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diseases and causal associations in OMIM missing from MONDO/Monarch
Diseases have MONDO IDs, but associations are missing from Monarch
SPCC1281.06c ole1 .0001 DEAFNESS, AUTOSOMAL DOMINANT 79 (1 family) (SCD5) MONDO:0033668 SPBC211.03c gea1 .0004 CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2GG (GBF1) MONDO:0011675 SPBC25H2.06c hrf1 .0004 KAYA-BARAKAT-MASSON SYNDROME (YIF1B) MONDO:0030878 SPAC57A10.03 cyp1 .0005 PONTOCEREBELLAR HYPOPLASIA, TYPE 14 (PPIL1) MONDO:0030258 SPBC1773.10c nrs1 .0006 NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, IMPAIRED LANGUAGE, AND GAIT ABNORMALITIES (NARS1) MONDO:0100348 SPAC3G9.06 frs2 .0002 RAJAB INTERSTITIAL LUNG DISEASE WITH BRAIN CALCIFICATIONS 2 (1 patient) (FARSA) MONDO:0100220 SPBC4C3.06 syp1 .0006 IMMUNODEFICIENCY 76 (FCHO1) MONDO:0030898 SPAC30C2.07 fnp1 .0006 IMMUNODEFICIENCY 93 AND HYPERTROPHIC CARDIOMYOPATHY (FNIP1) MONDO:0030528 SPAC637.12c mst1 .0003 NEURODEVELOPMENTAL DISORDER WITH DYSMORPHIC FACIES, SLEEP DISTURBANCE, AND BRAIN ABNORMALITIES (KAT5) MONDO:0030852 SPBC1347.10 cdc23 .0004 IMMUNODEFICIENCY 80 WITH CONGENITAL CARDIOMYOPATHY (MCM10) MONDO:0030266 SPCC1753.03c rec7 .0002 OOCYTE MATURATION DEFECT 10 (REC114) MONDO:0030925 SPCC132.01c mtr1 .0007 INTELLECTUAL DEVELOPMENTAL DISORDER WITH SPEECH DELAY AND AXONAL PERIPHERAL NEUROPATHY (NEMF) MONDO:0030849 SPAC144.08 jac1 .0002 ANEMIA, SIDEROBLASTIC, 5 (1 patient) (HSCB) MONDO:0030436 SPAC1486.08 cox16 .0001 MITOCHONDRIAL COMPLEX IV DEFICIENCY, NUCLEAR TYPE 22 (COX16) MONDO:0032626 SPBC713.02c ubp15 .0005 HAO-FOUNTAIN SYNDROME (USP7) MONDO:0014805 SPBC4.05 mlo2 .0001 LI-CAMPEAU SYNDROME (UBR7) MONDO:0030963 SPCC1739.03 hrr1 .0001 IMMUNODEFICIENCY 91 AND HYPERINFLAMMATION (ZNFX1) MONDO:0030491 SPBC776.17 rrp7 .0001 MICROCEPHALY 28, PRIMARY, AUTOSOMAL RECESSIVE (1 family) (RRP7) MONDO:0030339 SPAC1F3.07c rsc58 .0001 ENDOVE SYNDROME, LIMB-BRAIN TYPE (1 patient) (EN1) MONDO:0030979 SPAC1834.11c sec18 .0002 DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 96 (NSF) MONDO:0023659 SPAC6B12.18 gon7 .0002 GALLOWAY-MOWAT SYNDROME 9 (GON7) MONDO:0030471 SPCC895.03c sua5 .0001 GALLOWAY-MOWAT SYNDROME 10 (YRDC) MONDO:0030476 SPBC2G5.06c hmt2 .0002 SULFIDE:QUINONE OXIDOREDUCTASE DEFICIENCY (SQOR) MONDO:0030982 SPCC663.11 saf1 .0003 VERTEBRAL, CARDIAC, TRACHEOESOPHAGEAL, RENAL, AND LIMB DEFECTS (WBP11) MONDO:0030987 SPBC6B1.10 prp17 .0001 PONTOCEREBELLAR HYPOPLASIA, TYPE 15 (1 patient) (CDDC40) MONDO:0030259 SPAC17A5.02c dbr1 .0004 ENCEPHALITIS, ACUTE, INFECTION-INDUCED (VIRAL), SUSCEPTIBILITY TO, 11 (DBR1) MONDO:0030334 SPAC3H1.02c sdd3 .0002 SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 30 (PITRM1) MONDO:0030318 SPCC61.04c .0001 MICROCEPHALY, EPILEPSY, AND DIABETES SYNDROME 2 (YIPF5) MONDO:0025690 SPCC16C4.12 naa20 .0002 INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 73 (NAA20) MONDO:0030533
Have no MONDO term SPAC17H9.10c ddb1 .0005 WHITE-KERNOHAN SYNDROME (DDB1) NO_MONDO_TERM SPCP1E11.06 apl4 --.0005 USMANI-RIAZUDDIN SYNDROME, AUTOSOMAL RECESSIVE (AP1G1) --.0003 USMANI-RIAZUDDIN SYNDROME, AUTOSOMAL DOMINANT (AP1G1) NO_MONDO_TERM SPCC16C4.02c .0002 NEURODEVELOPMENTAL DISORDER WITH INFANTILE EPILEPTIC SPASMS (NCDN) NO_MONDO_TERM SPBC115.01c rrp46 .0005 CEREBELLAR ATAXIA, BRAIN ABNORMALITIES, AND CARDIAC CONDUCTION DEFECTS (EXOSC5) NO_MONDO_TERM SPMIT.10 atp9 .0001 DYSTONIA, EARLY-ONSET, AND/OR SPASTIC PARAPLEGIA (ATP5MC3) NO_MONDO_TERM SPAC17C9.05c pmc3 .0007 NEURODEVELOPMENTAL DISORDER WITH SPASTICITY, CATARACTS, AND CEREBELLAR HYPOPLASIA (MED27) NO_MONDO_TERM SPCC622.11 .0002 DEVELOPMENTAL DELAY WITH VARIABLE NEUROLOGIC AND BRAIN ABNORMALITIES (LMBRD2) NO_MONDO_TERM SPBP8B7.19 spt16 .0003 NEURODEVELOPMENTAL DISORDER WITH DYSMORPHIC FACIES AND THIN CORPUS CALLOSUM (SUPT16H) NO_MONDO_TERM SPBC336.10c tif512 .0004 FAUNDES-BANKA SYNDROME (EIF5A) NO_MONDO_TERM SPAC1F5.06 lsh1 .0002 IMMUNODEFICIENCY 59 AND HYPOGLYCEMIA (HYOU1) NO_MONDO_TERM SPAC824.05 vps16 .0005 DYSTONIA 3 (VPS16) NO_MONDO_TERM
Also SPAC15A10.04c zpr1 **Defects in this gene or the SMN1 gene can cause spinal muscular atrophy MONARCH, but human (ZPR1) has no disease assignment
In each case human ortholog is in parentheses.
https://github.com/pombase/curation/issues/3274
Another missing association Mtx2 .0005 MANDIBULOACRAL DYSPLASIA PROGEROID SYNDROME (MONDO:0030880)
For the SPAC15A10.04c zpr1 **Defects in this gene or the SMN1 gene can cause spinal muscular atrophy MONARCH, but human (ZPR1) has no disease assignment
one, this appears to be a disease modifier. This would be a useful tag to include in Mondo. It seems a shame not to capture this connections to "spinal muscular atrophy" but I don't want to mix with the causal.
Another ECM10 MONDO:0031011 .0001 NEURODEVELOPMENTAL DISORDER WITH DYSMORPHIC FACIES AND VARIABLE SEIZURES
@nicolevasilevsky and @matentzn These diseases have Equivalent to OMIM, but the gene associations were not added to Mondo. This might be an issue at the level of the import with OMIM. Should I update the gene associations manually, or should we use this issue to review the omim import/synchronization pipeline? Please advice. Thank you!
Are these disease defining genes, or just associated genes? If the latter, aren't they added through the OMIM monarch ingest?
They are causal for the disease (or at least they seem to be). Most are single-gene diseases.
@sabrinatoro Do we have a documentation page that describes exactly under which condition a disease-gene relationship is imported? As far as I understand, causal is not enough, I though the gene must be used to define the disease. A mere known causal relation to some gene is (afaik) not enough, only if a variant of the gene is necessarily causing the disease.
@matentzn I do not have documentation. I remember an issue (I will look for it) where this exact question was asked, but I don't know whether we import the disease-gene relation in mondo and/or whether we have specific conditions to do so (and if we know, what these conditions are). We should discuss this at our next Mondo call.
@matentzn What do you mean by causal? To me causal means that it is demonstrated that a variation causes the disease?
I dont really want to get into deep into content discussions :) Sorry for barging in here. But just to make that last point: Any relationship with Some/Some semantics does not belong in Mondo (or any ontology for that matter), but in evidence-based knowledge graphs like Monarch. A some/some relationship reads like this:
"Some instances of Disease X are caused by (some instance of) Gene X."
Ontologies only contain "all/some", which reads:
"All instances of Disease X are caused by Gene X" or "Disease X, whenever it occurs, is always caused by Gene X".
Are the causal relationships you are talking about always of the latter kind?
We discussed this on a Mondo call:
- [x] Sabrina will check these terms to see if they are in OMIM
- [ ] Nico is working on updating the OMIM slurp pipeline to bring in the one-to-one gene to disease associations from OMIM
We'll use this list from you @ValWood as a reference to make sure our pipeline is working.
related to https://github.com/monarch-initiative/mondo/issues/2343
related: https://github.com/monarch-initiative/mondo-ingest/issues/47 https://github.com/monarch-initiative/mondo-ingest/issues/48
Note:
- all the Mondo terms without genes are in OMIM
- the terms that are not in Mondo will probably be added during the next omim slurp (note to self: check after the next slurp)
Update discussion on Technical call on 11/11/22.
- these gene-disease should be included in the omim import (we can check the list)
- these gene associations to existing Mondo terms that are equivalent to OMIM need to be pushed. This is not a priority at the moment, but these should be in Monarch.