Closed nicolevasilevsky closed 3 years ago
@nicolevasilevsky MONDO:0021001 hemochromatosis type 1 may be a similar case, see https://github.com/EBISPOT/efo/issues/568.
I think you are on top of this, do you need me to do anything here?
@paolaroncaglia has been reporting individual issues, but do you think we should look at all of the only-ordo supported is-as relationships? Is there an easy way to generate a list of all of these terms/relationships?
@zoependlington and I discussed the issue of incorrect Orphanet-derived superclasses with @nicolevasilevsky at our monthly EFO-Mondo call today. Zoe will try to query the problematic terms and their superclasses from Mondo for Nicole to look at. If necessary, we may ask Nico or Chris for help. Then we'll go from there.
Here's another example of incorrect Orphanet-derived superclasses in Mondo (that EFO inherits too):
MONDO:0009169 endocardial fibroelastosis
comment: Editor notes: ORDO classifies as both familial and non-familial
def: Endomyocardial fibroelastosis is a cause of unexplained childhood cardiac insufficiency. It results from diffuse thickening of the endocardium leading to dilated myocardiopathy in the majority of cases and restrictive myocardiopathy in rare cases. It may occur as a primary disorder or may be secondary to another cardiac malformation, notably aortic stenosis or atresia.
Subclass of: familial restrictive cardiomyopathy endocardium disease non-familial restrictive cardiomyopathy familial dilated cardiomyopathy non-familial dilated cardiomyopathy
It follows from the def (and is supported by the editor's comment) that the only correct superclass is 'endocardium disease', and that all other superclasses should be deleted.
(Re. reviewing Orphanet-derived incorrect parentage) While we wait for the agreed action item on EFO's part, I'll also make a note here that in some cases a disease term is correctly placed in EFO and has an EFO namespace, but gains incorrect Orphanet-derived parentage via Mondo because Mondo got the term directly from Orphanet. See e.g. 'Sneddon syndrome' that is a subclass of 'vascular disease' only in EFO, but gains 7 parents from Mondo, most of which look incorrect.
See spreadsheet
@cmungall could you do a SPARQL query to give us a list of all the Mondo classes that only have Orphanet as the source for the subClass Of assertion?
thank you!
@ShahimEssaid could you do a SPARQL query to give us a list of all the Mondo classes that only have Orphanet as the source for the subClassOf assertion.
Zoe and I are going to review the is_a overloading and create tickets as needed. She has a spreadsheet with over 6000 terms in EFO that come from Orphanet, and have multiple parents.
@ShahimEssaid I think we talked about this SPARQL query before the holidays but I can't remember where it stands now. Would you be able to do this soon? Thanks!
@nicolevasilevsky @ShahimEssaid Hi, @zoependlington and I met with Open Targets today and they asked if there are any updates on this please. Many thanks!
@nicolevasilevsky to make sure I get this right, if there is a Mondo class A that has more than one parent, lets say B and C, should A be listed in the result if ALL the subclass axioms are only from Orphanet or if ANY of the subclass axioms are only from Orphanet? In other words, if A subclassof B only comes from Orphanet but A subclassof C comes from somewhere else with or without Orphanet, should A be listed? This is the "ANY" case.
Also, there are few subclassof axioms annotated with: source="MONDO:Entailed" source="MONDO:Redundant"
Would these axioms exclude the class since they aren't really Orphanet only?
About my earlier comment, this is an example of a Mondo class that has a "is_a" that is only coming from source="ORDO:*" but there is another "is_a" that is not only from ORDO. Should this class be in the result or not?
[Term]
id: MONDO:0007060
name: spermatogenic failure 6
def: "Any azoospermia in which the cause of the disease is a mutation in the SPATA16 gene." [MONDO:patterns/disease_series_by_gene]
synonym: "acrosome malformation of spermatozoa" RELATED [OMIM:102530]
synonym: "azoospermia caused by mutation in SPATA16" EXACT [MONDO:design_pattern]
synonym: "globozoospermia" RELATED [OMIM:102530]
synonym: "round-headed spermatozoa" RELATED [OMIM:102530]
synonym: "SPATA16 azoospermia" EXACT [MONDO:design_pattern, MONDO:patterns/disease_series_by_gene]
synonym: "spermatogenic failure 6" EXACT [MONDO:Lexical, OMIM:102530]
synonym: "spermatogenic failure 6; SPGF6" RELATED [OMIM:102530]
synonym: "spermatogenic failure type 6" EXACT [MONDORULE:1, OMIM:102530]
synonym: "spermatozoa, round-headed" RELATED [OMIM:102530]
synonym: "SPGF6" RELATED [MONDO:Lexical, OMIM:102530]
xref: DOID:0070167 {source="MONDO:equivalentTo"}
xref: OMIM:102530 {source="MONDO:equivalentTo"}
xref: Orphanet:171709 {source="MONDO:subClassOf", source="OMIM:102530"}
xref: Orphanet:399808 {source="MONDO:subClassOf", source="OMIM:102530"}
xref: SCTID:236818008 {source="MONDO:equivalentTo", source="MONDO:kboom-pr-1.00/0.74/5.95"}
xref: UMLS:C0403825 {source="NCBI:mim2gene_medline", source="MONDO:notFoundInDiseaseSubset", source="OMIM:102530"}
here:
is_a: MONDO:0004983 {source="DC-OMIM:102530", source="MONDO:Redundant", source="OMIM:102530"} ! azoospermia
is_a: MONDO:0015746 {source="ORDO:171709/btnt"} ! male infertility due to globozoospermia
@ShahimEssaid @nicolevasilevsky Thanks Shahim for your feedback! Your example above highlights that, ultimately, we're interested in all cases where there is at least one "is_a" that is only coming from source="ORDO:*". ('azoospermia' is a correct parent, while 'male infertility due to globozoospermia' is likely incorrect and should be reptresented as a phenotype instead.) So your "ANY" case above. (@zoependlington , if you have any objection, please feel free to comment.) As for your question on source="MONDO:Entailed" source="MONDO:Redundant" I'll leave that to @nicolevasilevsky and/or @cmungall . Thanks! Paola
Agreed with @paolaroncaglia, we'd be interested in the "ANY" case. So no objection from me. Thank you for getting back to us!
Addendum: I guess if the results are too numerous, we would then probably want to start working on the results subset corresponding to the "ALL" case above. The "ALL" case is the one we had in mind first, as a first step in fixing the issue; but ultimately, the "ANY" case will need to be examined too to carry out a thorough cleanup. Maybe we could re-assess the strategy when we have an idea of numbers from Shahim's results. Any opinion @cmungall?
@paolaroncaglia and @zoependlington Shahim put together this list of Mondo terms for us. There are over 900 terms. I'm not sure what the best approach for this is? We could discuss further on our next call.
@nicolevasilevsky Thanks! I had a quick look at the first 2-3 terms in Shahim's list and, yes, I believe they need work. The best strategy probably needs discussion as it's going to be a significant amount of work. Zoë is away until Tuesday, so I'll catch up with her next week, and we can surely discuss with you on our next call on Feb 18th if not sooner. Thanks.
sounds good!
Making a note that MONDO:0019170 'polyarteritis nodosa' also seems to have some questionable superclasses. Full list: a) arteritis [ok based on def] b) systemic inflammatory disease associated with an acquired peripheral neuropathy [probably not ok, unless the disease is always associated with an acquired peripheral neuropathy; otherwise that's just a symptom] c) neurovascular disease [not ok; symptom] d) secondary glomerular disease [not ok; symptom] Note that the term has exactMatch not only with ORDO but also with other resources. Thanks.
Note that after this process we will want to find ORDO-only groupings that have no children and remove these
I recommend: switch this. prepare a set of ORDO-only grouping classes for obsoletion. obsolete all these, finding new homes for any that become orphans.
I'm thinking of combinatorial ones, e.g. 'ectodermal malformation syndrome associated with ocular features'. these are just repeating phenotypes in a grouping.
This is how I would get ORDO-onlies:
obo-grep.pl -r 'xref: Orph' mondo-edit.obo | obo-grep.pl --neg -r '(NCIT|OMIM|DOID)' - | obo-grep.pl -r _group -|grep ^name:
@cmungall @nicolevasilevsky (cc @zoependlington ) Zoe and I agree with your suggested strategy and will try to help. For us, it'd be easier to work through a shared spreadsheet than via Mondo PRs. If you could please provide the spreadsheet, Zoe and I will then look into it and make further suggestions as appropriate. To help find the biggest offenders/grouping terms/prioritize the obsoletions, could the spreadsheet please contain:
Mondo ID ORDO ID of the exact match label definition number of children number of parents Mondo ID and label(s) of parent(s) (a single field separated by pipes would work)
We could then add a column with our suggestions (e.g. remove parents x and y; place under z instead, etc.) in a formatted/useful manner to be agreed upon. Feel free to comment, and thank you!
Paola and Zoe
Parent | label | Child | label |
---|---|---|---|
MONDO:0015135 | primary immunodeficiency due to a genetic defect in innate immunity | MONDO:0015133 | quantitative and/or qualitative congenital phagocyte defect |
MONDO:0015135 | primary immunodeficiency due to a genetic defect in innate immunity | MONDO:0018545 | primary immunodeficiency with predisposition to severe viral infection |
MONDO:0015219 | non-syndromic central nervous system malformation | MONDO:0017104 | central nervous system cystic malformation |
MONDO:0015227 | non-syndromic limb malformation | MONDO:0017430 | non-syndromic congenital joint dislocations |
MONDO:0015227 | non-syndromic limb malformation | MONDO:0017431 | non-syndromic limb overgrowth |
MONDO:0015227 | non-syndromic limb malformation | MONDO:0019714 | non-syndromic polydactyly, syndactyly and/or hyperphalangy |
MONDO:0015490 | predominantly small-vessel vasculitis | MONDO:0015491 | immune complex mediated vasculitis |
MONDO:0015502 | pinnae and external auditory canal anomaly | MONDO:0044702 | X-linked external auditory canal atresia-dilated internal auditory canal-facial dysmorphism syndrome |
MONDO:0015594 | non-paraneoplastic limbic encephalitis | MONDO:0044683 | limbic encephalitis with neurexin-3 antibodies |
MONDO:0015642 | benign partial infantile seizures | MONDO:0015641 | benign infantile focal epilepsy with midline spikes and wave during sleep |
MONDO:0015652 | chromosomal anomaly with epilepsy as a major feature | MONDO:0044641 | 9q33.3q34.11 microdeletion syndrome |
MONDO:0015756 | myeloid hemopathy | MONDO:0015688 | myeloid neoplasms associated with eosinophilia and abnormality of PDGFRA, PDGFRB or FGFR1 |
MONDO:0015860 | anomaly of puberty or/and menstrual cycle | MONDO:0044660 | menstrual cycle-dependent periodic fever |
MONDO:0015915 | cerebellar malformation | MONDO:0020130 | malformation of the cerebellar vermis |
MONDO:0015921 | ARX-related epileptic encephalopathy | MONDO:0018496 | ARX-related encephalopathy-brain malformation spectrum |
MONDO:0015923 | acquired peripheral neuropathy | MONDO:0016137 | acute and subacute inflammatory demyelinating polyneuropathy |
MONDO:0015923 | acquired peripheral neuropathy | MONDO:0016172 | acquired sensory ganglionopathy |
MONDO:0015923 | acquired peripheral neuropathy | MONDO:0016178 | peripheral neuropathy associated with monoclonal gammopathy |
MONDO:0015923 | acquired peripheral neuropathy | MONDO:0016179 | acquired amyloid peripheral neuropathy |
MONDO:0015932 | non-syndromic urogenital tract malformation of female | MONDO:0015829 | non-syndromic uterovaginal malformation |
MONDO:0015933 | non-syndromic urogenital tract malformation of male | MONDO:0044644 | congenital agenesis of the scrotum |
MONDO:0015961 | genetic head and neck malformation | MONDO:0015482 | otomandibular dysplasia |
MONDO:0015961 | genetic head and neck malformation | MONDO:0018562 | genetic otorhinolaryngological malformation |
MONDO:0016148 | qualitative or quantitative defects of collagen 6 | MONDO:0016111 | non-dystrophic myopathy with collagen 6 anomaly |
MONDO:0016155 | qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan | MONDO:0016156 | qualitative or quantitative defects of FKRP |
MONDO:0016155 | qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan | MONDO:0016157 | qualitative or quantitative defects of fukutin |
MONDO:0016155 | qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan | MONDO:0016183 | qualitative or quantitative defects of protein glycosyltransferase-like |
MONDO:0016155 | qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan | MONDO:0016184 | qualitative or quantitative defects of protein O-mannosyltransferase 1 |
MONDO:0016155 | qualitative or quantitative defects of protein involved in O-glycosylation of alpha-dystroglycan | MONDO:0016185 | qualitative or quantitative defects of protein O-mannosyltransferase 2 |
MONDO:0016172 | acquired sensory ganglionopathy | MONDO:0016173 | non-paraneoplastic sensory ganglionopathy |
MONDO:0016186 | qualitative or quantitative defects of myofibrillar proteins | MONDO:0016187 | qualitative or quantitative defects of desmin |
MONDO:0016186 | qualitative or quantitative defects of myofibrillar proteins | MONDO:0016188 | qualitative or quantitative defects of alphaB-cristallin |
MONDO:0016186 | qualitative or quantitative defects of myofibrillar proteins | MONDO:0016189 | qualitative or quantitative defects of filamin C |
MONDO:0016186 | qualitative or quantitative defects of myofibrillar proteins | MONDO:0016190 | qualitative or quantitative defects of protein ZASP |
MONDO:0016221 | temporomandibular joint anomaly | MONDO:0018793 | primary condylar hyperplasia |
MONDO:0016925 | partial trisomy/tetrasomy of chromosome 5 | MONDO:0016942 | partial trisomy/tetrasomy of the short arm of chromosome 5 |
MONDO:0016930 | partial trisomy/tetrasomy of chromosome 9 | MONDO:0016960 | partial trisomy of the long arm of chromosome 9 |
MONDO:0016936 | partial trisomy/tetrasomy of chromosome 18 | MONDO:0016951 | partial trisomy/tetrasomy of the short arm of chromosome 18 |
MONDO:0016999 | X chromosome number anomaly | MONDO:0017000 | X chromosome number anomaly with female phenotype |
MONDO:0016999 | X chromosome number anomaly | MONDO:0017001 | X chromosome number anomaly with male phenotype |
MONDO:0017000 | X chromosome number anomaly with female phenotype | MONDO:0017002 | polysomy of X chromosome |
MONDO:0017083 | lipoma associated with neurospinal dysraphism | MONDO:0017084 | leptomyelolipoma |
MONDO:0017104 | central nervous system cystic malformation | MONDO:0017105 | glioependymal/ependymal cyst |
MONDO:0017344 | Epstein-Barr virus-associated carcinoma | MONDO:0017348 | lymphoepithelial-like carcinoma |
MONDO:0017595 | aggressive B-cell non-Hodgkin lymphoma | MONDO:0015818 | aggressive primary cutaneous B-cell lymphoma |
MONDO:0017595 | aggressive B-cell non-Hodgkin lymphoma | MONDO:0018813 | high grade B-cell lymphoma with MYC and/ or BCL2 and/or BCL6 rearrangement |
MONDO:0017653 | epilepsy and/or ataxia with myoclonus as major feature | MONDO:0017654 | non progressive epilepsy and/or ataxia with myoclonus as a major feature |
MONDO:0017653 | epilepsy and/or ataxia with myoclonus as major feature | MONDO:0017655 | progressive epilepsy and/or ataxia with myoclonus as a major feature |
MONDO:0017710 | congenital systemic veins anomaly | MONDO:0018811 | congenital portosystemic shunt |
MONDO:0018230 | primary bone dysplasia | MONDO:0018231 | primary bone dysplasia with progressive ossification of skin, skeletal muscle, fascia, tendons and ligaments |
MONDO:0018230 | primary bone dysplasia | MONDO:0018232 | primary bone dysplasia with micromelia |
MONDO:0018230 | primary bone dysplasia | MONDO:0019694 | spondylodysplastic dysplasia |
MONDO:0018230 | primary bone dysplasia | MONDO:0019699 | slender bone dysplasia |
MONDO:0018230 | primary bone dysplasia | MONDO:0019700 | primary bone dysplasia with multiple joint dislocations |
MONDO:0018230 | primary bone dysplasia | MONDO:0019704 | primary bone dysplasia with decreased bone density |
MONDO:0018230 | primary bone dysplasia | MONDO:0019705 | primary bone dysplasia with defective bone mineralization |
MONDO:0018230 | primary bone dysplasia | MONDO:0019707 | primary osteolysis |
MONDO:0018230 | primary bone dysplasia | MONDO:0019708 | primary bone dysplasia with disorganized development of skeletal components |
MONDO:0018230 | primary bone dysplasia | MONDO:0019709 | cleidocranial dysplasia and isolated cranial ossification defect |
MONDO:0018230 | primary bone dysplasia | MONDO:0019718 | lethal chondrodysplasia |
MONDO:0018230 | primary bone dysplasia | MONDO:0028741 | overgrowth or tall stature syndrome with skeletal involvement |
MONDO:0018454 | dysostosis of genetic origin | MONDO:0019710 | dysostosis with predominant craniofacial involvement |
MONDO:0018454 | dysostosis of genetic origin | MONDO:0019711 | dysostosis with predominant vertebral and costal involvement |
MONDO:0018454 | dysostosis of genetic origin | MONDO:0019712 | patellar dysostosis |
MONDO:0018455 | dysostosis of genetic origin with limb anomaly as a major feature | MONDO:0017429 | joint formation defects |
MONDO:0018455 | dysostosis of genetic origin with limb anomaly as a major feature | MONDO:0017433 | dysostosis with combined reduction defects of upper and lower limbs |
MONDO:0018455 | dysostosis of genetic origin with limb anomaly as a major feature | MONDO:0018236 | dysostosis with limb and face anomalies as a major feature |
MONDO:0018455 | dysostosis of genetic origin with limb anomaly as a major feature | MONDO:0019714 | non-syndromic polydactyly, syndactyly and/or hyperphalangy |
MONDO:0018562 | genetic otorhinolaryngological malformation | MONDO:0015502 | pinnae and external auditory canal anomaly |
MONDO:0018652 | biological anomaly without phenotypic characterization | MONDO:0018651 | lipoyl transferase 2 deficiency |
MONDO:0019063 | vascular anomaly | MONDO:0016235 | complex vascular malformation with associated anomalies |
MONDO:0019213 | cerebral organic aciduria | MONDO:0017686 | inborn aminoacylase deficiency |
MONDO:0019704 | primary bone dysplasia with decreased bone density | MONDO:0044675 | LRP5-related primary osteoporosis |
MONDO:0019712 | patellar dysostosis | MONDO:0044641 | 9q33.3q34.11 microdeletion syndrome |
MONDO:0020001 | respiratory or thoracic malformation | MONDO:0015929 | thoracic malformation |
MONDO:0020001 | respiratory or thoracic malformation | MONDO:0015930 | respiratory malformation |
MONDO:0020019 | digestive tract malformation | MONDO:0019513 | esophageal malformation |
MONDO:0020019 | digestive tract malformation | MONDO:0019998 | gastroduodenal malformation |
MONDO:0020019 | digestive tract malformation | MONDO:0019999 | intestinal malformation |
MONDO:0020020 | visceral malformation of the liver, biliary tract, pancreas or spleen | MONDO:0015213 | non-syndromic visceral malformation |
MONDO:0020052 | partial autosomal trisomy/tetrasomy | MONDO:0016925 | partial trisomy/tetrasomy of chromosome 5 |
MONDO:0020052 | partial autosomal trisomy/tetrasomy | MONDO:0016930 | partial trisomy/tetrasomy of chromosome 9 |
MONDO:0020052 | partial autosomal trisomy/tetrasomy | MONDO:0016936 | partial trisomy/tetrasomy of chromosome 18 |
MONDO:0020052 | partial autosomal trisomy/tetrasomy | MONDO:0016972 | partial duplication of the long arm of chromosome 22 |
MONDO:0020059 | gonosome number anomaly | MONDO:0016999 | X chromosome number anomaly |
MONDO:0020059 | gonosome number anomaly | MONDO:0017005 | Y chromosome number anomaly |
MONDO:0020133 | posterior fossa malformation | MONDO:0015915 | cerebellar malformation |
MONDO:0020138 | ataxia with dementia | MONDO:0020139 | early-onset ataxia with dementia |
MONDO:0020138 | ataxia with dementia | MONDO:0020140 | late-onset ataxia with dementia |
MONDO:0020152 | rare eyelid malformation | MONDO:0020155 | eyelid border anomaly |
MONDO:0020216 | secondary dysgenetic glaucoma | MONDO:0020221 | secondary glaucoma due to a proliferation and differentiation anomaly |
MONDO:0020217 | secondary dysgenetic glaucoma associated with neural crest cell migration anomaly | MONDO:0020219 | corneogoniodysgenesis |
MONDO:0020217 | secondary dysgenetic glaucoma associated with neural crest cell migration anomaly | MONDO:0020220 | corneoiridogoniodysgenesis |
MONDO:0020223 | lens and zonula anomaly | MONDO:0020235 | lens size anomaly |
MONDO:0020223 | lens and zonula anomaly | MONDO:0020237 | lens shape anomaly |
MONDO:0020262 | nervous system anomaly with eye involvement | MONDO:0020263 | spinocerebellar ataxia with oculomotor anomaly |
MONDO:0020262 | nervous system anomaly with eye involvement | MONDO:0020264 | spinocerebellar degenerescence and spastic paraparesis with an oculomotor anomaly |
MONDO:0020266 | genodermatosis with ocular features | MONDO:0016997 | hereditary epidermolysis bullosa associated with ocular features |
MONDO:0020266 | genodermatosis with ocular features | MONDO:0020271 | phakomatosis with eye involvement |
MONDO:0020285 | transposition of the great arteries and conotruncal cardiac anomaly | MONDO:0020286 | aortic malformation |
MONDO:0020285 | transposition of the great arteries and conotruncal cardiac anomaly | MONDO:0020287 | pulmonary artery or pulmonary branch anomaly |
MONDO:0022410 | retinal ciliopathy | MONDO:0022397 | retinal ciliopathy due to mutation in the retinitis pigmentosa-1 gene |
MONDO:0022410 | retinal ciliopathy | MONDO:0022399 | retinal ciliopathy due to mutation in the rpgr gene |
MONDO:0022410 | retinal ciliopathy | MONDO:0022400 | retinal ciliopathy due to mutation in the rpgrip gene |
MONDO:0022410 | retinal ciliopathy | MONDO:0022404 | retinal ciliopathy due to mutation in usher gene |
MONDO:0022410 | retinal ciliopathy | MONDO:0022405 | retinal ciliopathy due to mutation in nephronophthisis gene |
MONDO:0022410 | retinal ciliopathy | MONDO:0022407 | retinal ciliopathy due to mutation in bardet-biedl gene |
MONDO:0044685 | autoimmune/inflammatory optic neuropathy | MONDO:0044687 | chronic relapsing inflammatory optic neuropathy |
MONDO:0044685 | autoimmune/inflammatory optic neuropathy | MONDO:0044688 | isolated optic neuritis |
MONDO:0044685 | autoimmune/inflammatory optic neuropathy | MONDO:0044689 | recurrent idiopathic neuroretinitis |
@cmungall Any chance you could export the table above as a Google spreadsheet, please? Ignore me if you're still working on it. Thanks.
I can do it! Here is a spreadsheet
Thanks @nicolevasilevsky and @cmungall . We'll work on it over the next few days and will add comments in the spreadsheet. Will ping you when we're done and go from there.
@cmungall I have a question on the spreadsheet already please. My understanding is that you have extracted Mondo terms that only have ORDO evidence. MONDO:0016172 acquired sensory ganglionopathy is one such term (in the spreadsheet) and has 2 children, both of which only have ORDO evidence, but only 1 of the 2 children is in the spreadsheet. Same for MONDO:0015860 anomaly of puberty or/and menstrual cycle - has several children and >1 ORDO-only, but only 1 child is in the spreadsheet. May I please make sure if I'm missing anything before I keep going? Thanks, and have a good weekend!
@cmungall @nicolevasilevsky Sorry to disturb you again about this (do let me know if you can't address this right now). I was hoping to start work on the list/spreadsheet of ORDO terms that you prepared, but I came across an issue, see my earlier comment in this ticket. If you have a chance, could you please address my question there? Thanks! :-)
The question is for @cmungall, right?
Everything is okay in Portland (so far), I am more worried about you! Feel free to ping us anytime @paolaroncaglia.
@nicolevasilevsky and @cmungall
The question is for @cmungall, right?
Right :-) Thank you for your concern and availability! All the best, Paola
I'm investigating
This was a quick query intended just to give high profile candidates for obsoletion. There may be better ways of doing this
perhaps @ShahimEssaid could help with a query?
@cmungall Thank you for following up on this. May I please ask if you or @nicolevasilevsky heard back from @ShahimEssaid about possibly helping with a query? I understand if the health emergency makes it difficult to progress on this. When you can, please let me know where we are with this; because if you need more time, no problem at all, I'm happy to start looking at the list of high profile candidates for obsoletion you provided, and I'll look up their children myself via OLS or Protege. Asking just so we can avoid duplication of efforts. Thank you all, and take care.
I just pinged @ShahimEssaid again. I know he has a lot of deadlines right now, so you could proceed without him @paolaroncaglia that would be great. Hopefully Shahim will be able to comment here soon.
Thanks!
@nicolevasilevsky Based on https://github.com/monarch-initiative/mondo/issues/1283#issuecomment-604033234, Zoe and I fear that any work on current Orphanet terms in Mondo may risk being "over-written" by an upcoming update of the Orphanet ingest. So the tasks discussed in recent comments in this thread may best be delayed. We'll discuss internally at EFO, and will then catch up with you at our next EFO-Mondo call. Of course, if there's any concern or urgency on either side, we can discuss sooner. Thanks!
Good point! It is my understanding that the new Orphanet ingest will not override any work that has currently been done though (as we've made a lot of changes already.)
I hope you don't mind putting this off. it's okay to delay on our end.
@nicolevasilevsky
Good point! It is my understanding that the new Orphanet ingest will not override any work that has currently been done though (as we've made a lot of changes already.)
That would make sense to me too! I'll aim at looking at the list of grouping terms before our next EFO-Mondo call, so we can hopefully discuss then.
I hope you don't mind putting this off. it's okay to delay on our end.
It's a bit of a priority on our end, for Open Targets, so now that I'm reassured that the work wouldn't be overwritten, I'll try to spend some time on it. I'm just sticking to non-committal phrasing because you never know these days. Thanks, take care and speak soon!
Making a note here that another (Orphanet-derived) problematic term is MONDO:0016575 'primary ciliary dyskinesia'. 3 of its 5 parents represent symptoms, and it has 41 children, that inherit the incorrect ancestry. Notably, 'primary ciliary dyskinesia' is not inSubset ordo_group_of_disorders. Its parent 'ciliopathy' is, but its own parents are fine, so focusing on ORDO grouping terms alone may be of limited use - need to go deeper too.
For a quick fix while I'm looking into this, you may want to
Thanks!
@nicolevasilevsky @cmungall Quick update on the ORDO grouping terms you highlighted in https://github.com/monarch-initiative/mondo/issues/834#issuecomment-595322698. I looked at a subset of those (8/57), and added comments in https://docs.google.com/spreadsheets/d/1KRAoGoj1O2-nm0ll5vlDMzm-9bsgMvvNza9wFIz6REA/edit#gid=656900674 (tab "Paola's summary"). The rows in red are for terms I'd suggest prioritizing for obsoletion. (Note, those 3 terms weren't in your list originally, but are their parents or ancestors.) The comment columns for those contains some general consideration and tips I hope you'll find useful. It's still a work in progress, but I wanted to write down some notes for your consideration in case I can't come back to this before our meeting on Monday. Thanks!
The parent 'rare pulmonary disease' is also suspicious and should be deleted.
This term is obsoleted: MONDO_0015118
closing this, duplicate with https://github.com/monarch-initiative/mondo/issues/704
@sabrinatoro and I are working on this.
also related to https://github.com/monarch-initiative/mondo/issues/324
In #824, there was a note about a need to review the only-ordo supported is-as relationships?
It also came up in https://github.com/EBISPOT/efo/issues/553 MONDO_0009061 'Cystic fibrosis': from @paolaroncaglia: of all its current parents in EFO, only 'autosomal recessive disease' should stay; all other parents should be deleted bcs they represent symptoms/phenotypes, CF is a multi-systemic disease.