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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:Calculi
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Accession:DOID:9005602 term browser browse the term
Definition:An abnormal concretion occurring mostly in the urinary and biliary tracts, usually composed of mineral salts. Also called stones.
Synonyms:exact_synonym: Biliary or Urinary Stones;   Calculus
 primary_id: MESH:D002137;   RDO:0005094
For additional species annotation, visit the Alliance of Genome Resources.


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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_004955410:20,428,531...20,459,482 JBrowse link
Gallstones term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcg8 ATP binding cassette subfamily G member 8 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17632509 NCBI chrNW_004955441:10,982,307...11,004,789
Ensembl chrNW_004955441:10,982,307...11,009,116
JBrowse link
G Cck cholecystokinin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1631261 NCBI chrNW_004955420:28,438,806...28,443,458
Ensembl chrNW_004955420:28,438,806...28,443,458
JBrowse link
G Hmgcr 3-hydroxy-3-methylglutaryl-CoA reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:7461467 NCBI chrNW_004955425:25,362,165...25,380,611
Ensembl chrNW_004955425:25,359,884...25,380,745
JBrowse link
G Smad4 SMAD family member 4 ISO mRNA,protein:decreased expression:intrahepatic bile duct RGD PMID:16917866 RGD:18936999 NCBI chrNW_004955402:35,956,080...36,001,746
Ensembl chrNW_004955402:35,961,165...35,994,538
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_004955545:2,381,091...2,382,114
Ensembl chrNW_004955545:2,381,156...2,381,978
JBrowse link
G Ca2 carbonic anhydrase 2 ISO RGD PMID:10977795 RGD:1600710 NCBI chrNW_004955417:3,388,110...3,402,798
Ensembl chrNW_004955417:3,386,087...3,402,363
JBrowse link
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004955422:11,783,973...11,826,970
Ensembl chrNW_004955422:11,781,835...11,827,464
JBrowse link
G Cd44 CD44 molecule (Indian blood group) ISO RGD PMID:16850024 RGD:2289370 NCBI chrNW_004955422:11,106,061...11,189,951 JBrowse link
G Cldn14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chrNW_004955407:35,641,560...35,728,105
Ensembl chrNW_004955407:35,641,560...35,728,105
JBrowse link
G F2 coagulation factor II, thrombin susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chrNW_004955422:1,356,675...1,367,788
Ensembl chrNW_004955422:1,356,769...1,367,517
JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004955422:17,914,228...17,916,918
Ensembl chrNW_004955422:17,914,305...17,917,428
JBrowse link
G Ifng interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chrNW_004955458:14,643,333...14,648,020
Ensembl chrNW_004955458:14,643,313...14,648,045
JBrowse link
G Mgp matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chrNW_004955413:11,614,851...11,618,090
Ensembl chrNW_004955413:11,615,078...11,618,024
JBrowse link
G Mpo myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chrNW_004955451:4,743,744...4,753,358
Ensembl chrNW_004955451:4,743,744...4,753,358
JBrowse link
G Pomc proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chrNW_004955469:7,217,233...7,220,401
Ensembl chrNW_004955469:7,217,363...7,220,386
JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004955407:31,261,451...31,267,657
Ensembl chrNW_004955407:31,263,863...31,267,727
JBrowse link
G Spp1 secreted phosphoprotein 1 ISO CTD Direct Evidence: marker/mechanism RGD
CTD
PMID:8325891 PMID:10890885 PMID:15954903 PMID:16105024 PMID:21378157 RGD:1581334 RGD:1581372 RGD:6903839 NCBI chrNW_004955474:1,914,477...1,922,025
Ensembl chrNW_004955474:1,913,829...1,922,016
JBrowse link
G Trpm7 transient receptor potential cation channel subfamily M member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chrNW_004955409:3,690,722...3,787,139
Ensembl chrNW_004955409:3,691,039...3,785,908
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_004955420:25,580,449...25,604,277
Ensembl chrNW_004955420:25,580,359...25,604,331
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 OMIM NCBI chrNW_004955422:20,555,458...20,561,818
Ensembl chrNW_004955422:20,556,098...20,596,012
JBrowse link
G Slc2a9 solute carrier family 2 member 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18989453 PMID:22132990 NCBI chrNW_004955514:5,479,585...5,625,328
Ensembl chrNW_004955514:5,479,585...5,625,223
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_004955422:11,783,973...11,826,970
Ensembl chrNW_004955422:11,781,835...11,827,464
JBrowse link
G Gsr glutathione-disulfide reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004955463:7,130,459...7,153,631
Ensembl chrNW_004955463:7,131,364...7,153,583
JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004955422:17,914,228...17,916,918
Ensembl chrNW_004955422:17,914,305...17,917,428
JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004955407:31,261,451...31,267,657
Ensembl chrNW_004955407:31,263,863...31,267,727
JBrowse link
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_004955485:1,216,435...1,273,275
Ensembl chrNW_004955485:1,216,435...1,353,953
JBrowse link
G F2 coagulation factor II, thrombin ISO RGD PMID:22494008 RGD:6893519 NCBI chrNW_004955422:1,356,675...1,367,788
Ensembl chrNW_004955422:1,356,769...1,367,517
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_004955470:1,145,022...1,159,413
Ensembl chrNW_004955470:1,144,810...1,159,471
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_004955474:1,914,477...1,922,025
Ensembl chrNW_004955474:1,913,829...1,922,016
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 12680
    Pathological Conditions, Signs and Symptoms 8330
      Anatomical Pathological Conditions 1659
        Calculi 25
          Dental Calculus 0
          Gallstones + 4
          Salivary Calculi + 0
          Testicular Microlithiasis 0
          Urinary Calculi + 21
paths to the root