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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_004936546:3,737,908...3,783,492 JBrowse link
Gallbladder Disease 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcb4 ATP binding cassette subfamily B member 4 ISO OMIM NCBI chrNW_004936763:1,339,849...1,415,528 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_004936508:8,074,697...8,093,424 JBrowse link
G Cck cholecystokinin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1631261 NCBI chrNW_004936695:2,776,705...2,782,280 JBrowse link
G Hmgcr 3-hydroxy-3-methylglutaryl-CoA reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:7461467 NCBI chrNW_004936549:1,378,536...1,400,501 JBrowse link
G LOC101971027 neuroendocrine secretory protein 55 ISO CTD Direct Evidence: marker/mechanism CTD PMID:21823526 NCBI chrNW_004936530:1,353,432...1,407,437 JBrowse link
G Smad4 SMAD family member 4 ISO mRNA,protein:decreased expression:intrahepatic bile duct RGD PMID:16917866 RGD:18936999 NCBI chrNW_004936497:12,242,869...12,278,012 JBrowse link
Kidney Calculi term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ca2 carbonic anhydrase 2 ISO RGD PMID:10977795 RGD:1600710 NCBI chrNW_004936544:362,591...379,151 JBrowse link
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004936533:3,601,270...3,637,128 JBrowse link
G Cd44 CD44 molecule (Indian blood group) ISO RGD PMID:16850024 RGD:2289370 NCBI chrNW_004936533:2,949,026...3,033,166 JBrowse link
G Cldn14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chrNW_004936500:6,207,856...6,227,582 JBrowse link
G F2 coagulation factor II, thrombin susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chrNW_004936562:2,371,725...2,388,617 JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004936599:2,197,681...2,200,642 JBrowse link
G Ifng interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chrNW_004936545:6,139,130...6,144,543 JBrowse link
G LOC101976563 matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chrNW_004936587:2,601,419...2,605,848 JBrowse link
G LOC101978603 bone gamma-carboxyglutamate protein ISO RGD PMID:12674322 RGD:7207412 NCBI chrNW_004936580:5,480,023...5,482,288 JBrowse link
G Mpo myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chrNW_004936490:4,809,773...4,819,070 JBrowse link
G Pomc proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chrNW_004936493:7,060,747...7,065,276 JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004936500:10,345,154...10,352,873 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_004936905:148,956...156,023 JBrowse link
G Trpm7 transient receptor potential cation channel subfamily M member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chrNW_004936471:12,564,617...12,666,229 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_004936596:344,287...373,788 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_004936599:4,693,493...4,698,556 JBrowse link
G Slc2a9 solute carrier family 2 member 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18989453 PMID:22132990 NCBI chrNW_004936477:16,700,915...16,836,424 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_004936533:3,601,270...3,637,128 JBrowse link
G Gsr glutathione-disulfide reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004936792:531,076...579,083 JBrowse link
G Gstp1 glutathione S-transferase pi 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004936599:2,197,681...2,200,642 JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chrNW_004936500:10,345,154...10,352,873 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_004936486:928,956...1,042,168 JBrowse link
G F2 coagulation factor II, thrombin ISO RGD PMID:22494008 RGD:6893519 NCBI chrNW_004936562:2,371,725...2,388,617 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_004936783:1,447,158...1,466,331 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_004936905:148,956...156,023 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 12943
    Pathological Conditions, Signs and Symptoms 8505
      Anatomical Pathological Conditions 1681
        Calculi 27
          Dental Calculus 0
          Gallstones + 6
          Salivary Calculi + 0
          Testicular Microlithiasis 0
          Urinary Calculi + 21
paths to the root