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Lookup for "diabetes type ..." takes more than a minute, and gives a wrong result #140

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vemonet opened this issue Jan 18, 2024 · 1 comment
Open

Lookup for "diabetes type ..." takes more than a minute, and gives a wrong result #140

vemonet opened this issue Jan 18, 2024 · 1 comment
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NameRes November ...

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@vemonet
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vemonet commented Jan 18, 2024 •
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The API takes more than 1 minute when searching for diabetes type 2, and the results give "Diabetes type" first, then "Diabetes type 2" second (we face the same problem with diabetes type 1, or if we shuffle the order of the words, e.g. type 2 diabetes)

Also note that the synonyms of diabetes type 2 (MONDO:0005148) are quite overloaded: a lot of repetitions of the same terms just with a change in the case of the first letter of a word. Maybe this could be the cause of the slow response?

Note that searching for diabetes or diabetes type respond in less than 2s

[
  {
    "curie": "UMLS:C1320657",
    "label": "Diabetes type",
    "synonyms": [
      "diabete type",
      "type diabetes",
      "diabetes type",
      "Diabetes type",
      "diabetes types",
      "Diabetes type (observable entity)"
    ],
    "types": [
      "biolink:PhenotypicFeature",
      "biolink:DiseaseOrPhenotypicFeature",
      "biolink:BiologicalEntity",
      "biolink:ThingWithTaxon",
      "biolink:NamedThing",
      "biolink:Entity"
    ],
    "score": 101.836205
  },
  {
    "curie": "MONDO:0005148",
    "label": "type 2 diabetes mellitus",
    "synonyms": [
      "MOD",
      "T2D",
      "AODM",
      "aodm",
      "MODY",
      "MVCD5",
      "niddm",
      "NIDDM",
      "NCDMM",
      "diabetes",
      "diabete type 2",
      "Type 2 Diabetes",
      "diabetes type 2",
      "Diabetes;Type 2",
      "NIDDM; diabetes",
      "type 2 diabetes",
      "Diabetes Type 2",
      "diabetes; NIDDM",
      "Type 2 diabetes",
      "Type II Diabetes",
      "diabetes type ii",
      "type II diabetes",
      "diabetes, type 2",
      "Type II diabetes",
      "Diabetes, Type 2",
      "diabetes, type ii",
      "type II; diabetes",
      "diabetes; type II",
      "Diabetes, Type II",
      "insulin resistance",
      "late onset diabetes",
      "Diabetes;adult onset",
      "nonketotic; diabetes",
      "Adult Onset Diabetes",
      "diabetes; nonketotic",
      "adult onset diabetes",
      "adult-onset diabetes",
      "Adult-Onset Diabetes",
      "DIABETES, ADULT ONSET",
      "adult-onset; diabetes",
      "diabetes; adult-onset",
      "MATURITY-ONSET DIABETES",
      "maturity-onset diabetes",
      "Maturity Onset Diabetes",
      "NIDDM diabetes mellitus",
      "Maturity onset diabetes",
      "maturity onset diabetes",
      "Maturity-Onset Diabetes",
      "Type 2 Diabetes Mellitus",
      "type 2 diabetes mellitus",
      "Stable Diabetes Mellitus",
      "diabetes mellitis type 2",
      "maturity-onset; diabetes",
      "Diabetes, Maturity-Onset",
      "diabetes; maturity-onset",
      "Type 2 diabetes mellitus",
      "TYPE 2 DIABETES MELLITUS",
      "Diabetes mellitus type 2",
      "DIABETES, MATURITY ONSET",
      "diabetes mellitus type 2",
      "diabetes mellitus type ii",
      "Diabetes mellitus Type II",
      "diabetes mellitus, type 2",
      "Diabetes mellitus (NIDDM)",
      "DIABETES MELLITUS, TYPE 2",
      "type ii diabetes mellitus",
      "type II diabetes mellitus",
      "Diabetes mellitus type II",
      "Type II Diabetes Mellitus",
      "Diabetes Mellitus, Type 2",
      "Type II diabetes mellitus",
      "Diabetes mellitus, Type 2",
      "Diabetes Mellitus, Stable",
      "diabetes mellitis type II",
      "Diabetes mellitus, type 2",
      "Diabetes Mellitus, Type II",
      "diabetes mellitus, type II",
      "Diabetes mellitus, type II",
      "DIABETES MELLITUS, TYPE II",
      "ketosis resistant diabetes",
      "Diabetes;non insulin depend",
      "DIABETES, KETOSIS RESISTANT",
      "Slow-Onset Diabetes Mellitus",
      "Diabetes Mellitus, Slow-Onset",
      "Noninsulin Dependent Diabetes",
      "ADULT ONSET DIABETES MELLITUS",
      "Noninsulin-dependent diabetes",
      "Diabetes Mellitus, Slow Onset",
      "adult onset diabetes mellitus",
      "noninsulin dependent diabetes",
      "Adult-Onset Diabetes Mellitus",
      "Non-insulin-dependent diabetes",
      "non-insulin dependent diabetes",
      "Diabetes Mellitus, Adult Onset",
      "Diabetes Mellitus, Adult-Onset",
      "Non-insulin dependent diabetes",
      "Non-Insulin Dependent Diabetes",
      "Diabetes non-insulin dependent",
      "non insulin dependent diabetes",
      "T2DM - type 2 diabetes mellitus",
      "DIABETES MELLITUS (ADULT ONSET)",
      "non-insulin-dependent; diabetes",
      "T2DM - diabetes mellitus type 2",
      "T2DM - Type 2 Diabetes mellitus",
      "diabetes; non-insulin-dependent",
      "Diabetes mellitus - adult onset",
      "Maturity onset diabetes mellitus",
      "Maturity-Onset Diabetes Mellitus",
      "DIABETES MELLITUS NOS LATE ONSET",
      "Maturity Onset Diabetes Mellitus",
      "Diabetes mellitus maturity onset",
      "Diabetes Mellitus, Maturity-Onset",
      "insulin resistance susceptibility",
      "Diabetes Mellitus, Maturity Onset",
      "DIABETES MELLITUS NON INSULIN-DEP",
      "obsolete_type II diabetes mellitus",
      "PON1 ENZYME ACTIVITY, VARIATION IN",
      "insulin resistance, severe, digenic",
      "Diabetes mellitus, adult onset type",
      "Ketosis-Resistant Diabetes Mellitus",
      "Diabetes mellitus type 2 (disorder)",
      "Diabetes Mellitus, Ketosis-Resistant",
      "Diabetes Mellitus, Ketosis Resistant",
      "Type 2 diabetes mellitus (diagnosis)",
      "insulin resistance, susceptibility to",
      "INSULIN RESISTANCE, SUSCEPTIBILITY TO",
      "Noninsulin-Dependent Diabetes Mellitus",
      "noninsulin-dependent diabetes mellitus",
      "noninsulin dependent diabetes mellitus",
      "Noninsulin dependent diabetes mellitus",
      "Noninsulin-dependent diabetes mellitus",
      "NONINSULIN-DEPENDENT DIABETES MELLITUS",
      "Noninsulin Dependent Diabetes Mellitus",
      "Non-insulin dependent diabetes mellitus",
      "Diabetes mellitus non-insulin-dependent",
      "Non-Insulin Dependent Diabetes Mellitus",
      "Non-Insulin-Dependent Diabetes Mellitus",
      "Diabetes Mellitus, Noninsulin-Dependent",
      "Non-insulin-dependent diabetes mellitus",
      "Diabetes Mellitus, Noninsulin Dependent",
      "non-insulin dependent diabetes mellitus",
      "Diabetes mellitus, noninsulin-dependent",
      "non-insulin-dependent diabetes mellitus",
      "DIABETES MELLITUS NON INSULIN DEPENDENT",
      "diabetes mellitus, noninsulin-dependent",
      "DIABETES MELLITUS, NONINSULIN-DEPENDENT",
      "RETINOPATHY, DIABETIC, SUSCEPTIBILITY TO",
      "Diabetes Mellitus, Non Insulin Dependent",
      "DIABETES MELLITUS, NON-INSULIN DEPENDENT",
      "Diabetes Mellitus, Non-Insulin-Dependent",
      "diabetes mellitus, noninsulin-dependent, 2",
      "CORONARY ARTERY DISEASE, SUSCEPTIBILITY TO",
      "CORONARY ARTERY SPASM 2, SUSCEPTIBILITY TO",
      "type 2 diabetes mellitus, susceptibility to",
      "ORGANOPHOSPHATE POISONING, SUSCEPTIBILITY TO",
      "diabetes mellitus, type 2, susceptibility to",
      "TYPE 2 DIABETES MELLITUS, PROTECTION AGAINST",
      "DIABETES MELLITUS, TYPE 2, PROTECTION AGAINST",
      "insulin resistance susceptibility (diagnosis)",
      "diabetes mellitus, type 2, protection against",
      "diabetes mellitus, type II, susceptibility to",
      "type 2 diabetes mellitus non-insulin dependent",
      "Type 2 Diabetes Mellitus Non-Insulin Dependent",
      "NIDDM - Non-insulin dependent diabetes mellitus",
      "diabetes mellitus, noninsulin-dependent, late onset",
      "diabetes mellitus, noninsulin-dependent, association with",
      "diabetes mellitus, noninsulin-dependent, susceptibility to",
      "diabetes mellitus, non-insulin-dependent, susceptibility to",
      "hypertension, insulin resistance-related, susceptibility to",
      "MICROVASCULAR COMPLICATIONS OF DIABETES, SUSCEPTIBILITY TO, 5",
      "MICROVASCULAR COMPLICATIONS OF DIABETES, SUSCEPTIBILITY TO, 5 (finding)"
    ],
    "types": [
      "biolink:Disease",
      "biolink:DiseaseOrPhenotypicFeature",
      "biolink:BiologicalEntity",
      "biolink:ThingWithTaxon",
      "biolink:NamedThing",
      "biolink:Entity"
    ],
    "score": 23.155197
  },
@vemonet vemonet changed the title Lookup for "diabetes type ..." takes more than a minute Lookup for "diabetes type ..." takes more than a minute and give wrong result Jan 18, 2024
@vemonet vemonet changed the title Lookup for "diabetes type ..." takes more than a minute and give wrong result Lookup for "diabetes type ..." takes more than a minute, and gives a wrong result Jan 18, 2024
@vemonet
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vemonet commented Jan 19, 2024

Another note related to diabetes: there seems to be some "diabetes type 2" as synonyms of "maturity-onset diabetes of the young type 1"

I think it's probably more related to Babel though, should I open an issue on the Babel repo?

{
    "curie": "MONDO:0007452",
    "label": "maturity-onset diabetes of the young type 1",
    "synonyms": [
      "MODY1",
      "MODY type 1",
      "MODY, type 1",
      "MODY, type I",
      "MODY, Type 1",
      "MODY, TYPE 1",
      "MODY HNF4A related",
      "Diabetes Mellitus Type 2",
      "diabetes mellitus type 2",

@gaurav gaurav added this to the NameRes May 2024 milestone May 18, 2024
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