MONDO:####-obsoleted used for source

sabrinatoro commented 1 year ago

(there is probably another issue with this, but I couldn't find it)

What are "MONDO:####-obsoleted" used for source? What do they represent?

Eg: MONDO:0013626 - 'psoriasis 14, pustular'

is_a ‘epidermal disease’ [source: MONDO:0019274-obsoleted]
is_a ‘skin disorder’ [source: MONDO:0019275-obsoleted]

It looks like they are often the source of bad classification for example:

Do we need these sources? Can we remove them? Can/should we remove the whole axiom if the only source is a MONDO:###-obsoleted?

sabrinatoro commented 1 year ago

@cmungall (CC @nicolevasilevsky )

sabrinatoro commented 1 year ago

from the call on March 2nd, 2023 : these MONDO:###-obsoleted are keeping track of Mondo terms that were obsoleted. We should query to see how many of these sources we have and assess whether it would make sense to remove these sources. We could also remove the axiom with only MONDO:###-obsoleted as source and check whether we end up with orphan terms. (this would help with the error in classification as shown in the comment above)

cmungall commented 1 year ago

you will specifically see these where the obsolete was an intermediate and the axioms were rewired

On Thu, Mar 2, 2023 at 6:49 PM sabrinatoro @.***> wrote:

from the call on March 2nd, 2023 : these MONDO:###-obsoleted are keeping track of Mondo terms that were obsoleted. We should query to see how many of these sources we have and assess whether it would make sense to remove these sources. We could also remove the axiom with only MONDO:###-obsoleted as source and check whether we end up with orphan terms. (this would help with the error in classification as shown in the comment above)

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nicolevasilevsky commented 1 year ago

we don't need to keep these IDs but we should review these superclasses first.

nicolevasilevsky commented 2 months ago

discussed on the curation call on 2024-04-04:

Decision

We will remove all of the superclass assertions that have MONDO:XXXXXXX-obsoleted
- - in cases where there is only on superclass assertion that has the source MONDO:XXXXXXX-obsoleted, we will review these and manually add a new superclass
We will remove all of the relationship: excluded_subClassOf annotations that have MONDO:XXXXXXX-obsoleted

To do's

[ ] @twhetzel please write a script and generate a report that shows:
1. all of the classes that have a superclass where the source is only MONDO:XXXXXXX-obsoleted (eg is_a: MONDO:0005093 {source="MONDO:0018798-obsoleted"} ! skin disorder (on MONDO:0007118).
[ ] Nicole will review these and confirm it is okay to delete these.
[ ] Next, @twhetzel write a script to delete all of these superclass assertions
1. of these classes above, we need a list of the classes where these superclasses are the only superclass for that term.
[ ] In these cases, Nicole will manually review these and add new parents

See example below:

[Term]
id: MONDO:0007852
name: palmoplantar keratoderma-deafness syndrome
def: "Palmoplantar keratoderma-deafness syndrome is a keratinization disorder characterized by focal or diffuse palmoplantar keratoderma. A patchy distribution is observed with accentuation on the thenars, hypothenars and the arches of the feet. The disease becomes apparent in infancy and is associated with sensorineural hearing loss that shows a variable age of onset. Due to genetic and clinical similarities, it has been proposed that palmoplantar keratoderma-deafness syndrome, knuckle pads-leukonychia-sensorineural deafness-palmoplantar hyperkeratosis syndrome and keratoderma hereditarium mutilans may represent variants of one broad disorder of syndromic deafness with heterogeneous phenotype. The disease is transmitted in an autosomal dominant manner with incomplete penetrance." [Orphanet:2202]
subset: gard_rare {source="GARD:3094"}
subset: nord_rare {source="MONDO:NORD"}
subset: ordo_disease {source="Orphanet:2202"}
subset: orphanet_rare {source="Orphanet:2202"}
subset: rare
synonym: "diffuse palmoplantar keratoderma with deafness (subtype)" RELATED [GARD:0003094]
synonym: "focal palmoplantar keratoderma with sensorineural deafness (subtype)" RELATED [GARD:0003094]
synonym: "hereditary palmoplantar keratoderma with deafness (subtype)" RELATED [GARD:0003094]
synonym: "keratoderma palmoplantar deafness" RELATED [GARD:0003094]
synonym: "keratoderma palmoplantar, with deafness" RELATED [GARD:0003094]
synonym: "keratoderma, palmoplantar, with deafness" RELATED [OMIM:148350]
synonym: "palmoplantar hyperkeratosis-deafness syndrome" EXACT [Orphanet:2202]
synonym: "palmoplantar hyperkeratosis-hearing loss syndrome" EXACT [Orphanet:2202]
synonym: "palmoplantar keratoderma and sensorineural deafness" RELATED [GARD:0003094]
synonym: "palmoplantar keratoderma-hearing loss syndrome" EXACT [Orphanet:2202]
synonym: "PPK-deafness syndrome" EXACT [Orphanet:2202]
xref: DOID:0111505 {source="MONDO:equivalentTo"}
xref: GARD:3094 {source="Orphanet:2202"}
xref: ICD10CM:Q82.8 {source="Orphanet:2202/attributed", source="Orphanet:2202/ntbt", source="Orphanet:2202"}
xref: MESH:C536152 {source="Orphanet:2202", source="MONDO:equivalentTo", source="Orphanet:2202/e"}
xref: OMIM:148350 {source="Orphanet:2202", source="MONDO:equivalentTo", source="Orphanet:2202/e"}
xref: Orphanet:2202 {source="OMIM:148350", source="MONDO:equivalentTo"}
xref: UMLS:C1835672 {source="OMIM:148350", source="Orphanet:2202", source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="Orphanet:2202/e"}
is_a: MONDO:0017666 {source="MONDO:0020094-obsoleted"} ! diffuse palmoplantar keratoderma
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/4284 {source="MONDO:mim2gene_medgen"} ! GJB2
property_value: confidence "3.7222222222222223" xsd:double

there are some cases where there is additional support for the superclass assertion from other sources, such as is_a: MONDO:0031166 {source="MONDO:0020243-obsoleted", source="OMIM:136550", source="https://github.com/monarch-initiative/mondo/pull/2571/"} ! macular dystrophy, retinal (on MONDO:0007630)
- [ ] In these cases, we just want to delete the MONDO:XXXXXXX-obsoleted, but leave the other source(s) and the superclass assertion.
- in this particular case, the GitHub URL needs to moved to the 'term tracker item' annotation (see below)
The MONDO:XXXXXXX-obsolete is in a lot of excluded_subclassOf annotations too. Could we please have a list of these in the report
- [ ] Nicole will review
- [ ] next, @twhetzel should remove exlcuded_subclassOf annotations with only MONDO:XXXXXXX-obsolete

example: relationship: excluded_subClassOf MONDO:0100036 {source="MONDO:0017655-obsoleted", source="https://orcid.org/0000-0001-5208-3432"} ! variable age onset epilepsy (on MONDO:0008045).

There are some cases where the GitHub link is included in the source annotation (eg is_a: MONDO:0018075 {source="MONDO:0017085-obsoleted", source="https://github.com/monarch-initiative/mondo/pull/2571/"} ! neural tube defect (on MONDO:0007316).
- [ ] We'd like to clean these up and move the GitHub URL to be a term tracker item annotation (egproperty_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/2571" xsd:anyURI)

sabrinatoro commented 4 weeks ago

based on the last comment, I am assigning to @twhetzel .

monarch-initiative / mondo

MONDO:####-obsoleted used for source #6004

Decision

To do's