diff --git a/Cargo.lock b/Cargo.lock index e2fac0d..e38e3f9 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -261,7 +261,7 @@ dependencies = [ "futures", "hmac", "include_dir", - "itertools", + "itertools 0.12.1", "jsonwebtoken", "kiddo", "lazy_static", @@ -292,6 +292,18 @@ dependencies = [ "wasm-bindgen", ] +[[package]] +name = "biomedgps-graph" +version = "0.1.0" +dependencies = [ + "getrandom 0.2.13", + "rustworkx-core", + "serde", + "serde-wasm-bindgen", + "wasm-bindgen", + "wasm-bindgen-test", +] + [[package]] name = "bitflags" version = "1.3.2" @@ -421,6 +433,16 @@ dependencies = [ "unicode-width", ] +[[package]] +name = "console_error_panic_hook" +version = "0.1.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a06aeb73f470f66dcdbf7223caeebb85984942f22f1adb2a088cf9668146bbbc" +dependencies = [ + "cfg-if", + "wasm-bindgen", +] + [[package]] name = "convert_case" version = "0.4.0" @@ -897,6 +919,12 @@ dependencies = [ "typenum", ] +[[package]] +name = "fixedbitset" +version = "0.4.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80" + [[package]] name = "fnv" version = "1.0.7" @@ -1539,6 +1567,7 @@ checksum = "168fb715dda47215e360912c096649d23d58bf392ac62f73919e831745e40f26" dependencies = [ "equivalent", "hashbrown 0.14.3", + "rayon", ] [[package]] @@ -1571,6 +1600,15 @@ version = "2.9.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "8f518f335dce6725a761382244631d86cf0ccb2863413590b31338feb467f9c3" +[[package]] +name = "itertools" +version = "0.11.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b1c173a5686ce8bfa551b3563d0c2170bf24ca44da99c7ca4bfdab5418c3fe57" +dependencies = [ + "either", +] + [[package]] name = "itertools" version = "0.12.1" @@ -1638,7 +1676,7 @@ dependencies = [ "fixed", "generator", "init_with", - "itertools", + "itertools 0.12.1", "log", "num-traits", "ordered-float 4.2.0", @@ -2312,6 +2350,16 @@ version = "2.3.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e3148f5046208a5d56bcfc03053e3ca6334e51da8dfb19b6cdc8b306fae3283e" +[[package]] +name = "petgraph" +version = "0.6.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b4c5cc86750666a3ed20bdaf5ca2a0344f9c67674cae0515bec2da16fbaa47db" +dependencies = [ + "fixedbitset", + "indexmap 2.2.6", +] + [[package]] name = "phf" version = "0.8.0" @@ -2873,6 +2921,16 @@ version = "0.1.1" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "925383efa346730478fb4838dbe9137d2a47675ad789c546d150a6e1dd4ab31c" +[[package]] +name = "priority-queue" +version = "1.4.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a0bda9164fe05bc9225752d54aae413343c36f684380005398a6a8fde95fe785" +dependencies = [ + "autocfg", + "indexmap 1.9.3", +] + [[package]] name = "proc-macro-crate" version = "1.3.1" @@ -2972,7 +3030,7 @@ dependencies = [ "rand_chacha 0.2.2", "rand_core 0.5.1", "rand_hc", - "rand_pcg", + "rand_pcg 0.2.1", ] [[package]] @@ -3052,6 +3110,15 @@ dependencies = [ "rand_core 0.5.1", ] +[[package]] +name = "rand_pcg" +version = "0.3.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "59cad018caf63deb318e5a4586d99a24424a364f40f1e5778c29aca23f4fc73e" +dependencies = [ + "rand_core 0.6.4", +] + [[package]] name = "rayon" version = "1.10.0" @@ -3062,6 +3129,17 @@ dependencies = [ "rayon-core", ] +[[package]] +name = "rayon-cond" +version = "0.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "059f538b55efd2309c9794130bc149c6a553db90e9d99c2030785c82f0bd7df9" +dependencies = [ + "either", + "itertools 0.11.0", + "rayon", +] + [[package]] name = "rayon-core" version = "1.12.1" @@ -3362,6 +3440,25 @@ version = "1.0.14" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "7ffc183a10b4478d04cbbbfc96d0873219d962dd5accaff2ffbd4ceb7df837f4" +[[package]] +name = "rustworkx-core" +version = "0.14.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "529027dfaa8125aa61bb7736ae9484f41e8544f448af96918c8da6b1def7f57b" +dependencies = [ + "ahash 0.8.11", + "fixedbitset", + "hashbrown 0.14.3", + "indexmap 2.2.6", + "num-traits", + "petgraph", + "priority-queue", + "rand 0.8.5", + "rand_pcg 0.3.1", + "rayon", + "rayon-cond", +] + [[package]] name = "ryu" version = "1.0.17" @@ -3386,6 +3483,12 @@ dependencies = [ "windows-sys 0.52.0", ] +[[package]] +name = "scoped-tls" +version = "1.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e1cf6437eb19a8f4a6cc0f7dca544973b0b78843adbfeb3683d1a94a0024a294" + [[package]] name = "scopeguard" version = "1.2.0" @@ -3470,6 +3573,17 @@ dependencies = [ "serde", ] +[[package]] +name = "serde-wasm-bindgen" +version = "0.6.5" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8302e169f0eddcc139c70f139d19d6467353af16f9fce27e8c30158036a1e16b" +dependencies = [ + "js-sys", + "serde", + "wasm-bindgen", +] + [[package]] name = "serde_derive" version = "1.0.197" @@ -3651,7 +3765,7 @@ version = "0.2.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ce81b7bd7c4493975347ef60d8c7e8b742d4694f4c49f93e0a12ea263938176c" dependencies = [ - "itertools", + "itertools 0.12.1", "nom", "unicode_categories", ] @@ -4583,6 +4697,31 @@ version = "0.2.92" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96" +[[package]] +name = "wasm-bindgen-test" +version = "0.3.42" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "d9bf62a58e0780af3e852044583deee40983e5886da43a271dd772379987667b" +dependencies = [ + "console_error_panic_hook", + "js-sys", + "scoped-tls", + "wasm-bindgen", + "wasm-bindgen-futures", + "wasm-bindgen-test-macro", +] + +[[package]] +name = "wasm-bindgen-test-macro" +version = "0.3.42" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b7f89739351a2e03cb94beb799d47fb2cac01759b40ec441f7de39b00cbf7ef0" +dependencies = [ + "proc-macro2", + "quote", + "syn 2.0.58", +] + [[package]] name = "wasm-streams" version = "0.4.0" diff --git a/Cargo.toml b/Cargo.toml index a782c52..c71f2de 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,3 +1,8 @@ +[workspace] +members = [ + "wasm" +] + [package] authors = ["Jingcheng Yang "] documentation = "https://github.com/yjcyxky/biomedgps/blob/master/README.md" diff --git a/studio/src/pages/KnowledgeTable/index.less b/studio/src/pages/KnowledgeTable/index.less index 8c7ba7b..ce71e9b 100644 --- a/studio/src/pages/KnowledgeTable/index.less +++ b/studio/src/pages/KnowledgeTable/index.less @@ -9,6 +9,7 @@ .ant-collapse { width: 100%; + .ant-collapse-item:nth-child(1), .ant-collapse-item:nth-child(2) { .ant-collapse-header { border-bottom: 1px solid #f0f0f0; @@ -27,7 +28,7 @@ .ant-collapse-header, .ant-collapse-content-box { - border-radius: 0; + border-radius: 0 !important; padding: 20px 0; } } diff --git a/wasm/Cargo.toml b/wasm/Cargo.toml new file mode 100644 index 0000000..c935b83 --- /dev/null +++ b/wasm/Cargo.toml @@ -0,0 +1,22 @@ +[package] +name = "biomedgps-graph" +description = "" +version = "0.1.0" +authors = ["Jingcheng Yang "] +edition = "2021" + +[lib] +crate-type = ["cdylib"] + +[dependencies] +rustworkx-core = "0.14.2" +serde = { version = "1.0", features = ["derive"] } +wasm-bindgen = "0.2" +serde-wasm-bindgen = "0.6.5" +getrandom = { version = "0.2", features = ["js"] } + +[dev-dependencies] +wasm-bindgen-test = "0.3" + +[profile.release] +opt-level = "s" diff --git a/wasm/README.md b/wasm/README.md new file mode 100644 index 0000000..af978c2 --- /dev/null +++ b/wasm/README.md @@ -0,0 +1,35 @@ +# BiomedGPS Graph + +This project provides a Rust implementation for calculating various centrality measures of a graph, compiled to WebAssembly (Wasm) for use in a web frontend. + +## Getting Started + +### Prerequisites + +Ensure you have the following tools installed: + +- [Rust](https://www.rust-lang.org/tools/install) +- [wasm-pack](https://rustwasm.github.io/wasm-pack/installer/) + +### Build Instructions + +1. Clone the repository: + + ```sh + git clone https://github.com/yjcyxky/biomedgps.git + cd biomedgps/wasm + ``` + +2. Build the project: + + ```sh + wasm-pack build --target web + ``` + +3. Run example.js: + + ```sh + python3 -m http.server 8000 + ``` + + Open `http://localhost:8000` in your browser and see the output. diff --git a/wasm/index.html b/wasm/index.html new file mode 100644 index 0000000..d462347 --- /dev/null +++ b/wasm/index.html @@ -0,0 +1,105 @@ + + + + + + + DataTables Example + + + + + +

WebAssembly Centrality Calculation

+ + + + + + + + + + + + + + + +
Entity IDEntity TypeEntity NameBetweenness ScoreDegree ScoreCloseness ScoreEigenvector ScorePageRank Score
+ + + + + + + + \ No newline at end of file diff --git a/wasm/mecfs_subgraph.json b/wasm/mecfs_subgraph.json new file mode 100644 index 0000000..950e72a --- /dev/null +++ b/wasm/mecfs_subgraph.json @@ -0,0 +1,56262 @@ +[ + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Orthostatic Intolerance", + "score": 0.9405058622, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D054971" + }, + { + "reltype": "Hetionet::DpS::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Orthostatic Intolerance", + "score": 0.8495634198, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D054971" + }, + { + "reltype": "Hetionet::DpS::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "cough", + "score": 0.91563344, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0000614" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "cough", + "score": 0.5360760093, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0000614" + }, + { + "reltype": "Hetionet::DpS::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "nausea", + "score": 0.911737144, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0000458" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "nausea", + "score": 0.5261166692, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0000458" + }, + { + "reltype": "Hetionet::DpS::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "decreased appetite", + "score": 0.9090417027, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0000245" + }, + { + "reltype": "Hetionet::DpS::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "breathing problems", + "score": 0.9075162411, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0000868" + }, + { + "reltype": "Hetionet::DpS::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "chills", + "score": 0.9025090933, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0019174" + }, + { + "reltype": "Hetionet::DpS::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "palpitation", + "score": 0.8891083002, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0000530" + }, + { + "reltype": "Hetionet::DpS::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "tinnitus", + "score": 0.8834840655, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0000393" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Pain", + "score": 0.7702038884, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D010146" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Fatigue", + "score": 0.768619597, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D005221" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Body Weight", + "score": 0.7619843483, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D001835" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Abdominal Pain", + "score": 0.7541909814, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D015746" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Hypocapnia", + "score": 0.7489036322, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D016857" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Mental Fatigue", + "score": 0.7377772927, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D005222" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Arthralgia", + "score": 0.7317040563, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D018771" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Sleep Deprivation", + "score": 0.7316759825, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D012892" + }, + { + "reltype": "Hetionet::DpS::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "sleep disturbance", + "score": 0.7311056256, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0000566" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "sleep disturbance", + "score": 0.2647121847, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "SYMP:0000566" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Asthenia", + "score": 0.7292813063, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D001247" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Olfaction Disorders", + "score": 0.7292035222, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D000857" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Dyspnea", + "score": 0.7256531715, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D004417" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Memory Disorders", + "score": 0.7244253755, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D008569" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Bulimia", + "score": 0.7214690447, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D002032" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Obesity", + "score": 0.7209241986, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D009765" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic encephalomeyelitis\/chronic fatigue syndrome", + "target_name": "Hyperalgesia", + "score": 0.7201797962, + "source_type": "Disease", + "target_type": "Symptom", + "source_id": "MONDO:0005404", + "target_id": "MESH:D006930" + }, + { + "reltype": "HSDN::has_symptom::Disease:Symptom", + "source_name": "myalgic 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+ "target_name": "PPARG", + "score": 0.7549638748, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00313", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "Hetionet::CuG::Compound:Gene", + "source_name": "TRIAMCINOLONE", + "target_name": "PPARG", + "score": 0.7017259002, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00620", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "GNBR::N::Compound:Gene", + "source_name": "TESTOSTERONE", + "target_name": "PPARG", + "score": 0.758338511, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00624", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "GNBR::N::Compound:Gene", + "source_name": "HYDROCORTISONE", + "target_name": "PPARG", + "score": 0.7441446781, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00741", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "Hetionet::CuG::Compound:Gene", + "source_name": "TRETINOIN", + "target_name": "PPARG", + "score": 0.831479907, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00755", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "GNBR::O::Compound:Gene", + "source_name": "ESTRADIOL", + "target_name": "PPARG", + "score": 0.8138648868, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00783", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "Hetionet::CuG::Compound:Gene", + "source_name": "Budesonide", + "target_name": "PPARG", + "score": 0.7473050356, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB01222", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "DEXAMETHASONE", + "target_name": "PPARG", + "score": 0.7691184878, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB01234", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "Hetionet::DaG::Disease:Gene", + "source_name": "type 2 diabetes mellitus", + "target_name": "PPARG", + "score": 0.9362075925, + "source_type": "Disease", + "target_type": "Gene", + "source_id": "MONDO:0005148", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "INTACT::DIRECT INTERACTION::Gene:Gene", + "source_name": "PF4", + "target_name": "PF4", + "score": 0.9988586903, + "source_type": "Gene", + "target_type": "Gene", + "source_id": "ENTREZ:5196", + "target_id": "ENTREZ:5196" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "NICOTINE", + "target_name": "POMC", + "score": 0.8030239344, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00184", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "VALPROIC ACID", + "target_name": "POMC", + "score": 0.8024657369, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00313", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "INDOMETHACIN", + "target_name": "POMC", + "score": 0.8052337766, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00328", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "METHADONE", + "target_name": "POMC", + "score": 0.7759832144, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00333", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::K::Compound:Gene", + "source_name": "METHADONE", + "target_name": "POMC", + "score": 0.7820868492, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00333", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "NOREPINEPHRINE", + "target_name": "POMC", + "score": 0.8548738956, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00368", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::K::Compound:Gene", + "source_name": "NOREPINEPHRINE", + "target_name": "POMC", + "score": 0.8566397429, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00368", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::N::Compound:Gene", + "source_name": "PROGESTERONE", + "target_name": "POMC", + "score": 0.8169198036, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00396", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "LEVOTHYROXINE", + "target_name": "POMC", + "score": 0.8236854672, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00451", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::K::Compound:Gene", + "source_name": "LEVOTHYROXINE", + "target_name": "POMC", + "score": 0.8074041605, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00451", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "PROPRANOLOL", + "target_name": "POMC", + "score": 0.8435637355, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00571", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "CLONIDINE", + "target_name": "POMC", + "score": 0.7899121642, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00575", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::K::Compound:Gene", + "source_name": "CLONIDINE", + "target_name": "POMC", + "score": 0.788451314, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00575", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "TESTOSTERONE", + "target_name": "POMC", + "score": 0.8903133273, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00624", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::O::Compound:Gene", + "source_name": "TESTOSTERONE", + "target_name": "POMC", + "score": 0.7920438647, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00624", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "EPINEPHRINE", + "target_name": "POMC", + "score": 0.8782302737, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00668", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::K::Compound:Gene", + "source_name": "EPINEPHRINE", + "target_name": "POMC", + "score": 0.8730282187, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00668", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "HYDROCORTISONE", + "target_name": "POMC", + "score": 0.9000060558, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00741", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::K::Compound:Gene", + "source_name": "HYDROCORTISONE", + "target_name": "POMC", + "score": 0.9022701979, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00741", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "ESTRADIOL", + "target_name": "POMC", + "score": 0.8672583103, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00783", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::K::Compound:Gene", + "source_name": "ESTRADIOL", + "target_name": "POMC", + "score": 0.8622447848, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00783", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "ALCOHOL", + "target_name": "POMC", + "score": 0.83385849, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00898", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::K::Compound:Gene", + "source_name": "ALCOHOL", + "target_name": "POMC", + "score": 0.8442081809, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB00898", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::K::Compound:Gene", + "source_name": "MELATONIN", + "target_name": "POMC", + "score": 0.825417161, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB01065", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::E::Compound:Gene", + "source_name": "DEXAMETHASONE", + "target_name": "POMC", + "score": 0.851149857, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB01234", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "GNBR::K::Compound:Gene", + "source_name": "DEXAMETHASONE", + "target_name": "POMC", + "score": 0.863702774, + "source_type": "Compound", + "target_type": "Gene", + "source_id": "DrugBank:DB01234", + "target_id": "ENTREZ:5443" + }, + { + "reltype": "Hetionet::Gr>G::Gene:Gene", + "source_name": "USP6NL", + "target_name": "PPARD", + "score": 0.5038150549, + "source_type": "Gene", + "target_type": "Gene", + "source_id": "ENTREZ:9712", + "target_id": "ENTREZ:5467" + }, + { + "reltype": "GNBR::B::Gene:Gene", + "source_name": "IL2", + "target_name": "PPARG", + "score": 0.6548278928, + "source_type": "Gene", + "target_type": "Gene", + "source_id": "ENTREZ:3558", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "GNBR::Q::Gene:Gene", + "source_name": "PPARD", + "target_name": "PPARG", + "score": 0.9478077888, + "source_type": "Gene", + "target_type": "Gene", + "source_id": "ENTREZ:5467", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "bioarx::HumGenHumGen::Gene:Gene", + "source_name": "PPARG", + "target_name": "PPARG", + "score": 0.9994243383, + "source_type": "Gene", + "target_type": "Gene", + "source_id": "ENTREZ:5468", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "INTACT::ASSOCIATION::Gene:Gene", + "source_name": "PPARG", + "target_name": "PPARG", + "score": 0.9990384579, + "source_type": "Gene", + "target_type": "Gene", + "source_id": "ENTREZ:5468", + "target_id": "ENTREZ:5468" + }, + { + "reltype": "INTACT::PHYSICAL ASSOCIATION::Gene:Gene", + "source_name": "PPARG", + "target_name": "PPARG", + "score": 0.9997935891, + "source_type": "Gene", + "target_type": "Gene", + "source_id": "ENTREZ:5468", + "target_id": "ENTREZ:5468" + } +] \ No newline at end of file diff --git a/wasm/src/lib.rs b/wasm/src/lib.rs new file mode 100644 index 0000000..01f8de9 --- /dev/null +++ b/wasm/src/lib.rs @@ -0,0 +1,191 @@ +use rustworkx_core::centrality::{ + betweenness_centrality, closeness_centrality, eigenvector_centrality, katz_centrality, +}; +use rustworkx_core::petgraph::graph::EdgeReference; +use rustworkx_core::petgraph::graph::NodeIndex; +use rustworkx_core::petgraph::graph::{DiGraph, UnGraph}; +use serde::{Deserialize, Serialize}; +use serde_wasm_bindgen::{from_value, to_value}; +use std::collections::HashMap; +use wasm_bindgen::prelude::*; + +#[derive(Serialize, Deserialize, Debug, Clone)] +struct Relation { + reltype: String, + source_name: String, + source_type: String, + source_id: String, + target_name: String, + target_type: String, + target_id: String, + score: f64, +} + +#[derive(Serialize, Deserialize, Debug, Clone)] +struct CentralityResult { + entity_id: String, + entity_type: String, + entity_name: String, + betweenness_score: f64, + degree_score: f64, + closeness_score: f64, + eigenvector_score: f64, + pagerank_score: f64, +} + +fn calculate_centralities(relations: Vec) -> Vec { + // let mut graph = DiGraph::::new(); + let mut graph = UnGraph::::new_undirected(); + let mut node_indices: HashMap = HashMap::new(); + + for rel in &relations { + let source_id = &rel.source_id; + let target_id = &rel.target_id; + if !node_indices.contains_key(source_id) { + let node_index = graph.add_node(source_id.clone()); + node_indices.insert(source_id.clone(), node_index); + } + if !node_indices.contains_key(target_id) { + let node_index = graph.add_node(target_id.clone()); + node_indices.insert(target_id.clone(), node_index); + } + let source_index = node_indices[source_id]; + let target_index = node_indices[target_id]; + graph.add_edge(source_index, target_index, rel.score); + } + + let betweenness_scores = betweenness_centrality(&graph, false, true, 100); + let closeness_scores = closeness_centrality(&graph, false); + // More details on the parameters for eigenvector_centrality can be found at https://docs.rs/rustworkx-core/latest/rustworkx_core/centrality/fn.eigenvector_centrality.html + let eigenvector_scores = match eigenvector_centrality( + &graph, + |edge: EdgeReference| -> Result { Ok(*edge.weight()) }, + None, + None, + ) { + Ok(scores) => scores.unwrap_or(vec![]), + Err(_) => vec![], + }; + + // let degree_scores = degree_centrality(&graph); + // let pagerank_scores = pagerank(&graph, 0.85, 0.0001).unwrap(); + + let mut results = Vec::new(); + for (node, index) in node_indices.iter() { + let entity_id = node.clone(); + let entity_info = relations + .iter() + .find(|r| &r.source_id == node || &r.target_id == node); + + let (entity_type, entity_name) = match entity_info { + Some(relation) => { + if &relation.source_id == node { + (relation.source_type.clone(), relation.source_name.clone()) + } else { + (relation.target_type.clone(), relation.target_name.clone()) + } + } + None => ("Unknown".to_string(), "Unknown".to_string()), + }; + let betweenness_score = match *betweenness_scores.get(index.index()).unwrap_or(&None) { + Some(score) => score, + None => 0.0, + }; + let closeness_score = match *closeness_scores.get(index.index()).unwrap_or(&None) { + Some(score) => score, + None => 0.0, + }; + let eigenvector_score = *eigenvector_scores.get(index.index()).unwrap_or(&0.0); + + let degree_score = 0.0; + let pagerank_score = 0.0; + + // let degree_score = *degree_scores.get(index.index()).unwrap_or(&0.0); + // let pagerank_score = *pagerank_scores.get(index.index()).unwrap_or(&0.0); + + results.push(CentralityResult { + entity_id, + entity_type, + entity_name, + betweenness_score, + closeness_score, + eigenvector_score, + degree_score, + pagerank_score, + }); + } + + results +} + +#[wasm_bindgen] +pub fn calculate_centrality(relations: JsValue) -> JsValue { + let relations: Vec = from_value(relations).unwrap(); + let results = calculate_centralities(relations); + to_value(&results).unwrap() +} + +#[cfg(test)] +mod tests { + use super::*; + + #[test] + fn test_calculate_centralities() { + let relations = vec![ + Relation { + reltype: "related".to_string(), + source_name: "A".to_string(), + source_type: "Person".to_string(), + source_id: "A".to_string(), + target_name: "B".to_string(), + target_type: "Person".to_string(), + target_id: "B".to_string(), + score: 0.5, + }, + Relation { + reltype: "related".to_string(), + source_name: "A".to_string(), + source_type: "Person".to_string(), + source_id: "A".to_string(), + target_name: "C".to_string(), + target_type: "Person".to_string(), + target_id: "C".to_string(), + score: 0.5, + }, + Relation { + reltype: "related".to_string(), + source_name: "B".to_string(), + source_type: "Person".to_string(), + source_id: "B".to_string(), + target_name: "C".to_string(), + target_type: "Person".to_string(), + target_id: "C".to_string(), + score: 0.5, + }, + ]; + + let results = calculate_centralities(relations); + for result in &results { + println!( + "entity_id: {}, entity_type: {}, betweenness_score: {}, closeness_score: {}, eigenvector_score: {}, degree_score: {}, pagerank_score: {}", + result.entity_id, + result.entity_type, + result.betweenness_score, + result.closeness_score, + result.eigenvector_score, + result.degree_score, + result.pagerank_score, + ); + } + + assert_eq!(results.len(), 3); + + let a_node = results.iter().find(|r| r.entity_id == "A").unwrap(); + assert_eq!(a_node.entity_type, "Person"); + assert_eq!(a_node.betweenness_score, 2.0); + assert_eq!(a_node.closeness_score, 0.0); + assert_eq!(a_node.eigenvector_score, 0.0); + assert_eq!(a_node.degree_score, 0.0); + assert_eq!(a_node.pagerank_score, 0.0); + } +}