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test_rtx.py
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test_rtx.py
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x= { # this edge was extracted to make diff results interesting.
"relation": "RO:0002200",
"target_id": "MONDO:0018874",
"edge_source": "biolink.phenotype_get_disease",
"publications": [
"PMID:16039247",
"PMID:6591864",
"PMID:7049597",
"PMID:8241983",
"PMID:8404130"
],
"id": "1820642",
"predicate_id": "RO:0002200",
"source_database": "BioLink", #diff "biolink",
"source_id": "HP:0002105",
"type": "has_phenotype",
"ctime": 1543707244.3735547,
"relation_label": "has phenotype",
"weight": 0.8093606487732907
}#,
answer = {
"question_graph": {
"edges": [
{
"id": "e0",
"source_id": "n1",
"target_id": "n2"
},
{
"id": "e1",
"source_id": "n2",
"target_id": "n3"
}
],
"nodes": [
{
"id": "n1",
"type": "phenotypic_feature",
"curie": "HP:0002105"
},
{
"id": "n2",
"type": "disease"
},
{
"id": "n3",
"type": "gene"
}
]
},
"knowledge_graph": {
"nodes": [
{
"equivalent_identifiers": [
"MEDDRA:10005806",
"MEDDRA:10011234",
"HP:0002105",
"MEDDRA:10019523",
"MEDDRA:10018964",
"UMLS:C0019079",
"MEDDRA:10041804"
],
"name": "Hemoptysis",
"id": "HP:0002105",
"type": "phenotypic_feature",
"omnicorp_article_count": 10902
},
{
"name": "acute myeloid leukemia",
"id": "MONDO:0018874",
"equivalent_identifiers": [
"MEDDRA:10000884",
"MEDDRA:10024291",
"MEDDRA:10000886",
"MEDDRA:10051003",
"MEDDRA:10054296",
"MEDDRA:10028552",
"DOID:9119",
"MEDDRA:10024346",
"MESH:D015470",
"UMLS:C0023467",
"MEDDRA:10029551",
"MEDDRA:10060394",
"MEDDRA:10000878",
"MEDDRA:10060354",
"ORPHANET:519",
"MEDDRA:10060557",
"MONDO:0018874",
"MEDDRA:10029549",
"MEDDRA:10060553",
"MEDDRA:10028557",
"OMIM:601626",
"UMLS:C1879321",
"MEDDRA:10000801",
"MEDDRA:10000880",
"MEDDRA:10001941"
],
"type": "disease",
"rare disease": True,
"syndromic disease": True,
"omnicorp_article_count": 40008
},
{
"name": "tuberculosis",
"id": "MONDO:0018076",
"equivalent_identifiers": [
"MEDDRA:10044755",
"MEDDRA:10071157",
"MONDO:0018076",
"MEDDRA:10044766",
"DOID:399",
"MEDDRA:10021868",
"MEDDRA:10021870",
"MEDDRA:10044756",
"UMLS:C0151332",
"UMLS:C0041296",
"ORPHANET:3389",
"MEDDRA:10043148",
"MESH:D014376"
],
"transmissible disease": True,
"type": "disease",
"rare disease": True,
"omnicorp_article_count": 210883
},
{
"equivalent_identifiers": [
"MESH:D002289",
"UMLS:C0007131",
"MEDDRA:10061873",
"MONDO:0005233",
"DOID:3908",
"MEDDRA:10029514"
],
"name": "non-small cell lung carcinoma (disease)",
"id": "MONDO:0005233",
"type": "disease",
"omnicorp_article_count": 44014
},
{
"name": "hepatocellular carcinoma",
"id": "MONDO:0007256",
"equivalent_identifiers": [
"MEDDRA:10073071",
"DOID:686",
"MEDDRA:10007416",
"OMIM:114550",
"UMLS:C2239176",
"ORPHANET:88673",
"MEDDRA:10019838",
"DOID:684",
"MEDDRA:10049010",
"MEDDRA:10048491",
"MONDO:0007256",
"UMLS:C1867955",
"UMLS:C1862761",
"MEDDRA:10024658",
"MESH:D006528"
],
"type": "disease",
"rare disease": True,
"omnicorp_article_count": 105682
},
{
"name": "cystic fibrosis",
"monogenic disease": True,
"autosomal genetic disease": True,
"id": "MONDO:0009061",
"equivalent_identifiers": [
"UMLS:C0010674",
"MEDDRA:10011762",
"MEDDRA:10011764",
"DOID:1485",
"OMIM:219700",
"MEDDRA:10028141",
"MESH:D003550",
"ORPHANET:586",
"MONDO:0009061"
],
"type": "disease",
"rare disease": True,
"autosomal recessive disease": True,
"omnicorp_article_count": 50748
},
{
"name": "pulmonary hypertension",
"id": "MONDO:0005149",
"equivalent_identifiers": [
"UMLS:C3203102",
"MEDDRA:10036727",
"UMLS:C2973725",
"UMLS:C0152171",
"MONDO:0005149",
"MEDDRA:10020787",
"MONDO:0015924",
"MESH:D006976",
"ORPHANET:182090",
"MEDDRA:10037403",
"ORPHANET:275766",
"MEDDRA:10065151",
"MEDDRA:10037401",
"MESH:D065627",
"MESH:C536282",
"UMLS:C0020542",
"MONDO:0017147",
"DOID:6432",
"MEDDRA:10064911",
"UMLS:CN202574",
"UMLS:CN200519",
"MEDDRA:10037400",
"MEDDRA:10037405"
],
"type": "disease",
"rare disease": True,
"omnicorp_article_count": 26734
},
{
"name": "amyloidosis (disease)",
"systemic or rheumatic disease": True,
"nutritional or metabolic disease": True,
"id": "MONDO:0019065",
"equivalent_identifiers": [
"MEDDRA:10002023",
"UMLS:C0002726",
"MEDDRA:10002024",
"MEDDRA:10002021",
"MESH:D000686",
"DOID:9120",
"ORPHANET:69",
"MONDO:0019065",
"MEDDRA:10002022"
],
"type": "disease",
"omnicorp_article_count": 77839
},
{
"name": "influenza",
"id": "MONDO:0005812",
"equivalent_identifiers": [
"MESH:D007251",
"DOID:8469",
"MONDO:0005812"
],
"transmissible disease": True,
"type": "disease",
"omnicorp_article_count": 78620
},
{
"id": "MONDO:0005279",
"equivalent_identifiers": [
"DOID:9477",
"MEDDRA:10014521",
"MEDDRA:10037380",
"MEDDRA:10050071",
"MEDDRA:10034191",
"MONDO:0005279",
"MEDDRA:10014537",
"MESH:D011655",
"MEDDRA:10037377",
"UMLS:C0034065"
],
"name": "pulmonary embolism (disease)",
"type": "disease",
"omnicorp_article_count": 48125
},
{
"equivalent_identifiers": [
"OMIM:608437",
"OMIM:613145",
"OMIM:609903",
"OMIM:612253",
"UMLS:C1835309",
"UMLS:C1835308",
"OMIM:610927",
"OMIM:605480",
"OMIM:612254",
"OMIM:601744",
"OMIM:152700",
"OMIM:605218",
"UMLS:C0242380",
"OMIM:609939",
"MeSH:D008180",
"Orphanet:536",
"UMLS:C0024141",
"OMIM:610065",
"OMIM:612378",
"OMIM:610066",
"OMIM:300809",
"MONDO:0007915",
"EFO:0002690",
"OMIM:614420",
"UMLS:C2895176",
"Orphanet:93552",
"DOID:9074",
"OMIM:612251"
],
"name": "systemic lupus erythematosus (disease)",
"id": "MONDO:0007915",
"type": "disease",
"omnicorp_article_count": 62089
},
{
"id": "MONDO:0002076",
"name": "pneumothorax (disease)",
"equivalent_identifiers": [
"MEDDRA:10035759",
"DOID:1673",
"MESH:D011030",
"MONDO:0002076",
"MEDDRA:10035763",
"MEDDRA:10035762",
"UMLS:C0149781",
"UMLS:C0032326"
],
"type": "disease",
"omnicorp_article_count": 23805
},
{
"id": "MONDO:0004492",
"name": "mediastinitis",
"equivalent_identifiers": [
"UMLS:C0025064",
"MEDDRA:10027082",
"DOID:819",
"MESH:D008480",
"MONDO:0004492"
],
"type": "disease",
"omnicorp_article_count": 4403
},
{
"id": "MONDO:0004670",
"name": "lupus erythematosus",
"equivalent_identifiers": [
"MEDDRA:10025134",
"UMLS:C0409974",
"DOID:8857",
"MEDDRA:10025131",
"MONDO:0004670"
],
"type": "disease",
"omnicorp_article_count": 29831
},
{
"name": "sarcoidosis",
"systemic or rheumatic disease": True,
"nutritional or metabolic disease": True,
"id": "MONDO:0019338",
"equivalent_identifiers": [
"DOID:13402",
"MONDO:0005764",
"MONDO:0006804",
"UMLS:C0036202",
"DOID:626",
"MedDRA:10039486",
"OMIM:612387",
"MONDO:0003832",
"MONDO:0006611",
"UMLS:C0036204",
"UMLS:C0036203",
"UMLS:C0036205",
"MONDO:0001708",
"Orphanet:797",
"DOID:11335",
"DOID:13406",
"UMLS:C0477322",
"OMIM:181000",
"OMIM:612388",
"MONDO:0019338",
"UMLS:C0348826",
"MeSH:D012507"
],
"type": "disease",
"rare disease": True,
"syndromic disease": True,
"omnicorp_article_count": 28946
},
{
"id": "MONDO:0005275",
"name": "lung disease",
"equivalent_identifiers": [
"MEDDRA:10013259",
"MONDO:0005275",
"MESH:D008171",
"MEDDRA:10025083",
"MEDDRA:10051054",
"UMLS:C0024115",
"MEDDRA:10037373",
"MEDDRA:10013235",
"MEDDRA:10048522",
"MEDDRA:10049490",
"MEDDRA:10025082",
"DOID:850",
"UMLS:C4021760"
],
"type": "disease",
"omnicorp_article_count": 115966
},
{
"congenital abnormality": True,
"name": "patent ductus arteriosus",
"id": "MONDO:0011827",
"equivalent_identifiers": [
"DOID:13832",
"UMLS:C0013274",
"MONDO:0011827",
"MESH:D004374"
],
"type": "disease",
"rare disease": True,
"omnicorp_article_count": 6974
},
{
"name": "lung lymphangioleiomyomatosis",
"id": "MONDO:0006277",
"equivalent_identifiers": [
"OMIM:606690",
"DOID:3319",
"ORPHANET:538",
"MESH:D018192",
"UMLS:C0751674",
"UMLS:C0238399",
"MEDDRA:10049462",
"MEDDRA:10049459",
"MONDO:0006277"
],
"type": "disease",
"rare disease": True,
"omnicorp_article_count": 327
},
{
"name": "glomerulonephritis (disease)",
"id": "MONDO:0002462",
"equivalent_identifiers": [
"MONDO:0002462",
"MEDDRA:10029143",
"MEDDRA:10018375",
"UMLS:C0017658",
"MEDDRA:10018364",
"DOID:2921",
"MESH:D005921"
],
"type": "disease",
"rare disease": True,
"omnicorp_article_count": 40524
},
{
"congenital abnormality": True,
"name": "hereditary hemorrhagic telangiectasia",
"monogenic disease": True,
"autosomal genetic disease": True,
"autosomal dominant disease": True,
"systemic or rheumatic disease": True,
"id": "MONDO:0019180",
"equivalent_identifiers": [
"MEDDRA:10019883",
"MEDDRA:10019887",
"MONDO:0019180",
"UMLS:C0039445",
"MEDDRA:10031132",
"MESH:D013683",
"MEDDRA:10020023",
"ORPHANET:774",
"DOID:1270",
"MEDDRA:10038554"
],
"type": "disease",
"rare disease": True,
"omnicorp_article_count": 2660
},
{
"id": "MONDO:0002363",
"name": "papilloma",
"equivalent_identifiers": [
"MEDDRA:10033715",
"MONDO:0002363",
"MEDDRA:10033713",
"MESH:D010212",
"UMLS:C0030354",
"MEDDRA:10033725",
"DOID:2615"
],
"type": "disease",
"omnicorp_article_count": 19600
},
{
"id": "MONDO:0003781",
"name": "bronchitis",
"equivalent_identifiers": [
"UMLS:C0006277",
"MEDDRA:10006462",
"MEDDRA:10066672",
"MEDDRA:10006451",
"MONDO:0003781",
"MEDDRA:10006461",
"MESH:D001991",
"MEDDRA:10006452",
"UMLS:C0149514",
"MEDDRA:10000687",
"MEDDRA:10006453",
"DOID:6132"
],
"type": "disease",
"omnicorp_article_count": 30298
},
{
"name": "antiphospholipid syndrome",
"id": "MONDO:0007140",
"equivalent_identifiers": [
"MONDO:0007140",
"MEDDRA:10002817",
"DOID:2988",
"UMLS:C0085278",
"OMIM:107320",
"MESH:D016736"
],
"type": "disease",
"syndromic disease": True,
"omnicorp_article_count": 9233
},
{
"id": "MONDO:0001243",
"equivalent_identifiers": [
"MEDDRA:10013441",
"MESH:D004211",
"UMLS:C0012739",
"MONDO:0001243",
"MEDDRA:10012126",
"DOID:11247",
"MEDDRA:10010785",
"MEDDRA:10012769",
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