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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 chr 9:86,511,866...86,555,950
Ensembl chr 9:86,511,369...86,555,943
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 chr 9:93,171,371...93,262,124 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 chr 3:96,596,975...96,616,224
Ensembl chr 3:96,594,778...96,616,229
JBrowse link
G CCK cholecystokinin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1631261 NCBI chr13:25,940,674...25,945,879
Ensembl chr13:25,937,645...25,946,197
JBrowse link
G GNAS GNAS complex locus ISO CTD Direct Evidence: marker/mechanism CTD PMID:21823526 NCBI chr17:58,985,580...59,053,022
Ensembl chr17:58,998,981...59,053,021
JBrowse link
G HMGCR 3-hydroxy-3-methylglutaryl-CoA reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:7461467 NCBI chr 2:84,380,245...84,401,117
Ensembl chr 2:84,380,225...84,402,956
JBrowse link
G SMAD4 SMAD family member 4 ISO mRNA,protein:decreased expression:intrahepatic bile duct RGD PMID:16917866 RGD:18936999 NCBI chr 1:100,521,843...100,633,501
Ensembl chr 1:100,514,791...100,628,029
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 chr 4:51,194,686...51,211,436
Ensembl chr 4:51,193,755...51,211,259
JBrowse link
G CAT catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 2:26,493,664...26,533,881
Ensembl chr 2:26,487,653...26,581,452
JBrowse link
G CD44 CD44 molecule ISO RGD PMID:16850024 RGD:2289370 NCBI chr 2:25,788,699...25,884,209
Ensembl chr 2:25,788,704...25,884,153
JBrowse link
G CLDN14 claudin 14 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19561606 NCBI chr13:200,121,796...200,201,712
Ensembl chr13:200,128,475...200,145,526
JBrowse link
G F2 coagulation factor II, thrombin susceptibility ISO DNA:haplotypes: : RGD PMID:21067798 RGD:6893526 NCBI chr 2:15,793,257...15,819,151
Ensembl chr 2:15,791,451...15,819,138
JBrowse link
G IFNG interferon gamma ISO associated with type 2 diabetes mellitus; mRNA:increased expression:kidney RGD PMID:21514417 RGD:6893463 NCBI chr 5:32,477,906...32,482,670
Ensembl chr 5:32,477,848...32,482,752
JBrowse link
G LOC100739163 glutathione S-transferase P-like ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 2:4,978,761...4,982,233 JBrowse link
G MGP matrix Gla protein ISO RGD PMID:10460895 RGD:1582511 NCBI chr 5:57,665,272...57,669,360
Ensembl chr 5:57,665,248...57,669,764
JBrowse link
G MPO myeloperoxidase ISO protein:increased activity:blood RGD PMID:18022927 RGD:7174700 NCBI chr12:34,557,031...34,570,091
Ensembl chr12:34,556,408...34,567,904
JBrowse link
G POMC proopiomelanocortin ISO CTD Direct Evidence: marker/mechanism CTD PMID:1324751 NCBI chr 3:113,661,712...113,668,558 JBrowse link
G SOD1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr13:195,326,573...195,335,273
Ensembl chr13:195,326,649...195,337,749
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 chr 8:131,077,786...131,085,334
Ensembl chr 8:131,077,786...131,085,340
JBrowse link
G TRPM7 transient receptor potential cation channel subfamily M member 7 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24291744 NCBI chr 1:121,146,093...121,250,227
Ensembl chr 1:121,146,115...121,250,224
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 chr13:29,413,886...29,445,751
Ensembl chr13:29,413,886...29,445,737
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 chr 2:7,557,822...7,565,801
Ensembl chr 2:7,557,827...7,565,895
JBrowse link
G SLC2A9 solute carrier family 2 member 9 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18989453 PMID:22132990 NCBI chr 8:6,211,143...6,367,530
Ensembl chr 8:6,210,477...6,367,990
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 2:26,493,664...26,533,881
Ensembl chr 2:26,487,653...26,581,452
JBrowse link
G GSR glutathione-disulfide reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr15:54,382,564...54,433,989
Ensembl chr15:54,382,567...54,433,989
JBrowse link
G LOC100739163 glutathione S-transferase P-like ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr 2:4,978,761...4,982,233 JBrowse link
G SOD1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:24360074 NCBI chr13:195,326,573...195,335,273
Ensembl chr13:195,326,649...195,337,749
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 chr14:120,451,421...120,583,725
Ensembl chr14:120,451,573...120,583,723
JBrowse link
G F2 coagulation factor II, thrombin ISO RGD PMID:22494008 RGD:6893519 NCBI chr 2:15,793,257...15,819,151
Ensembl chr 2:15,791,451...15,819,138
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
G SPP1 secreted phosphoprotein 1 no_association ISO DNA:polymorphism: :p.N9171S (human)
DNA:polymorphism: :p.R9402H (human)
RGD PMID:16145474 RGD:1581368 NCBI chr 8:131,077,786...131,085,334
Ensembl chr 8:131,077,786...131,085,340
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 13599
    Pathological Conditions, Signs and Symptoms 8905
      Anatomical Pathological Conditions 1768
        Calculi 26
          Dental Calculus 0
          Gallstones + 6
          Salivary Calculi + 0
          Testicular Microlithiasis 0
          Urinary Calculi + 20
paths to the root