diff --git a/frontend/README.md b/frontend/README.md index 987ecdb1f..81c432229 100644 --- a/frontend/README.md +++ b/frontend/README.md @@ -114,7 +114,7 @@ const iframe = document.querySelector("iframe"); iframe.contentWindow.postMessage({ source: ["abc"], target: ["def"] }, "*"); ``` -#### Emits `MessageEvent` +#### Emits `MessageEvent<{ width: number; height: number; }>` Emitted when the size of the widget changes and on load. Useful for setting the dimensions of your iframe container, for example: diff --git a/frontend/fixtures/index.ts b/frontend/fixtures/index.ts index 1c1c06294..b22081654 100644 --- a/frontend/fixtures/index.ts +++ b/frontend/fixtures/index.ts @@ -157,38 +157,8 @@ export const handlers = [ ), /** any other request */ - rest.get(/.*/, (req, res, ctx) => { - /** for certain exceptions, passthrough (let browser make a real request) */ - const exceptions = [ - /\.vue$/, - /\.js$/, - /\.ts$/, - /\.css$/, - /\.scss$/, - /\.html$/, - /\.mp4$/, - /\.svg$/, - /\.png$/, - /\.jpg$/, - /\.jpeg$/, - /\.gif$/, - /\.bmp$/, - /\.tiff$/, - /\.woff$/, - /\.json$/, - /\.jsonld$/, - /\.txt$/, - /site\.webmanifest/, - /medium\.com/, - /fonts\.googleapis\.com/, - ]; - if (exceptions.some((exception) => req.url.href.match(exception))) - return req.passthrough(); - - /** - * otherwise, throw error to make sure we never hit any api when mocking is - * enabled - */ - return res(ctx.status(500, "Non-mocked request " + req.url.pathname)); + rest.get(/.*/, (req) => { + console.info("Non-mocked request", req.url.pathname); + return req.passthrough(); }), ]; diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json index c27309721..b19a253ec 100644 --- a/frontend/fixtures/phenotype-explorer-compare.json +++ b/frontend/fixtures/phenotype-explorer-compare.json @@ -1,261 +1,4291 @@ { "subject_termset": { - "MP:0005391": { - "id": "MP:0005391", - "label": "vision/eye phenotype (MPO)" + "HP:0200055": { + "id": "HP:0200055", + "label": "Small hand (HPO)" }, - "MP:0005367": { - "id": "MP:0005367", - "label": "renal/urinary system phenotype (MPO)" + "HP:0008065": { + "id": "HP:0008065", + "label": "Aplasia/Hypoplasia of the skin (HPO)" }, - "MP:0002169": { - "id": "MP:0002169", - "label": "no abnormal phenotype detected (MPO)" + "HP:0002209": { + "id": "HP:0002209", + "label": "Sparse scalp hair (HPO)" }, - "MP:0010771": { - "id": "MP:0010771", - "label": "integument phenotype (MPO)" + "HP:0002861": { + "id": "HP:0002861", + "label": "Melanoma (HPO)" }, - "MP:0005389": { - "id": "MP:0005389", - "label": "reproductive system phenotype (MPO)" + "HP:0000275": { + "id": "HP:0000275", + "label": "Narrow face (HPO)" + }, + "HP:0001608": { + "id": "HP:0001608", + "label": "Abnormality of the voice (HPO)" + }, + "HP:0005177": { + "id": "HP:0005177", + "label": "Premature arteriosclerosis (HPO)" + }, + "HP:0001635": { + "id": "HP:0001635", + "label": "Congestive heart failure (HPO)" + }, + "HP:0003777": { + "id": "HP:0003777", + "label": "Pili torti (HPO)" + }, + "HP:0000518": { + "id": "HP:0000518", + "label": "Cataract (HPO)" + }, + "HP:0002216": { + "id": "HP:0002216", + "label": "Premature graying of hair (HPO)" + }, + "HP:0004322": { + "id": "HP:0004322", + "label": "Short stature (HPO)" + }, + "HP:0010721": { + "id": "HP:0010721", + "label": "Abnormal hair whorl (HPO)" + }, + "HP:0001601": { + "id": "HP:0001601", + "label": "Laryngomalacia (HPO)" + }, + "HP:0001620": { + "id": "HP:0001620", + "label": "High pitched voice (HPO)" + }, + "HP:0000819": { + "id": "HP:0000819", + "label": "Diabetes mellitus (HPO)" + }, + "HP:0000869": { + "id": "HP:0000869", + "label": "Secondary amenorrhea (HPO)" + }, + "HP:0002669": { + "id": "HP:0002669", + "label": "Osteosarcoma (HPO)" + }, + "HP:0002858": { + "id": "HP:0002858", + "label": "Meningioma (HPO)" + }, + "HP:0002211": { + "id": "HP:0002211", + "label": "White forelock (HPO)" + }, + "HP:0002155": { + "id": "HP:0002155", + "label": "Hypertriglyceridemia (HPO)" + }, + "HP:0004349": { + "id": "HP:0004349", + "label": "Reduced bone mineral density (HPO)" + }, + "HP:0001533": { + "id": "HP:0001533", + "label": "Slender build (HPO)" + }, + "HP:0009726": { + "id": "HP:0009726", + "label": "Renal neoplasm (HPO)" + }, + "HP:0005978": { + "id": "HP:0005978", + "label": "Type II diabetes mellitus (HPO)" + }, + "HP:0007703": { + "id": "HP:0007703", + "label": "Abnormality of retinal pigmentation (HPO)" + }, + "HP:0100324": { + "id": "HP:0100324", + "label": "Scleroderma (HPO)" + }, + "HP:0100578": { + "id": "HP:0100578", + "label": "Lipoatrophy (HPO)" + }, + "HP:0012056": { + "id": "HP:0012056", + "label": "Cutaneous melanoma (HPO)" + }, + "HP:0002621": { + "id": "HP:0002621", + "label": "Atherosclerosis (HPO)" + }, + "HP:0001838": { + "id": "HP:0001838", + "label": "Rocker bottom foot (HPO)" + }, + "HP:0007618": { + "id": "HP:0007618", + "label": "Subcutaneous calcification (HPO)" + }, + "HP:0031956": { + "id": "HP:0031956", + "label": "Elevated circulating aspartate aminotransferase concentration (HPO)" + }, + "HP:0002293": { + "id": "HP:0002293", + "label": "Alopecia of scalp (HPO)" + }, + "HP:0003419": { + "id": "HP:0003419", + "label": "Low back pain (HPO)" + }, + "HP:0000962": { + "id": "HP:0000962", + "label": "Hyperkeratosis (HPO)" + }, + "HP:0012060": { + "id": "HP:0012060", + "label": "Acral lentiginous melanoma (HPO)" + }, + "HP:0000939": { + "id": "HP:0000939", + "label": "Osteoporosis (HPO)" + }, + "HP:0003202": { + "id": "HP:0003202", + "label": "Skeletal muscle atrophy (HPO)" + }, + "HP:0010468": { + "id": "HP:0010468", + "label": "Aplasia/Hypoplasia of the testes (HPO)" + }, + "HP:0000546": { + "id": "HP:0000546", + "label": "Retinal degeneration (HPO)" + }, + "HP:0100649": { + "id": "HP:0100649", + "label": "Neoplasm of the oral cavity (HPO)" + }, + "HP:0002860": { + "id": "HP:0002860", + "label": "Squamous cell carcinoma (HPO)" + }, + "HP:0003002": { + "id": "HP:0003002", + "label": "Breast carcinoma (HPO)" + }, + "HP:0000035": { + "id": "HP:0000035", + "label": "Abnormal testis morphology (HPO)" + }, + "HP:0009125": { + "id": "HP:0009125", + "label": "Lipodystrophy (HPO)" + }, + "HP:0100526": { + "id": "HP:0100526", + "label": "Neoplasm of the lung (HPO)" + }, + "HP:0200042": { + "id": "HP:0200042", + "label": "Skin ulcer (HPO)" + }, + "HP:0004415": { + "id": "HP:0004415", + "label": "Pulmonary artery stenosis (HPO)" + }, + "HP:0002890": { + "id": "HP:0002890", + "label": "Thyroid carcinoma (HPO)" + }, + "HP:0007495": { + "id": "HP:0007495", + "label": "Prematurely aged appearance (HPO)" + }, + "HP:0000765": { + "id": "HP:0000765", + "label": "Abnormal thorax morphology (HPO)" + }, + "HP:0011001": { + "id": "HP:0011001", + "label": "Increased bone mineral density (HPO)" + }, + "HP:0000444": { + "id": "HP:0000444", + "label": "Convex nasal ridge (HPO)" + }, + "HP:0000135": { + "id": "HP:0000135", + "label": "Hypogonadism (HPO)" + }, + "HP:0000822": { + "id": "HP:0000822", + "label": "Hypertension (HPO)" + }, + "HP:0000934": { + "id": "HP:0000934", + "label": "Chondrocalcinosis (HPO)" + }, + "HP:0100242": { + "id": "HP:0100242", + "label": "Sarcoma (HPO)" + }, + "HP:0100615": { + "id": "HP:0100615", + "label": "Ovarian neoplasm (HPO)" + }, + "HP:0100585": { + "id": "HP:0100585", + "label": "Telangiectasia of the skin (HPO)" + }, + "HP:0100659": { + "id": "HP:0100659", + "label": "Abnormal cerebral vascular morphology (HPO)" + }, + "HP:0000320": { + "id": "HP:0000320", + "label": "Bird-like facies (HPO)" + }, + "HP:0040217": { + "id": "HP:0040217", + "label": "Elevated hemoglobin A1c (HPO)" + }, + "HP:0000855": { + "id": "HP:0000855", + "label": "Insulin resistance (HPO)" + }, + "HP:0001387": { + "id": "HP:0001387", + "label": "Joint stiffness (HPO)" + }, + "HP:0031964": { + "id": "HP:0031964", + "label": "Elevated circulating alanine aminotransferase concentration (HPO)" + }, + "HP:0100833": { + "id": "HP:0100833", + "label": "Neoplasm of the small intestine (HPO)" + }, + "HP:0002672": { + "id": "HP:0002672", + "label": "Gastrointestinal carcinoma (HPO)" + }, + "HP:0005328": { + "id": "HP:0005328", + "label": "Progeroid facial appearance (HPO)" + }, + "HP:0000144": { + "id": "HP:0000144", + "label": "Decreased fertility (HPO)" + }, + "HP:0002664": { + "id": "HP:0002664", + "label": "Neoplasm (HPO)" + }, + "HP:0100679": { + "id": "HP:0100679", + "label": "Lack of skin elasticity (HPO)" } }, "object_termset": { - "HP:0004325": { - "id": "HP:0004325", - "label": "Decreased body weight (HPO)" + "HP:0012378": { + "id": "HP:0012378", + "label": "Fatigue (HPO)" + }, + "HP:0002315": { + "id": "HP:0002315", + "label": "Headache (HPO)" + }, + "HP:0000023": { + "id": "HP:0000023", + "label": "Inguinal hernia (HPO)" + }, + "HP:0001653": { + "id": "HP:0001653", + "label": "Mitral regurgitation (HPO)" + }, + "HP:0001760": { + "id": "HP:0001760", + "label": "Abnormal foot morphology (HPO)" + }, + "HP:0005294": { + "id": "HP:0005294", + "label": "Arterial dissection (HPO)" + }, + "HP:0006243": { + "id": "HP:0006243", + "label": "Phalangeal dislocation (HPO)" + }, + "HP:0001704": { + "id": "HP:0001704", + "label": "Tricuspid valve prolapse (HPO)" + }, + "HP:0003771": { + "id": "HP:0003771", + "label": "Pulp calcification (HPO)" + }, + "HP:0001075": { + "id": "HP:0001075", + "label": "Atrophic scars (HPO)" + }, + "HP:0012450": { + "id": "HP:0012450", + "label": "Chronic constipation (HPO)" + }, + "HP:0000993": { + "id": "HP:0000993", + "label": "Molluscoid pseudotumors (HPO)" + }, + "HP:0001634": { + "id": "HP:0001634", + "label": "Mitral valve prolapse (HPO)" + }, + "HP:0001073": { + "id": "HP:0001073", + "label": "Cigarette-paper scars (HPO)" + }, + "HP:0000978": { + "id": "HP:0000978", + "label": "Bruising susceptibility (HPO)" + }, + "HP:0001065": { + "id": "HP:0001065", + "label": "Striae distensae (HPO)" + }, + "HP:0000286": { + "id": "HP:0000286", + "label": "Epicanthus (HPO)" + }, + "HP:0003083": { + "id": "HP:0003083", + "label": "Dislocated radial head (HPO)" + }, + "HP:0004872": { + "id": "HP:0004872", + "label": "Incisional hernia (HPO)" + }, + "HP:0004944": { + "id": "HP:0004944", + "label": "Dilatation of the cerebral artery (HPO)" + }, + "HP:0002035": { + "id": "HP:0002035", + "label": "Rectal prolapse (HPO)" + }, + "HP:0002616": { + "id": "HP:0002616", + "label": "Aortic root aneurysm (HPO)" + }, + "HP:0002761": { + "id": "HP:0002761", + "label": "Generalized joint laxity (HPO)" + }, + "HP:0009763": { + "id": "HP:0009763", + "label": "Limb pain (HPO)" + }, + "HP:0025014": { + "id": "HP:0025014", + "label": "Subcutaneous spheroids (HPO)" + }, + "HP:0001252": { + "id": "HP:0001252", + "label": "Hypotonia (HPO)" + }, + "HP:0031653": { + "id": "HP:0031653", + "label": "Abnormal heart valve physiology (HPO)" + }, + "HP:0001058": { + "id": "HP:0001058", + "label": "Poor wound healing (HPO)" + }, + "HP:0002829": { + "id": "HP:0002829", + "label": "Arthralgia (HPO)" + }, + "HP:0001324": { + "id": "HP:0001324", + "label": "Muscle weakness (HPO)" + }, + "HP:0003394": { + "id": "HP:0003394", + "label": "Muscle spasm (HPO)" + }, + "HP:0001537": { + "id": "HP:0001537", + "label": "Umbilical hernia (HPO)" + }, + "HP:0010750": { + "id": "HP:0010750", + "label": "Dermatochalasis (HPO)" + }, + "HP:0002999": { + "id": "HP:0002999", + "label": "Patellar dislocation (HPO)" + }, + "HP:0010754": { + "id": "HP:0010754", + "label": "Abnormality of the temporomandibular joint (HPO)" + }, + "HP:0031364": { + "id": "HP:0031364", + "label": "Ecchymosis (HPO)" + }, + "HP:0000974": { + "id": "HP:0000974", + "label": "Hyperextensible skin (HPO)" + }, + "HP:0001030": { + "id": "HP:0001030", + "label": "Fragile skin (HPO)" + }, + "HP:0000481": { + "id": "HP:0000481", + "label": "Abnormal cornea morphology (HPO)" + }, + "HP:0003834": { + "id": "HP:0003834", + "label": "Shoulder dislocation (HPO)" + }, + "HP:0000938": { + "id": "HP:0000938", + "label": "Osteopenia (HPO)" + }, + "HP:0003010": { + "id": "HP:0003010", + "label": "Prolonged bleeding time (HPO)" + }, + "HP:0007495": { + "id": "HP:0007495", + "label": "Prematurely aged appearance (HPO)" + }, + "HP:0001763": { + "id": "HP:0001763", + "label": "Pes planus (HPO)" + }, + "HP:0010749": { + "id": "HP:0010749", + "label": "Blepharochalasis (HPO)" + }, + "HP:0002020": { + "id": "HP:0002020", + "label": "Gastroesophageal reflux (HPO)" + }, + "HP:0030009": { + "id": "HP:0030009", + "label": "Cervical insufficiency (HPO)" + }, + "HP:0000139": { + "id": "HP:0000139", + "label": "Uterine prolapse (HPO)" + }, + "HP:0002013": { + "id": "HP:0002013", + "label": "Vomiting (HPO)" + }, + "HP:0001386": { + "id": "HP:0001386", + "label": "Joint swelling (HPO)" + }, + "HP:0001622": { + "id": "HP:0001622", + "label": "Premature birth (HPO)" + }, + "HP:0002758": { + "id": "HP:0002758", + "label": "Osteoarthritis (HPO)" + }, + "HP:0001762": { + "id": "HP:0001762", + "label": "Talipes equinovarus (HPO)" + }, + "HP:0025509": { + "id": "HP:0025509", + "label": "Piezogenic pedal papules (HPO)" + }, + "HP:0002650": { + "id": "HP:0002650", + "label": "Scoliosis (HPO)" + }, + "HP:0001063": { + "id": "HP:0001063", + "label": "Acrocyanosis (HPO)" + }, + "HP:0002827": { + "id": "HP:0002827", + "label": "Hip dislocation (HPO)" + }, + "HP:0001027": { + "id": "HP:0001027", + "label": "Soft, doughy skin (HPO)" + }, + "HP:0025019": { + "id": "HP:0025019", + "label": "Arterial rupture (HPO)" + }, + "HP:0004947": { + "id": "HP:0004947", + "label": "Arteriovenous fistula (HPO)" + }, + "HP:0001278": { + "id": "HP:0001278", + "label": "Orthostatic hypotension (HPO)" + }, + "HP:0002036": { + "id": "HP:0002036", + "label": "Hiatus hernia (HPO)" }, - "MP:0006144": { - "id": "MP:0006144", - "label": "increased systemic arterial systolic blood pressure (MPO)" + "HP:0000015": { + "id": "HP:0000015", + "label": "Bladder diverticulum (HPO)" }, - "HP:0000093": { - "id": "HP:0000093", - "label": "Proteinuria (HPO)" + "HP:0002018": { + "id": "HP:0002018", + "label": "Nausea (HPO)" + }, + "HP:0001788": { + "id": "HP:0001788", + "label": "Premature rupture of membranes (HPO)" + }, + "HP:0001270": { + "id": "HP:0001270", + "label": "Motor delay (HPO)" } }, "subject_best_matches": { - "MP:0002169": { - "match_source": "MP:0002169", - "match_source_label": "no abnormal phenotype detected (MPO)", - "match_target": "MP:0006144", - "match_target_label": "increased systemic arterial systolic blood pressure (MPO)", - "score": 4.26719956102326, + "HP:0000035": { + "match_source": "HP:0000035", + "match_source_label": "Abnormal testis morphology (HPO)", + "match_target": "HP:0030009", + "match_target_label": "Cervical insufficiency (HPO)", + "score": 10.48204782739082, "match_subsumer": null, "match_subsumer_label": null, "similarity": { - "subject_id": "MP:0002169", + "subject_id": "HP:0000035", "subject_label": null, "subject_source": null, - "object_id": "MP:0006144", + "object_id": "HP:0030009", "object_label": null, "object_source": null, - "ancestor_id": "MP:0000001", + "ancestor_id": "HP:0000812", "ancestor_label": "", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, - "ancestor_information_content": 4.26719956102326, - "jaccard_similarity": 0.12962962962962962, + "ancestor_information_content": 10.48204782739082, + "jaccard_similarity": 0.27941176470588236, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.7437442427684151 + "phenodigm_score": 1.7113759029455595 } }, - "MP:0005367": { - "match_source": "MP:0005367", - "match_source_label": "renal/urinary system phenotype (MPO)", - "match_target": "HP:0000093", - "match_target_label": "Proteinuria (HPO)", - "score": 6.936744601801884, + "HP:0000135": { + "match_source": "HP:0000135", + "match_source_label": "Hypogonadism (HPO)", + "match_target": "HP:0030009", + "match_target_label": "Cervical insufficiency (HPO)", + "score": 9.248307728351065, "match_subsumer": null, "match_subsumer_label": null, "similarity": { - "subject_id": "MP:0005367", + "subject_id": "HP:0000135", "subject_label": null, "subject_source": null, - "object_id": "HP:0000093", + "object_id": "HP:0030009", "object_label": null, "object_source": null, - "ancestor_id": "UBERON:0001008", + "ancestor_id": "HP:0000078", "ancestor_label": "", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, - "ancestor_information_content": 6.936744601801884, - "jaccard_similarity": 0.18181818181818182, + "ancestor_information_content": 9.248307728351065, + "jaccard_similarity": 0.3670886075949367, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.123043316723227 + "phenodigm_score": 1.8425385766951758 } }, - "MP:0005389": { - "match_source": "MP:0005389", - "match_source_label": "reproductive system phenotype (MPO)", - "match_target": "MP:0006144", - "match_target_label": "increased systemic arterial systolic blood pressure (MPO)", - "score": 4.26719956102326, + "HP:0000144": { + "match_source": "HP:0000144", + "match_source_label": "Decreased fertility (HPO)", + "match_target": "HP:0030009", + "match_target_label": "Cervical insufficiency (HPO)", + "score": 9.248307728351065, "match_subsumer": null, "match_subsumer_label": null, "similarity": { - "subject_id": "MP:0005389", + "subject_id": "HP:0000144", "subject_label": null, "subject_source": null, - "object_id": "MP:0006144", + "object_id": "HP:0030009", "object_label": null, "object_source": null, - "ancestor_id": "MP:0000001", + "ancestor_id": "HP:0000078", "ancestor_label": "", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, - "ancestor_information_content": 4.26719956102326, - "jaccard_similarity": 0.2962962962962963, + "ancestor_information_content": 9.248307728351065, + "jaccard_similarity": 0.38235294117647056, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.124435603086443 + "phenodigm_score": 1.8804567692026617 } }, - "MP:0005391": { - "match_source": "MP:0005391", - "match_source_label": "vision/eye phenotype (MPO)", - "match_target": "MP:0006144", - "match_target_label": "increased systemic arterial systolic blood pressure (MPO)", - "score": 4.26719956102326, + "HP:0000275": { + "match_source": "HP:0000275", + "match_source_label": "Narrow face (HPO)", + 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"ancestor_information_content": 14.418232729793377, + "jaccard_similarity": 0.972972972972973, + "cosine_similarity": null, + "dice_similarity": null, + "phenodigm_score": 3.7454706999419027 + } + }, + "HP:0009763": { + "match_source": "HP:0009763", + "match_source_label": "Limb pain (HPO)", + "match_target": "HP:0003419", + "match_target_label": "Low back pain (HPO)", + "score": 12.074278328576016, + "match_subsumer": null, + "match_subsumer_label": null, + "similarity": { + "subject_id": "HP:0009763", + "subject_label": null, + "subject_source": null, + "object_id": "HP:0003419", + "object_label": null, + "object_source": null, + "ancestor_id": "HP:0012531", + "ancestor_label": "", + "ancestor_source": null, + "object_information_content": null, + "subject_information_content": null, + "ancestor_information_content": 12.074278328576016, + "jaccard_similarity": 0.5185185185185185, + "cosine_similarity": null, + "dice_similarity": null, + "phenodigm_score": 2.5021464607639357 + } + }, + "HP:0010749": { + "match_source": "HP:0010749", + "match_source_label": "Blepharochalasis (HPO)", + "match_target": "HP:0000275", + "match_target_label": "Narrow face (HPO)", + "score": 12.311317525876866, + "match_subsumer": null, + "match_subsumer_label": null, + "similarity": { + "subject_id": "HP:0010749", + "subject_label": null, + "subject_source": null, + "object_id": "HP:0000275", + "object_label": null, + "object_source": null, + "ancestor_id": "HP:0001999", + "ancestor_label": "", + "ancestor_source": null, + "object_information_content": null, + "subject_information_content": null, + "ancestor_information_content": 12.311317525876866, + "jaccard_similarity": 0.37735849056603776, + "cosine_similarity": null, + "dice_similarity": null, + "phenodigm_score": 2.1554072001466684 + } + }, + "HP:0010750": { + "match_source": "HP:0010750", + "match_source_label": "Dermatochalasis (HPO)", + "match_target": "HP:0000546", + "match_target_label": "Retinal degeneration (HPO)", + "score": 7.709281511796768, + "match_subsumer": null, + "match_subsumer_label": null, + "similarity": { + "subject_id": "HP:0010750", + "subject_label": null, + "subject_source": null, + "object_id": "HP:0000546", + "object_label": null, + "object_source": null, + "ancestor_id": "HP:0000315", + "ancestor_label": "", + "ancestor_source": null, + "object_information_content": null, + "subject_information_content": null, + "ancestor_information_content": 7.709281511796768, + "jaccard_similarity": 0.57, + "cosine_similarity": null, + "dice_similarity": null, + "phenodigm_score": 2.096256296764343 + } + }, + "HP:0010754": { + "match_source": "HP:0010754", + "match_source_label": "Abnormality of the temporomandibular joint (HPO)", + "match_target": "HP:0100649", + "match_target_label": "Neoplasm of the oral cavity (HPO)", + "score": 9.152888163272383, + "match_subsumer": null, + "match_subsumer_label": null, + "similarity": { + "subject_id": "HP:0010754", + "subject_label": null, + "subject_source": null, + "object_id": "HP:0100649", + "object_label": null, + "object_source": null, + "ancestor_id": "HP:0031816", + "ancestor_label": "", + "ancestor_source": null, + "object_information_content": null, + "subject_information_content": null, + "ancestor_information_content": 9.152888163272383, + "jaccard_similarity": 0.41353383458646614, + "cosine_similarity": null, + "dice_similarity": null, + "phenodigm_score": 1.9455150833902846 + } + }, + "HP:0012378": { + "match_source": "HP:0012378", + "match_source_label": "Fatigue (HPO)", + "match_target": "HP:0003419", + "match_target_label": "Low back pain (HPO)", + "score": 11.324256581584363, + "match_subsumer": null, + "match_subsumer_label": null, + "similarity": { + "subject_id": "HP:0012378", + "subject_label": null, + "subject_source": null, + "object_id": "HP:0003419", + "object_label": null, + "object_source": null, + "ancestor_id": "HP:0025142", + "ancestor_label": "", + "ancestor_source": null, + "object_information_content": null, + "subject_information_content": null, + "ancestor_information_content": 11.324256581584363, + "jaccard_similarity": 0.36, + "cosine_similarity": null, + "dice_similarity": null, + "phenodigm_score": 2.0190919665459446 + } + }, + "HP:0012450": { + "match_source": "HP:0012450", + "match_source_label": "Chronic constipation (HPO)", + "match_target": "HP:0002672", + "match_target_label": "Gastrointestinal carcinoma (HPO)", + "score": 7.826350815132431, + "match_subsumer": null, + "match_subsumer_label": null, + "similarity": { + "subject_id": "HP:0012450", + "subject_label": null, + "subject_source": null, + "object_id": "HP:0002672", + "object_label": null, + "object_source": null, + "ancestor_id": "HP:0025031", + "ancestor_label": "", + "ancestor_source": null, + "object_information_content": null, + "subject_information_content": null, + "ancestor_information_content": 7.826350815132431, + "jaccard_similarity": 0.5106382978723404, + "cosine_similarity": null, + "dice_similarity": null, + "phenodigm_score": 1.9991084159672352 + } + }, + "HP:0025014": { + "match_source": "HP:0025014", + "match_source_label": "Subcutaneous spheroids (HPO)", + "match_target": "HP:0200042", + "match_target_label": "Skin ulcer (HPO)", + "score": 10.72635502515571, + "match_subsumer": null, + "match_subsumer_label": null, + "similarity": { + "subject_id": "HP:0025014", + "subject_label": null, + "subject_source": null, + "object_id": "HP:0200042", + "object_label": null, + "object_source": null, + "ancestor_id": "HP:0011355", + "ancestor_label": "", + "ancestor_source": null, + "object_information_content": null, + "subject_information_content": null, + "ancestor_information_content": 10.72635502515571, + "jaccard_similarity": 0.8974358974358975, + "cosine_similarity": null, + "dice_similarity": null, + "phenodigm_score": 3.102614389223492 + } + }, + "HP:0025019": { + "match_source": "HP:0025019", + "match_source_label": "Arterial rupture (HPO)", + "match_target": "HP:0001635", + "match_target_label": "Congestive heart failure (HPO)", + "score": 9.47121402147955, + "match_subsumer": null, + "match_subsumer_label": null, + "similarity": { + "subject_id": "HP:0025019", + "subject_label": null, + "subject_source": null, + "object_id": "HP:0001635", + "object_label": null, + "object_source": null, + "ancestor_id": "HP:0011025", + "ancestor_label": "", + "ancestor_source": null, + "object_information_content": null, + "subject_information_content": null, + "ancestor_information_content": 9.47121402147955, + "jaccard_similarity": 0.42028985507246375, + "cosine_similarity": null, + "dice_similarity": null, + "phenodigm_score": 1.995157930703213 + } + }, + "HP:0025509": { + "match_source": "HP:0025509", + "match_source_label": "Piezogenic pedal papules (HPO)", + "match_target": "HP:0008065", + "match_target_label": "Aplasia/Hypoplasia of the skin (HPO)", + "score": 10.72635502515571, + "match_subsumer": null, + "match_subsumer_label": null, + "similarity": { + "subject_id": "HP:0025509", + "subject_label": null, + "subject_source": null, + "object_id": "HP:0008065", + "object_label": null, + "object_source": null, + "ancestor_id": "HP:0011355", + "ancestor_label": "", + "ancestor_source": null, + "object_information_content": null, + "subject_information_content": null, + "ancestor_information_content": 10.72635502515571, + "jaccard_similarity": 0.8536585365853658, + "cosine_similarity": null, + "dice_similarity": null, + "phenodigm_score": 3.025994800667957 + } + }, + "HP:0030009": { + "match_source": "HP:0030009", + "match_source_label": "Cervical insufficiency (HPO)", + "match_target": "HP:0100615", + "match_target_label": "Ovarian neoplasm (HPO)", + "score": 11.350488123157543, "match_subsumer": null, "match_subsumer_label": null, "similarity": { - "subject_id": "HP:0000093", + "subject_id": "HP:0030009", "subject_label": null, "subject_source": null, - "object_id": "MP:0005367", + "object_id": "HP:0100615", "object_label": null, "object_source": null, - "ancestor_id": "UBERON:0001008", + "ancestor_id": "HP:0000008", "ancestor_label": "", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, - "ancestor_information_content": 6.936744601801884, - "jaccard_similarity": 0.18181818181818182, + "ancestor_information_content": 11.350488123157543, + "jaccard_similarity": 0.6301369863013698, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.123043316723227 + "phenodigm_score": 2.674390094764783 } }, - "HP:0004325": { - "match_source": "HP:0004325", - "match_source_label": "Decreased body weight (HPO)", - "match_target": "MP:0005389", - "match_target_label": "reproductive system phenotype (MPO)", - "score": 2.2728188647181566, + "HP:0031364": { + "match_source": "HP:0031364", + "match_source_label": "Ecchymosis (HPO)", + "match_target": "HP:0007618", + "match_target_label": "Subcutaneous calcification (HPO)", + "score": 14.533709947213314, "match_subsumer": null, "match_subsumer_label": null, "similarity": { - "subject_id": "HP:0004325", + "subject_id": "HP:0031364", "subject_label": null, "subject_source": null, - "object_id": "MP:0005389", + "object_id": "HP:0007618", "object_label": null, "object_source": null, - "ancestor_id": "UBERON:0000468", + "ancestor_id": "UBERON:0011818", "ancestor_label": "", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, - "ancestor_information_content": 2.2728188647181566, - "jaccard_similarity": 0.3333333333333333, + "ancestor_information_content": 14.533709947213314, + "jaccard_similarity": 0.4222222222222222, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8704058181327751 + "phenodigm_score": 2.47718697539076 } }, - "MP:0006144": { - "match_source": "MP:0006144", - "match_source_label": "increased systemic arterial systolic blood pressure (MPO)", - "match_target": "MP:0002169", - "match_target_label": "no abnormal phenotype detected (MPO)", - "score": 4.26719956102326, + "HP:0031653": { + "match_source": "HP:0031653", + "match_source_label": "Abnormal heart valve physiology (HPO)", + "match_target": "HP:0001635", + "match_target_label": "Congestive heart failure (HPO)", + "score": 9.47121402147955, "match_subsumer": null, "match_subsumer_label": null, "similarity": { - "subject_id": "MP:0006144", + "subject_id": "HP:0031653", "subject_label": null, "subject_source": null, - "object_id": "MP:0002169", + "object_id": "HP:0001635", "object_label": null, "object_source": null, - "ancestor_id": "MP:0000001", + "ancestor_id": "HP:0011025", "ancestor_label": "", "ancestor_source": null, "object_information_content": null, "subject_information_content": null, - "ancestor_information_content": 4.26719956102326, - "jaccard_similarity": 0.12962962962962962, + "ancestor_information_content": 9.47121402147955, + "jaccard_similarity": 0.3972602739726027, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.7437442427684151 + "phenodigm_score": 1.9397260314348834 } } }, - "average_score": 4.646681455846709, - "best_score": 6.936744601801884, + "average_score": 9.923734289544301, + "best_score": 17.11867244793447, "metric": "ancestor_information_content" } diff --git a/frontend/index.html b/frontend/index.html index 2f7332d36..d081eb4dd 100644 --- a/frontend/index.html +++ b/frontend/index.html @@ -1,4 +1,4 @@ - + @@ -42,15 +42,25 @@ - - + + diff --git a/frontend/package.json b/frontend/package.json index e2cb03535..f213134b2 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -25,6 +25,7 @@ "@vueuse/core": "^10.4.1", "apexcharts": "^3.42.0", "body-scroll-lock": "^4.0.0-beta.0", + "dom-to-image": "^2.6.0", "lodash": "^4.17.21", "micromark": "^4.0.0", "normalize.css": "^8.0.1", @@ -44,6 +45,7 @@ "@rushstack/eslint-patch": "^1.3.3", "@tsconfig/node18": "^18.2.1", "@types/body-scroll-lock": "^3.1.0", + "@types/dom-to-image": "^2.6.5", "@types/jsdom": "^21.1.2", "@types/lodash": "^4.14.198", "@types/node": "20", diff --git a/frontend/src/api/phenotype-explorer.ts b/frontend/src/api/phenotype-explorer.ts index e7e55aed1..608647551 100644 --- a/frontend/src/api/phenotype-explorer.ts +++ b/frontend/src/api/phenotype-explorer.ts @@ -1,6 +1,7 @@ import { pick } from "lodash"; import type { AssociationResults, + TermPairwiseSimilarity, TermSetPairwiseSimilarity, } from "@/api/model"; import type { Options, OptionsFunc } from "@/components/AppSelectTags.vue"; @@ -122,38 +123,61 @@ export const compareSetToSet = async ( ); summary.sort((a, b) => b.score - a.score); - /** get detailed phenogrid info */ - const cols = Object.values(response.object_termset || {}); - const rows = Object.values(response.subject_termset || {}); - - /** get detailed phenogrid info */ - const cells = cols.map((col) => - rows.map((row) => { - const match = Object.values(response.subject_best_matches || {}).find( - ({ match_source, match_target }) => - match_source === row.id && match_target === col.id, - ); + /** turn objects into array of cols */ + const cols = Object.values(response.object_termset || {}).map((col) => ({ + ...col, + total: 0, + })); + /** turn subjects into array of cols */ + const rows = Object.values(response.subject_termset || {}).map((row) => ({ + ...row, + total: 0, + })); - return { - score: match?.score || 0, + /** make map of col/row id to cells */ + const cells: { + [key: string]: { + score: number; + strength: number; + simInfo: Partial; + }; + } = {}; + + /** get subject matches */ + const matches = Object.values(response.subject_best_matches || {}); + + for (const col of cols) { + for (const row of rows) { + /** find match corresponding to col/row id */ + const { score = 0, similarity = {} } = + matches.find( + ({ match_source, match_target }) => + match_source === row.id && match_target === col.id, + ) || {}; + + /** sum up row and col scores */ + col.total += score; + row.total += score; + + /** assign cell */ + cells[col.id + row.id] = { + score: score || 0, strength: 0, - simInfo: pick(match?.similarity, [ + simInfo: pick(similarity, [ "ancestor_id", "jaccard_similarity", "phenodigm_score", ]), }; - }), - ); + } + } - /** get range of cell scores */ - const scores = cells.map((row) => row.map((col) => col.score)).flat(); + /** normalize cell scores to 0-1 */ + const scores = Object.values(cells).map((value) => value.score); const min = Math.min(...scores); const max = Math.max(...scores); - - /** normalize cell scores to 0-1 */ - cells.forEach((row) => - row.forEach((col) => (col.strength = (col.score - min) / (max - min))), + Object.values(cells).forEach( + (value) => (value.strength = (value.score - min) / (max - min)), ); return { summary, phenogrid: { cols, rows, cells } }; diff --git a/frontend/src/components/AppCheckbox.vue b/frontend/src/components/AppCheckbox.vue index 244e0f1ea..7bdd04dba 100644 --- a/frontend/src/components/AppCheckbox.vue +++ b/frontend/src/components/AppCheckbox.vue @@ -46,7 +46,7 @@ function onChange(event: Event) { display: inline-flex; position: relative; align-items: center; - padding: 10px; + padding: 2px 8px; gap: 10px; border-radius: $rounded; cursor: pointer; diff --git a/frontend/src/components/AppFlex.vue b/frontend/src/components/AppFlex.vue index b4fe4d89e..bbda736bd 100644 --- a/frontend/src/components/AppFlex.vue +++ b/frontend/src/components/AppFlex.vue @@ -6,6 +6,7 @@ diff --git a/frontend/src/pages/explore/TabPhenotypeExplorer.vue b/frontend/src/pages/explore/TabPhenotypeExplorer.vue index 76d5e2688..1493f5421 100644 --- a/frontend/src/pages/explore/TabPhenotypeExplorer.vue +++ b/frontend/src/pages/explore/TabPhenotypeExplorer.vue @@ -105,7 +105,7 @@ -