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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 chrNW_004624737:36,091,671...36,256,398 JBrowse link
G F2 coagulation factor II, thrombin ISO RGD PMID:22494008 RGD:6893519 NCBI chrNW_004624767:1,876,974...1,887,720
Ensembl chrNW_004624767:1,877,024...1,887,958
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 chrNW_004624749:13,210,365...13,224,471
Ensembl chrNW_004624749:13,210,476...13,225,890
JBrowse link
G Spp1 secreted phosphoprotein 1 no_association ISO DNA:polymorphism: :p.N9171S (human)
DNA:polymorphism: :p.R9402H (human)
RGD PMID:16145474 RGD:1581368 NCBI chrNW_004624872:4,505,796...4,513,247
Ensembl chrNW_004624872:4,505,522...4,513,742
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 chrNW_004624739:12,939,183...12,987,574
Ensembl chrNW_004624739:12,942,165...12,987,973
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 ISO RGD PMID:12674322 RGD:7207412 NCBI chrNW_004624885:1,526,625...1,528,235
Ensembl chrNW_004624885:1,527,538...1,528,109
JBrowse link
G Ca2 carbonic anhydrase 2 ISO RGD PMID:10977795 RGD:1600710 NCBI chrNW_004624744:6,168,030...6,183,407
Ensembl chrNW_004624744:6,167,606...6,183,538
JBrowse link
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004624767:12,680,940...12,715,468
Ensembl chrNW_004624767:12,680,953...12,715,739
JBrowse link
G Cd44 CD44 molecule (IN blood group) ISO RGD PMID:16850024 RGD:2289370 NCBI chrNW_004624767:11,938,452...12,024,970
Ensembl chrNW_004624767:11,938,028...12,025,069
JBrowse link
G Cldn14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chrNW_004624745:27,058,441...27,074,288
Ensembl chrNW_004624745:27,058,911...27,074,282
JBrowse link
G F2 coagulation factor II, thrombin susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chrNW_004624767:1,876,974...1,887,720
Ensembl chrNW_004624767:1,877,024...1,887,958
JBrowse link
G Ifng interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chrNW_004624802:163,261...166,534
Ensembl chrNW_004624802:163,261...166,534
JBrowse link
G Mgp matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chrNW_004624752:23,146,025...23,149,266
Ensembl chrNW_004624752:23,146,166...23,149,048
JBrowse link
G Mpo myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chrNW_004624871:121,026...131,433
Ensembl chrNW_004624871:121,026...131,323
JBrowse link
G Pomc proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chrNW_004624738:7,442,223...7,448,513
Ensembl chrNW_004624738:7,442,292...7,445,020
JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004624745:20,032,003...20,037,958
Ensembl chrNW_004624745:20,032,011...20,037,958
JBrowse link
G Spp1 secreted phosphoprotein 1 ISO CTD Direct Evidence: marker/mechanism CTD
RGD
PMID:8325891 PMID:10890885 PMID:15954903 PMID:16105024 PMID:21378157 RGD:1581334 RGD:1581372 RGD:6903839 NCBI chrNW_004624872:4,505,796...4,513,247
Ensembl chrNW_004624872:4,505,522...4,513,742
JBrowse link
G Trpm7 transient receptor potential cation channel subfamily M member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chrNW_004624731:9,490,885...9,588,255
Ensembl chrNW_004624731:9,491,157...9,588,346
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 chrNW_004624730:74,636,554...74,656,817
Ensembl chrNW_004624730:74,636,522...74,656,886
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 member 12 ISO ClinVar Annotator: match by term: Dalmatian hypouricemia | ClinVar Annotator: match by term: Renal hypouricemia OMIM
ClinVar
PMID:12024214 PMID:14655203 PMID:14694169 PMID:15054642 PMID:15327384 More... NCBI chrNW_004624767:21,771,137...21,780,305
Ensembl chrNW_004624767:21,772,744...21,779,230
JBrowse link
G Slc2a9 solute carrier family 2 member 9 ISO ClinVar Annotator: match by term: Dalmatian hypouricemia ClinVar NCBI chrNW_004624755:21,165,374...21,328,843
Ensembl chrNW_004624755:21,171,274...21,322,543
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 chrNW_004624767:12,680,940...12,715,468
Ensembl chrNW_004624767:12,680,953...12,715,739
JBrowse link
G Gsr glutathione-disulfide reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004624780:13,440,269...13,497,435
Ensembl chrNW_004624780:13,440,235...13,496,535
JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004624745:20,032,003...20,037,958
Ensembl chrNW_004624745:20,032,011...20,037,958
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 15960
    Pathological Conditions, Signs and Symptoms 10982
      Anatomical Pathological Conditions 2293
        Calculi 25
          Urinary Calculi 20
            Kidney Calculi + 13
            Renal Hypouricemia 2
            Ureteral Calculi 3
            lower urinary tract calculus + 2
Path 2
Term Annotations click to browse term
  disease 15960
    disease of anatomical entity 13723
      Urogenital Diseases 4362
        urinary system disease 2205
          urolithiasis 59
            Urinary Calculi 20
              Kidney Calculi + 13
              Renal Hypouricemia 2
              Ureteral Calculi 3
              lower urinary tract calculus + 2
paths to the root