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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.

Term:Urinary Calculi
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Accession:DOID:9003311 term browser browse the term
Definition:Low-density crystals or stones in any part of the URINARY TRACT. Their chemical compositions often include CALCIUM OXALATE, magnesium ammonium phosphate (struvite), CYSTINE, or URIC ACID.
Synonyms:exact_synonym: Urinary Calculus;   Urinary Stone;   Urinary Stones;   Urinary Tract Stone;   Urinary Tract Stones
 primary_id: MESH:D014545



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Urinary Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Add3 adducin 3 ISO RGD PMID:15329129 RGD:2317717 NCBI chr19:53,128,874...53,235,518
Ensembl chr19:53,128,874...53,235,830
JBrowse link
G F2 coagulation factor II ISO RGD PMID:22494008 RGD:6893519 NCBI chr 2:91,442,742...91,466,799
Ensembl chr 2:91,455,665...91,466,759
JBrowse link
G Il1rn interleukin 1 receptor antagonist susceptibility ISO DNA:repeats, haplotype:intron:IVS2+914_1000dup IL1RN*1, IL1RN*2 IL1RN*3 (human) RGD PMID:18186699 RGD:6907399 NCBI chr 2:24,226,872...24,241,503
Ensembl chr 2:24,226,865...24,241,506
JBrowse link
G Spp1 secreted phosphoprotein 1 no_association ISO DNA:polymorphism: :p.R9402H (human)
DNA:polymorphism: :p.N9171S (human)
RGD PMID:16145474 PMID:16145474 RGD:1581368, RGD:1581368 NCBI chr 5:104,582,977...104,588,919
Ensembl chr 5:104,582,984...104,588,916
JBrowse link
G Vdr vitamin D (1,25-dihydroxyvitamin D3) receptor ISO GAD PMID:15118671 RGD:1331525 NCBI chr15:97,752,308...97,806,177
Ensembl chr15:97,752,306...97,808,511
JBrowse link
bladder calculus term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ahr aryl-hydrocarbon receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:22232670 NCBI chr12:35,547,978...35,584,988
Ensembl chr12:35,547,973...35,585,037
JBrowse link
Kidney Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bglap bone gamma carboxyglutamate protein IDA RGD PMID:12674322 RGD:7207412 NCBI chr 3:88,290,802...88,291,773
Ensembl chr 3:88,290,808...88,291,771
JBrowse link
G Car2 carbonic anhydrase 2 ISO RGD PMID:10977795 RGD:1600710 NCBI chr 3:14,951,329...14,965,830
Ensembl chr 3:14,951,333...14,965,830
JBrowse link
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 2:103,284,249...103,315,498
Ensembl chr 2:103,284,194...103,315,505
JBrowse link
G Cd44 CD44 antigen ISO RGD PMID:16850024 RGD:2289370 NCBI chr 2:102,641,486...102,732,014
Ensembl chr 2:102,641,486...102,732,010
JBrowse link
G Cldn14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr16:93,715,919...93,809,733
Ensembl chr16:93,715,919...93,809,696
JBrowse link
G F2 coagulation factor II susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr 2:91,442,742...91,466,799
Ensembl chr 2:91,455,665...91,466,759
JBrowse link
G Gstp1 glutathione S-transferase, pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr19:4,085,411...4,087,912
Ensembl chr19:4,085,407...4,087,985
JBrowse link
G Ifng interferon gamma IEP associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr10:118,276,951...118,281,799
Ensembl chr10:118,276,951...118,281,797
JBrowse link
G Mgp matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chr 6:136,849,433...136,852,821
Ensembl chr 6:136,849,433...136,852,821
JBrowse link
G Mpo myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr11:87,684,610...87,695,238
Ensembl chr11:87,684,407...87,695,239
JBrowse link
G Pomc pro-opiomelanocortin-alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr12:4,004,945...4,010,643
Ensembl chr12:4,004,951...4,010,642
JBrowse link
G Sod1 superoxide dismutase 1, soluble ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr16:90,017,650...90,023,221
Ensembl chr16:90,017,642...90,023,217
JBrowse link
G Spp1 secreted phosphoprotein 1 ISO
IDA
CTD Direct Evidence: marker/mechanism CTD
RGD
PMID:8325891 PMID:10890885 PMID:15954903 PMID:21378157 PMID:16105024 RGD:1581372, RGD:6903839, RGD:1581334 NCBI chr 5:104,582,977...104,588,919
Ensembl chr 5:104,582,984...104,588,916
JBrowse link
G Trpm7 transient receptor potential cation channel, subfamily M, member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr 2:126,633,478...126,718,181
Ensembl chr 2:126,633,485...126,718,150
JBrowse link
prostate calculus term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ltf lactotransferrin ISO RGD PMID:19202053 RGD:7243107 NCBI chr 9:110,848,360...110,871,834
Ensembl chr 9:110,848,339...110,871,835
JBrowse link
Renal Hypouricemia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Slc22a12 solute carrier family 22 (organic anion/cation transporter), member 12 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Dalmatian hypouricemia | ClinVar Annotator: match by term: Renal hypouricemia
OMIM
CTD
ClinVar
PMID:12024214 PMID:14655203 PMID:14694169 PMID:15054642 PMID:15327384 More... NCBI chr19:6,585,884...6,593,100
Ensembl chr19:6,585,875...6,593,062
JBrowse link
G Slc2a9 solute carrier family 2 (facilitated glucose transporter), member 9 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Dalmatian hypouricemia
CTD
ClinVar
PMID:18989453 PMID:22132990 NCBI chr 5:38,506,616...38,660,488
Ensembl chr 5:38,506,616...38,660,486
JBrowse link
Ureteral Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 2:103,284,249...103,315,498
Ensembl chr 2:103,284,194...103,315,505
JBrowse link
G Gsr glutathione reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 8:34,143,266...34,188,190
Ensembl chr 8:34,142,551...34,188,191
JBrowse link
G Gstp1 glutathione S-transferase, pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr19:4,085,411...4,087,912
Ensembl chr19:4,085,407...4,087,985
JBrowse link
G Sod1 superoxide dismutase 1, soluble ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr16:90,017,650...90,023,221
Ensembl chr16:90,017,642...90,023,217
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 18300
    Pathological Conditions, Signs and Symptoms 12356
      Anatomical Pathological Conditions 2584
        Calculi 29
          Urinary Calculi 22
            Kidney Calculi + 14
            Renal Hypouricemia 2
            Ureteral Calculi 4
            lower urinary tract calculus + 2
Path 2
Term Annotations click to browse term
  disease 18300
    disease of anatomical entity 15630
      Urogenital Diseases 4892
        urinary system disease 2500
          urolithiasis 67
            Urinary Calculi 22
              Kidney Calculi + 14
              Renal Hypouricemia 2
              Ureteral Calculi 4
              lower urinary tract calculus + 2
paths to the root