/protocolbuffers/protobuf/releases/download/v${RELEASE}/protoc-${RELEASE}-${ARCH}.zip -apt-get update -apt-get install -y git cmake build-essential - -if [[ ! -e protobuf ]]; then - git clone https://github.com/protocolbuffers/protobuf.git -fi -cd protobuf -git submodule update --init --recursive - -cmake . -DCMAKE_INSTALL_PREFIX=$CMAKE_INSTALL_PREFIX -make -j 8 install +mkdir -p $PREFIX +cd $PREFIX +unzip /tmp/protoc-${RELEASE}-${ARCH}.zip From cf2180dc17caaa5fbdb974555263931481f83def Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Thu, 11 Jul 2024 10:11:15 +0200 Subject: [PATCH 4/6] wip --- build.rs | 2 +- openapi.yaml | 9 ++++++++- src/query/mod.rs | 2 +- src/server/run/hpo_omims.rs | 34 +++++++++++++++++++++++++++++----- src/server/run/mod.rs | 2 +- 5 files changed, 40 insertions(+), 9 deletions(-) diff --git a/build.rs b/build.rs index c5bc7cc..ee5e155 100644 --- a/build.rs +++ b/build.rs @@ -2,7 +2,7 @@ use std::{env, path::PathBuf}; fn main() -> Result<(), anyhow::Error> { let root = PathBuf::from(env!("CARGO_MANIFEST_DIR")).join("protos"); - let proto_files = vec!["viguno/v1/simulation.proto"] + let proto_files = ["viguno/v1/simulation.proto"] .iter() .map(|f| root.join(f)) .collect::>(); diff --git a/openapi.yaml b/openapi.yaml index a7aa3e8..f3964eb 100644 --- a/openapi.yaml +++ b/openapi.yaml @@ -81,12 +81,19 @@ paths: nullable: true - name: match_ in: query - description: The match mode. + description: The match mode, default is `Match::Exact`. required: false schema: allOf: - $ref: '#/components/schemas/Match' nullable: true + - name: ignore_case + in: query + description: Whether case is insentivie, default is `false`. + required: false + schema: + type: boolean + nullable: true - name: max_results in: query description: Maximal number of results to return. diff --git a/src/query/mod.rs b/src/query/mod.rs index f7bab3e..59ab314 100644 --- a/src/query/mod.rs +++ b/src/query/mod.rs @@ -316,7 +316,7 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: tracing::info!("Loading HGNC xlink..."); let before_load_xlink = Instant::now(); let path_hgnc_xlink = format!("{}/hgnc_xlink.tsv", args.path_hpo_dir); - let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(&path_hgnc_xlink)?; + let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(path_hgnc_xlink)?; tracing::info!( "... done loading HGNC xlink in {:?}", before_load_xlink.elapsed() diff --git a/src/server/run/hpo_omims.rs b/src/server/run/hpo_omims.rs index 6efc642..ea4fbaa 100644 --- a/src/server/run/hpo_omims.rs +++ b/src/server/run/hpo_omims.rs @@ -39,9 +39,11 @@ pub struct Query { pub omim_id: Option, /// The disease name to search for. pub name: Option, - /// The match mode. + /// The match mode, default is `Match::Exact`. #[serde(alias = "match")] pub match_: Option, + /// Whether case is insentivie, default is `false`. + pub ignore_case: Option, /// Maximal number of results to return. #[serde(default = "_default_max_results")] pub max_results: usize, @@ -144,6 +146,7 @@ pub struct Result { /// Query for OMIM diseases in the HPO database. #[allow(clippy::unused_async)] +#[allow(clippy::too_many_lines)] #[utoipa::path( operation_id = "hpo_omims", params(Query), @@ -167,11 +170,22 @@ async fn handle( .map_err(|e| CustomError::new(anyhow::anyhow!(e)))?; ontology.omim_disease(&omim_id) } else if let Some(name) = &query.name { + let name = if query.ignore_case.unwrap_or_default() { + name.to_lowercase() + } else { + name.clone() + }; let mut omim_disease = None; let mut it = ontology.omim_diseases(); let mut tmp = it.next(); while tmp.is_some() && omim_disease.is_none() { - if tmp.expect("checked above").name() == name { + let tmp_name = tmp.expect("checked above").name(); + let tmp_name = if query.ignore_case.unwrap_or_default() { + tmp_name.to_lowercase() + } else { + tmp_name.to_string() + }; + if tmp_name == name { omim_disease = tmp; } tmp = it.next(); @@ -191,11 +205,21 @@ async fn handle( let mut it = ontology.omim_diseases(); let mut omim_disease = it.next(); while omim_disease.is_some() && result.len() < query.max_results { + let name = if query.ignore_case.unwrap_or_default() { + name.to_lowercase() + } else { + name.clone() + }; let omim_name = omim_disease.as_ref().expect("checked above").name(); + let omim_name = if query.ignore_case.unwrap_or_default() { + omim_name.to_lowercase() + } else { + omim_name.to_string() + }; let is_match = match query.match_.unwrap_or_default() { - Match::Prefix => omim_name.starts_with(name), - Match::Suffix => omim_name.ends_with(name), - Match::Contains => omim_name.contains(name), + Match::Prefix => omim_name.starts_with(&name), + Match::Suffix => omim_name.ends_with(&name), + Match::Contains => omim_name.contains(&name), Match::Exact => panic!("cannot happen here"), }; if is_match { diff --git a/src/server/run/mod.rs b/src/server/run/mod.rs index 2e67223..bf219b4 100644 --- a/src/server/run/mod.rs +++ b/src/server/run/mod.rs @@ -264,7 +264,7 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: tracing::info!("Loading HGNC xlink..."); let before_load_xlink = std::time::Instant::now(); let path_hgnc_xlink = format!("{}/hgnc_xlink.tsv", args.path_hpo_dir); - let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(&path_hgnc_xlink)?; + let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(path_hgnc_xlink)?; let hgnc_to_ncbi = crate::common::hgnc_xlink::inverse_hashmap(&ncbi_to_hgnc); tracing::info!( "... done loading HGNC xlink in {:?}", From 38b9817bf62863ca11f8511523a79d8aaaae9e9d Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Thu, 11 Jul 2024 10:13:24 +0200 Subject: [PATCH 5/6] linter --- build.rs | 2 +- src/query/mod.rs | 2 +- src/server/run/mod.rs | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/build.rs b/build.rs index c5bc7cc..ee5e155 100644 --- a/build.rs +++ b/build.rs @@ -2,7 +2,7 @@ use std::{env, path::PathBuf}; fn main() -> Result<(), anyhow::Error> { let root = PathBuf::from(env!("CARGO_MANIFEST_DIR")).join("protos"); - let proto_files = vec!["viguno/v1/simulation.proto"] + let proto_files = ["viguno/v1/simulation.proto"] .iter() .map(|f| root.join(f)) .collect::>(); diff --git a/src/query/mod.rs b/src/query/mod.rs index f7bab3e..59ab314 100644 --- a/src/query/mod.rs +++ b/src/query/mod.rs @@ -316,7 +316,7 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: tracing::info!("Loading HGNC xlink..."); let before_load_xlink = Instant::now(); let path_hgnc_xlink = format!("{}/hgnc_xlink.tsv", args.path_hpo_dir); - let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(&path_hgnc_xlink)?; + let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(path_hgnc_xlink)?; tracing::info!( "... done loading HGNC xlink in {:?}", before_load_xlink.elapsed() diff --git a/src/server/run/mod.rs b/src/server/run/mod.rs index 2e67223..bf219b4 100644 --- a/src/server/run/mod.rs +++ b/src/server/run/mod.rs @@ -264,7 +264,7 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: tracing::info!("Loading HGNC xlink..."); let before_load_xlink = std::time::Instant::now(); let path_hgnc_xlink = format!("{}/hgnc_xlink.tsv", args.path_hpo_dir); - let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(&path_hgnc_xlink)?; + let ncbi_to_hgnc = crate::common::hgnc_xlink::load_ncbi_to_hgnc(path_hgnc_xlink)?; let hgnc_to_ncbi = crate::common::hgnc_xlink::inverse_hashmap(&ncbi_to_hgnc); tracing::info!( "... done loading HGNC xlink in {:?}", From c83e9b9cd391b6d5916f50d4df80bfffcd60a853 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Thu, 11 Jul 2024 10:23:58 +0200 Subject: [PATCH 6/6] wip --- ...n__hpo_omims__test__hpo_omims_name_contains_no_hpo_terms.snap | 1 + ..._hpo_omims__test__hpo_omims_name_contains_with_hpo_terms.snap | 1 + ..._run__hpo_omims__test__hpo_omims_name_exact_no_hpo_terms.snap | 1 + ...un__hpo_omims__test__hpo_omims_name_exact_with_hpo_terms.snap | 1 + ...run__hpo_omims__test__hpo_omims_name_prefix_no_hpo_terms.snap | 1 + ...n__hpo_omims__test__hpo_omims_name_prefix_with_hpo_terms.snap | 1 + ...run__hpo_omims__test__hpo_omims_name_suffix_no_hpo_terms.snap | 1 + ...n__hpo_omims__test__hpo_omims_name_suffix_with_hpo_terms.snap | 1 + ...n__hpo_omims__test__hpo_omims_omim_id_exact_no_hpo_terms.snap | 1 + ..._hpo_omims__test__hpo_omims_omim_id_exact_with_hpo_terms.snap | 1 + 10 files changed, 10 insertions(+) diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_no_hpo_terms.snap index bf6fad2..cfe4f6c 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_no_hpo_terms.snap @@ -9,6 +9,7 @@ query: omim_id: ~ name: tel-Manzke syndro match_: contains + ignore_case: ~ max_results: 100 hpo_terms: false result: diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_with_hpo_terms.snap index a99d788..48ecb3d 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_contains_with_hpo_terms.snap @@ -9,6 +9,7 @@ query: omim_id: ~ name: tel-Manzke syndro match_: contains + ignore_case: ~ max_results: 100 hpo_terms: true result: diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_no_hpo_terms.snap index 33a14ad..21e40b4 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_no_hpo_terms.snap @@ -9,6 +9,7 @@ query: omim_id: ~ name: Catel-Manzke syndrome match_: ~ + ignore_case: ~ max_results: 100 hpo_terms: false result: diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_with_hpo_terms.snap index f78af79..c06ceb6 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_exact_with_hpo_terms.snap @@ -9,6 +9,7 @@ query: omim_id: ~ name: Catel-Manzke syndrome match_: ~ + ignore_case: ~ max_results: 100 hpo_terms: true result: diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_no_hpo_terms.snap index 42dae91..7abe192 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_no_hpo_terms.snap @@ -9,6 +9,7 @@ query: omim_id: ~ name: Catel-Manzke syndro match_: prefix + ignore_case: ~ max_results: 100 hpo_terms: false result: diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_with_hpo_terms.snap index 9022e08..d06e83a 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_prefix_with_hpo_terms.snap @@ -9,6 +9,7 @@ query: omim_id: ~ name: Catel-Manzke syndro match_: prefix + ignore_case: ~ max_results: 100 hpo_terms: true result: diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_no_hpo_terms.snap index 223d861..2d4f4df 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_no_hpo_terms.snap @@ -9,6 +9,7 @@ query: omim_id: ~ name: tel-Manzke syndrome match_: suffix + ignore_case: ~ max_results: 100 hpo_terms: false result: diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_with_hpo_terms.snap index d2564bb..41196eb 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_name_suffix_with_hpo_terms.snap @@ -9,6 +9,7 @@ query: omim_id: ~ name: tel-Manzke syndrome match_: suffix + ignore_case: ~ max_results: 100 hpo_terms: true result: diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_no_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_no_hpo_terms.snap index e4852d9..484b0b3 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_no_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_no_hpo_terms.snap @@ -9,6 +9,7 @@ query: omim_id: "616145" name: ~ match_: ~ + ignore_case: ~ max_results: 100 hpo_terms: false result: diff --git a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_with_hpo_terms.snap b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_with_hpo_terms.snap index e57a71f..83a2d7f 100644 --- a/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_with_hpo_terms.snap +++ b/src/server/run/snapshots/viguno__server__run__hpo_omims__test__hpo_omims_omim_id_exact_with_hpo_terms.snap @@ -9,6 +9,7 @@ query: omim_id: "616145" name: ~ match_: ~ + ignore_case: ~ max_results: 100 hpo_terms: true result: