Open andrewsu opened 5 years ago
stuppie
commented
5 years ago Bot code is here: https://github.com/SuLab/scheduled-bots/blob/master/scheduled_bots/phenotypes/mitodb_bot.py Code to scrape mitodb and match hpo phenotypes: https://github.com/SuLab/scheduled-bots/blob/master/scheduled_bots/phenotypes/download_mitodb.py
stuppie
commented
5 years ago Looking at one randomly chosen disease (http://mitodb.com/symptoms.php?oid=302060&symptoms=Show) with 26 phenotypes, 24 of them match 18 match an HPO label exactly, 2 match a synonym exactly, and 1 more matches a "related synonym".
stuppie
commented
5 years ago Over everything:
186 out of 524 unique symptoms are missing accounting for 437 out of 2155 links most used missing phenotypes [('hypotonia', 44), ('lactate accumulation', 37), ('hyperactive reflexes', 17), ('increased blood ck', 16), ('basal ganglia pathology', 15), ('increased blood transaminase', 14), ("babinski's sign", 13), ('psychiatric symptom', 11), ('hepatopathy', 10), ('skin pigmentation changes', 8)]
stuppie
commented
5 years ago Phenotypes missing, along with how they're used in MitoDB
| Pubmed id | disease | |
|---|---|---|
| Symptom/sign | ||
| 3-hydroxyglutaric aciduria | 21347589 | 231530 |
| 5-oxoprolinuria | 11445798 | 266130 |
| abnormal brain stem function | 18571143 | 612233 |
| acute chest syndrome | 10861320 | 603903 |
| air trapping | 17099020 | 219700 |
| alar grooves | 23470839 | 302950 |
| anterior stromal dystrophy | 1446772 | 163950 |
| aortic valvular insufficiency | 22829427 | 219100 |
| asphyxia | 1327585 | 608782 |
| babinski's sign | 15300460;21595125;24814845;2137962;18571143;21... | 277460;610246;610246;551500;612233;208920;2712... |
| basal ganglia pathology | 22683713;8392291;21266382;18972346;19135620;20... | 614739;220111;220111;168600;256000;551500;2787... |
| bleeding | 17435591;9159540 | 277900;130000 |
| bossed forehead | 21266382;22829427;18470892 | 220111;219100;230740 |
| brain stem pathology | 8392291;21266382 | 220111;220111 |
| brainstem haemangioblastoma | 8929948 | 193300 |
| bronchial hyperactivity | 11045837 | 604901 |
| bruising | 16990350;9159540 | 163950;130000 |
| bulbar dysfunction | 17296839 | 105400 |
| candidiasis | 8185357 | 300400 |
| cardiac conduction defect | 17439982;10480210;10208957;18256394;2858640;10... | 530000;312750;312750;176670;535000;115200;251880 |
| cardiac fibrosis | 10580070 | 115200 |
| cardiac structural defects | 18000968;15558842;11045837 | 219000;300000;604901 |
| central nuclei in myotubes | 17676042 | 255200 |
| cerebellar haemangioblastoma | 8929948 | 193300 |
| cerebellar syndrome | 20855850 | 250950 |
| ceruloplasmin levels low | 17435591 | 277900 |
| cervical spine abnormality | 23470839 | 302950 |
| chilblain-like lesions | 15883328 | 225750 |
| chondrodysplasia punctata | 23470839;7541833 | 302950;214100 |
| circumoral cyanosis | 18256394 | 176670 |
| claudicatio | 3652487;2012127 | 264800;264800 |
| cleft lip or palate | 10405446;23222957;18000968;8826887;15558842;15... | 242840;242840;219000;105650;300000;154500 |
| congenital blistering | 12668616 | 173650 |
| corpus callosum thining | 21911699 | 610532 |
| cortical dysgenesis | 10405446 | 242840 |
| cox negative fibres | 23352259 | 615156 |
| cox-negative muscle fibers | 17620490 | 609286 |
| csf elevated ifn-alpha | 24300241 | 225750 |
| csf elevated neopterin | 24300241 | 225750 |
| dark urine | 7110809;22147108 | 305900;203500 |
| death in the first months of life | 17486094 | 612075 |
| decreased brain naa to cr | 14586596 | 277700 |
| decreased gsh levels | 11445798 | 266130 |
| decreased recovery of rna synthesis after dna damage | 27004399 | 216400 |
| decreased serum bicarbonate | 8120710 | 201450 |
| decreased serum igf-1 | 16510863 | 502000 |
| delayed closure of anterior fontanel | 21932319 | 614008 |
| diabetes mellitus type 1 | 18581092;20972738 | 520000;222300 |
| diabetic retinopathy | 18581092 | 520000 |
| downward sloping palpebral apertures | 1446772;15340364 | 163950;154500 |
| dysplastic sphenoid wing | 9128932 | 162200 |
| ear canal atresia | 15340364 | 154500 |
| ear malformation | 18000968;15558842;15340364 | 219000;300000;154500 |
| ear pigmentation | 22147108 | 203500 |
| early death | 17668387;20693550 | 245400;245400 |
| emmetropia | 16876521 | 101200 |
| exacerbation during febrile episodes | 18571143 | 612233 |
| eye abnormalities | 16316432 | 176270 |
| eye pigmentation | 22147108 | 203500 |
| facial wrinkles | 7484729 | 502000 |
| fatty heart | 2658591 | 231680 |
| finger deformity | 16961075 | 270550 |
| fracture | 6496237;22585395 | 502000;176270 |
| gastric ulcers | 20142534 | 203700 |
| graying of hair | 11054058;7484729;16673358 | 127550;502000;277700 |
| haematuria | 11167767;11167767 | 306700;277480 |
| hearing loss due to cochlear malformation | 23033317 | 613398 |
| hepatocellular adenomas | 22678084 | 232200 |
| hepatopathy | 20370797;23222957;18695062;16909392;15781812;1... | 231680;242840;256810;256810;254780;203700;2037... |
| high serum igm | 24136356 | 615513 |
| hyperactive reflexes | 15955954;21595125;24814845;8602753;24532200;18... | 168600;610246;610246;256000;312080;612233;2722... |
| hypermobile joints | 8553383;18470892;2195034;16801035;17932957 | 154700;230740;300624;130000;160150 |
| hypersensitivity to dna cross-linking | 17426088 | 227650 |
| hypoplastic or absent clavicles | 21932319 | 614008 |
| hypospadia | 20335238;15558842 | 614052;300000 |
| hypotonia | 17977044;2658591;21266382;18819985;23352259;20... | 231680;231680;220111;609560;615156;614052;2560... |
| incontinence | 12557294 | 611105 |
| increased blood afp | 19696032;1377828 | 606002;208900 |
| increased blood bilirubin | 17435591 | 277900 |
| increased blood ck | 20370797;18819985;8652023;23313956;19722047;77... | 231680;609560;310200;615084;540000;201475;3002... |
| increased blood gammaglutamyltransferase | 8273986;11045837 | 232200;604901 |
| increased blood ldh | 8120710 | 201450 |
| increased blood transaminase | 17977044;23362058;8273986;17435591;8120710;164... | 231680;608594;232200;277900;201450;257200;2604... |
| increased fetal hemoglobin | 8759887 | 260400 |
| increased igm | 26271390 | 251260 |
| increased plasma hga | 12501223 | 203500 |
| increased urin collagen n-telopeptide | 12501223 | 203500 |
| increased urin hga | 12501223 | 203500 |
| increased urinary copper | 17435591 | 277900 |
| intertriginous freckling | 9128932 | 162200 |
| intracranial haemorrhage | 21114482;11167767;11167767 | 306700;306700;277480 |
| iridonesis | 8553383 | 154700 |
| iris transillumination | 8553383 | 154700 |
| ischaemic heart disease | 21663647;6496237 | 143890;502000 |
| joint bleeding | 11167767;11886463;11167767 | 306700;306700;277480 |
| joint effusion | 12501223 | 203500 |
| kidney calcifications | 8273986 | 232200 |
| kidney cysts | 8929948;19825331;7541833 | 193300;173900;214100 |
| kidney failure | 19825331 | 173900 |
| kidney stone | 19825331;22147108 | 173900;203500 |
| lactate accumulation | 22683713;21266382;18819985;10852545;20335238;8... | 614739;220111;609560;603041;614052;256000;2123... |
| laryngotracheoesophageal anomalies | 15558842 | 300000 |
| larynx atresia | 18000968 | 219000 |
| late visual disorientation | 15534185 | 104300 |
| leucoplakia | 11054058;12668616 | 127550;173650 |
| limb dyspraxia | 15534185 | 104300 |
| limb wasting | 17296839 | 105400 |
| long qt | 18256394;16055927 | 176670;610198 |
| low plasma carnitine | 6646897;9003853 | 201450;609016 |
| low serum igg | 24136356 | 615513 |
| low serum trypsinogen | 10393609 | 260400 |
| low-set umbilicus | 18000968 | 219000 |
| lumbar pain | 22147108 | 203500 |
| lung abscesses | 17099020 | 219700 |
| meningo-encephalocele | 18000968 | 219000 |
| methylsuccinic aciduria | 18054510 | 201470 |
| midfacial hypoplasia | 21266382;23470839;15885794 | 220111;302950;123500 |
| mosaic perfusion | 17099020;18403663 | 219700;244400 |
| mucous plugging | 17099020;18403663 | 219700;244400 |
| multiple sclerosis | 7735876;11523562 | 535000;535000 |
| muscle haematoma | 11167767;11167767 | 306700;277480 |
| narrowed thorax | 10393609 | 260400 |
| neuronal migration defect | 7541833 | 214100 |
| nk-cell reduction | 22105576 | 300400 |
| no head control | 18571143 | 612233 |
| non-progressive ventriculomegaly | 16691624 | 101200 |
| non-walking | 14649546 | 312750 |
| nose malformation | 18000968 | 219000 |
| oesophageal stricture | 11054058 | 127550 |
| orthodontic problem | 9733026 | 100800 |
| pacemakers implanted | 10580070;10939567 | 115200;181350 |
| pallesthesia | 21595125;12557294;23065789 | 610246;611105;607259 |
| pancreatic carcinoma | 8929948 | 193300 |
| peau d`orange lesions | 2012127 | 264800 |
| peribronchial thickening | 17099020;8633137;18403663 | 219700;613490;244400 |
| perioral melanocytic macules | 20126809 | 175200 |
| persistent foramen ovale | 23222957 | 242840 |
| phaeochromocytoma | 8929948 | 193300 |
| poor healing | 9159540 | 130000 |
| post-operative bleeding | 11167767;11167767 | 306700;277480 |
| post-partum bleeding | 11167767 | 277480 |
| prominent corneal nerves | 1446772 | 163950 |
| protruding auricles | 18470892 | 230740 |
| protruding lips | 18470892 | 230740 |
| pseudoanodontia | 18470892 | 230740 |
| psychiatric symptom | 17620490;23352259;15955954;23313956;11329229;1... | 609286;615156;168600;615084;520000;271245;5020... |
| pulmonary hypertension | 14985486 | 603903 |
| pyrosis | 11247006 | 312750 |
| radiosensitivity | 1256588;10799436 | 208900;251260 |
| ragged red fibres | 23352259 | 615156 |
| reflux | 23470839;22585395 | 302950;176270 |
| retinal angioma | 8929948 | 193300 |
| retinal cherry red spot | 16434659 | 257200 |
| retinal myelinated fibers | 16961075 | 270550 |
| septum pellucidum defect | 16691624 | 101200 |
| serum elevated ifn-alpha | 24300241 | 225750 |
| skin pigmentation changes | 11054058;21932319;18256394;17426088;2917181;20... | 127550;614008;176670;227650;227650;227650;2109... |
| skin redundancy | 18470892 | 230740 |
| skull ossification defect | 18000968 | 219000 |
| sleeping with eyes open | 18256394 | 176670 |
| spinal haemangioblastoma | 8929948 | 193300 |
| spontaneous bacterial peritonitis | 11045837 | 604901 |
| steatorrhoea | 10679949;10946006;10393609;10829988 | 200100;200100;260400;219700 |
| succinate accumulation | 19465911 | 252011 |
| t-cell reduction | 22105576 | 300400 |
| teeth pigmentation | 22147108 | 203500 |
| thin limbs | 21932319;16673358 | 614008;277700 |
| thorax deformity | 21932319 | 614008 |
| thumb abnormalities | 8826887;24635570;17426088 | 105650;268400;227650 |
| tonsillectomy | 9733026 | 100800 |
| tracheostoma | 15340364 | 154500 |
| tricuspid valvular insufficiency | 22829427 | 219100 |
| tubulopathy | 17439982;7581370;19138848;17442627 | 530000;557000;612075;607426 |
| ureter agenesis | 18000968 | 219000 |
| variceal bleeding | 11045837 | 604901 |
| ventricular arrythmia | 16847078 | 302060 |
| vermis hypoplasia | 10405446 | 242840 |
| visual acuity decrease | 15953402;20301646;6496237;22748208;15795345 | 277460;258501;502000;611726;203800 |
| wheelchair use | 21855841 | 607694 |
| white matter atrophy | 21911699 | 610532 |
| widened atrophic scars | 9159540 | 130000 |
| windswept deformity | 8725795 | 177170 |
| xanthomas | 21663647 | 143890 |
| xerophthalmus | 18256394;21480477 | 176670;216400 |
| yellowish papules | 3652487 | 264800 |
| zygomatic hypoplasia | 15340364 | 154500 |
Mitodb is a mitochondrial disease database described in this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3629291/
This site does not appear to have been updated since 2015. There is no structured download, but an email address exists that we could email. Alternatively, the relevant data looks like it could be scraped without too much effort.
There are ~100 diseases with data (for example: http://mitodb.com/symptoms.php?oid=302060&symptoms=Show). Diseases are normalized to OMIM. No obvious normalization of phenotypes/symptoms.