review terms that are obsolete in Mondo but "orphanet disorders"

[sabrinatoro]

Based on #7681 (comment)

Some obsolete classes have exact mappings to the orphanet:disorder.
We should review these obsoleted terms and check whether we still agree with this obsoletion or we should reinstate the term

Mondo ID	label
MONDO:0017049	obsolete hypomyelination neuropathy-arthrogryposis syndrome
MONDO:0034979	obsolete peripapillary staphyloma
MONDO:0029051	obsolete autosomal recessive nail dysplasia
MONDO:0035314	obsolete congenital tricuspid valve dysplasia
MONDO:0021690	obsolete congenital left ventricular aneurysm
MONDO:0018888	obsolete congenital cornea plana
MONDO:8000032	obsolete malformation syndrome
MONDO:0016250	obsolete rare adenocarcinoma of the breast
MONDO:0035250	obsolete anomalous aortic origin of the right coronary artery
MONDO:0009930	obsolete pulmonary arteriovenous malformation
MONDO:0018344	obsolete periodic paralysis with transient compartment-like syndrome
MONDO:0017173	obsolete non-syndromic male infertility due to sperm motility disorder
MONDO:0018393	obsolete male infertility with azoospermia or oligozoospermia due to single gene mutation
MONDO:0020256	obsolete congenital trochlear nerve palsy
MONDO:0032011	obsolete biological anomaly
MONDO:0015976	obsolete hyper-IgM syndrome without susceptibility to opportunistic infections
MONDO:0034028	obsolete symptomatic form of hemochromatosis type 1
MONDO:0014753	obsolete autosomal recessive optic atrophy
MONDO:0019138	obsolete bleeding diathesis due to a collagen receptor defect
MONDO:0016599	obsolete autosomal dominant secondary polycythemia
MONDO:0016665	obsolete unclassified vasculitis
MONDO:0018580	obsolete PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome
MONDO:0008347	obsolete idiopathic and/or familial pulmonary arterial hypertension
MONDO:0016579	obsolete dominant hypophosphatemia with nephrolithiasis or osteoporosis
MONDO:0026419	obsolete isolated corpus callosum agenesis
MONDO:0018532	obsolete adenocarcinoma of liver and intrahepatic biliary tract
MONDO:0015305	obsolete rare endometriosis
MONDO:0016173	obsolete non-paraneoplastic sensory ganglionopathy
MONDO:0020075	obsolete hereditary non-syndromic obesity
MONDO:0018112	obsolete isolated scaphocephaly
MONDO:0034980	obsolete isolated megalopapilla
MONDO:0035792	obsolete non-syndromic anorectal malformation with rectovaginal fistula
MONDO:0019176	obsolete trichorhinophalangeal syndrome type I or III
MONDO:0034819	obsolete familial intestinal malrotation
MONDO:0017581	obsolete familial infantile gigantism
MONDO:0035252	obsolete anomalous origin of coronary artery from the pulmonary artery
MONDO:0034981	obsolete optic disk pit
MONDO:0035788	obsolete non-syndromic anorectal malformation with anal stenosis
MONDO:0018598	obsolete neonatal adrenoleukodystrophy
MONDO:0035793	obsolete non-syndromic anorectal malformation with h-type fistula
MONDO:0016174	obsolete paraneoplastic sensory ganglionopathy
MONDO:0034977	obsolete isolated microspherophakia
MONDO:0017629	obsolete sodium channelopathy-related small fiber neuropathy
MONDO:0035789	obsolete non-syndromic anorectal malformation with pouch colon
MONDO:8000030	obsolete morphological anomaly
MONDO:0018114	obsolete isolated brachycephaly
MONDO:0044331	obsolete genetic transient congenital hypothyroidism
MONDO:0034733	obsolete cochlear nerve deficiency
MONDO:0035249	obsolete anomalous aortic origin of the left coronary artery
MONDO:0035267	obsolete quadricuspid aortic valve
MONDO:0017333	obsolete hypomyelinating leukodystrophy with or without oligondontia and/or hypogonadism
MONDO:0014424	obsolete congenital deficiency in alpha-fetoprotein
MONDO:0018340	obsolete hereditary isolated aplastic anemia
MONDO:0016352	obsolete idiopathic inherited hypercalciuria
MONDO:0100189	obsolete apolipoprotein A-I deficiency
MONDO:0013742	obsolete familial mesial temporal lobe epilepsy with febrile seizures
MONDO:0014425	obsolete hereditary persistence of alpha-fetoprotein
MONDO:0015975	obsolete hyper-IgM syndrome with susceptibility to opportunistic infections
MONDO:0015837	obsolete Unicervical bicornuate uterus
MONDO:0100229	obsolete Heimler syndrome
MONDO:0017241	obsolete AP4-related intellectual disability and spastic paraplegia
MONDO:0016589	obsolete progressive cerebello-cerebral atrophy
MONDO:0017447	obsolete congenital absence/hypoplasia of thumb
MONDO:0034024	obsolete kyphoscoliotic Ehlers-Danlos syndrome
MONDO:0016788	obsolete genetic hyperferritinemia without iron overload
MONDO:0010330	obsolete primary ciliary dyskinesia-retinitis pigmentosa syndrome
MONDO:0034217	obsolete resistance to thyroid hormone due to a mutation in thyroid hormone receptor beta
MONDO:0018337	obsolete severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency
MONDO:0018651	obsolete lipoyl transferase 2 deficiency
MONDO:0035451	obsolete left sided atrial isomerism
MONDO:0018574	obsolete intellectual disability-expressive aphasia-facial dysmorphism syndrome
MONDO:0019486	obsolete myoclonic epilepsy of infancy
MONDO:0019174	obsolete infantile Refsum disease
MONDO:0020548	obsolete ocular pemphigoid
MONDO:0033947	obsolete hereditary angioedema with normal C1Inh
MONDO:0034678	obsolete mirror-image polydactyly
MONDO:0032013	obsolete clinical syndrome
MONDO:0018575	obsolete microcephalic primordial dwarfism-insulin resistance syndrome
MONDO:0016520	obsolete isolated Klippel-Feil syndrome
MONDO:0035448	obsolete aprosencephaly/atelencephaly spectrum
MONDO:0032014	obsolete particular clinical situation in a disease or syndrome
MONDO:0015108	obsolete rare non-syndromic intellectual disability
MONDO:0035784	obsolete non-syndromic anorectal malformation with rectovesical fistula
MONDO:0011794	obsolete Dravet syndrome
MONDO:0018758	obsolete familial patent arterial duct
MONDO:0017057	obsolete hereditary thrombocytopenia with normal platelets
MONDO:0018277	obsolete congenital muscular dystrophy with cerebellar involvement
MONDO:0035785	obsolete non-syndromic anorectal malformation with vestibular fistula
MONDO:0035790	obsolete non-syndromic anorectal malformation with rectal atresia
MONDO:0019597	obsolete 46,XY disorder of sex development due to isolated 17,20-lyase deficiency
MONDO:0020313	obsolete unclassified myelodysplastic/myeloproliferative disease
MONDO:0016536	obsolete autosomal recessive lymphoproliferative disease
MONDO:0020207	obsolete rare isolated myopia
MONDO:0015470	obsolete familial isolated dilated cardiomyopathy
MONDO:0018222	obsolete X-linked intellectual disability due to GRIA3 anomalies
MONDO:0035541	obsolete split cord malformation type II
MONDO:0035786	obsolete non-syndromic cloacal malformation
MONDO:0015848	obsolete septate vagina
MONDO:0020315	obsolete unclassified myelodysplastic syndrome
MONDO:0036192	obsolete EN1-related dorsoventral syndrome
MONDO:0015586	obsolete benign familial mesial temporal lobe epilepsy
MONDO:0035791	obsolete non-syndromic anorectal malformation with rectal stenosis
MONDO:0015385	obsolete external auditory canal aplasia/hypoplasia
MONDO:0035581	obsolete lethal brain and heart developmental defects
MONDO:0018347	obsolete severe intellectual disability-progressive postnatal microcephaly- midline stereotypic hand movements syndrome
MONDO:0018649	obsolete cerebral visual impairment
MONDO:0035787	obsolete non-syndromic anorectal malformation without fistula
MONDO:0018279	obsolete congenital muscular dystrophy without intellectual disability
MONDO:0019150	obsolete familial isolated restrictive cardiomyopathy
MONDO:0010123	obsolete absent thumb-short stature-immunodeficiency syndrome
MONDO:0018560	obsolete anterior urethral valve
MONDO:0035780	obsolete non-syndromic anorectal malformation with perineal fistula
MONDO:0035398	obsolete hypomyelination of early myelinating structures
MONDO:0007464	obsolete isolated distichiasis
MONDO:0035557	obsolete intermediate atrioventricular septal defect
MONDO:0019482	obsolete dendritic cell sarcoma not otherwise specified
MONDO:0035781	obsolete non-syndromic anorectal malformation with rectourethral fistula

[sabrinatoro]

shareable spreadsheet here.

[sabrinatoro]

@matentzn Could you please add the orphanet ID to this spreadsheet?
I am assuming that we are looking at obsoleted Mondo terms which have an x-ref to a specific orphanet, however when looking at the spreadsheet, I have seen:

• Mondo obsoleted terms with no orphanet x-ref
• orphanet x-ref (that, based on name, could have been the one missing) that have been removed from orphanet.
• Mondo term (not obsoleted) with orphanet x-ref but the orphanet name is the same as an obsoleted Mondo term

Therefore I would like confirmation of

1. which orphanet x-ref is expected for these obsolete terms (ie which orphanet terms are actually mapped to Mondo obsoleted terms) based on the files used to create this spreadsheet.
2. where these mappings came from and how they were made (I suspect that some of them are only on term label)

Thank you!

[matentzn]

I have updated the table here (state yesterday):

https://docs.google.com/spreadsheets/d/1Sfj9zwKFXpZwaQNkJJGeQHXUFvyCU2P8YmyGaSXcLdE/edit#gid=1957301643

If the "exact_matches" column is empty, we have only a synchronicity problem: The subset sync pipeline and the mappings are intricately linked. So the issues will solve themselves with the next update.

[sabrinatoro]

AI tools are taking too long...
@matentzn Could you share an updated list with:

• all the MONDO id that are obsoleted and equivalent to an orphanet ordo_disorder term (ie obsolete Mondo term with the ordo_disorder subset annotation)
• For each orphanet ID (assuming it is easy to get that information), please list all the OMIM ID that orphanet map to the term).
• Extra points if you can add the corresponding Mondo to these OMIM IDs.

The table should have the following columns:

• Mondo ID
• Mondo label
• Orphanet ID
• reason for obsolescence in Mondo (this is the source annotation for the "has obsolescence reason" annotation)

In another spreadsheet (it is easier this way I think)

• Orphanet ID (from table above)
• OMIM x-ref for these IDs according to Orphanet
• MONDO IDs equivalent to the OMIM IDs.

(Orphanet ID could therefore be on several rows)

Thank you!

[sabrinatoro]

Strategy:
At this point, we have reviewed enough of these terms to realize that

• Orphanet considers a term as a disorder, but it looked like a grouping term to us because it was grouping several OMIM terms. In other words, the orphanet terms are the "lumped" disease entity according to Orphanet.
• Since Orphanet considers these terms as "disorder", these terms should be in Mondo (this way they are on the rare disease subset, and they represent the disease entity "according to orphanet")

The strategy is to use the robot template above to

1. de-obsolete the Mondo terms
2. add classification as needed
   (the spreadsheets above are at the base of several ROBOT templates that will allow this work to be done faster and more easily)