Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

review ORDO grouping classes #5114

Closed
nicolevasilevsky opened this issue Jun 29, 2022 · 14 comments
Closed

review ORDO grouping classes #5114

nicolevasilevsky opened this issue Jun 29, 2022 · 14 comments
Labels
effort-XL Ticket may take more than 2 hours complete mass obsoletion obsolete This includes both obsolete and merge requests ordo-project

Comments

@nicolevasilevsky
Copy link
Member

Consider obsoleting Orphanet grouping classes based on Mondo Exclusion reasons.

See spreadsheet.
@nicolevasilevsky nicolevasilevsky self-assigned this Jun 29, 2022
@nicolevasilevsky nicolevasilevsky added ordo-project obsolete This includes both obsolete and merge requests labels Jun 29, 2022
@nicolevasilevsky nicolevasilevsky added this to the September release milestone Jun 29, 2022
@nicolevasilevsky nicolevasilevsky mentioned this issue Jun 29, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Jul 1, 2022
@nicolevasilevsky
add superclasses
5ce48da 
 to terms that will lose their parent when we obsolete ORDO grouping classes

address #5114
@nicolevasilevsky nicolevasilevsky mentioned this issue Jul 1, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Jul 1, 2022
@nicolevasilevsky
add superclasses (#5124)
76f5be1 
* add superclasses

 to terms that will lose their parent when we obsolete ORDO grouping classes

address #5114

* revise parent

* revise superclass for 'pseudo-TORCH syndrome'

* add obs tag to sarcoglycanopathy
@ErinRiggs
Copy link
Collaborator

Hi @nicolevasilevsky - I got to this ticket from the obsoletion candidate report Larry Babb has prepared for ClinGen - the report indicated that you were considering obsoleting "syndromic intellectual disability" (MONDO:0000508). ClinGen currently has 21 gene-disease validity curations and 6 dosage sensitivity curations using this term. I can't access the linked spreadsheet for any further information, but just wanted to send a note immediately to say that we are interested in further discussion on this term! Let me know next steps.

@nicolevasilevsky
Copy link
Member Author

Hi @ErinRiggs - thanks for letting me know! We'll remove it from the obsoletion list since it is being used by ClinGen.

Please do let us know if there are any other terms in use by ClinGen on the obsoletion list and we'll keep them.

nicolevasilevsky added a commit that referenced this issue Jul 5, 2022
@nicolevasilevsky
remove syndromic intellectual disability as a obsoletion candidate
d84e2ce 
address #5114
@nicolevasilevsky nicolevasilevsky mentioned this issue Jul 5, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Jul 6, 2022
@nicolevasilevsky
remove syndromic intellectual disability as a obsoletion candidate (#…
8b7394b 
…5135)

address #5114
nicolevasilevsky added a commit that referenced this issue Jul 6, 2022
@nicolevasilevsky
revise superclasses for ORDO only is_a supported classes
dc35ed1 
address #5114
@nicolevasilevsky nicolevasilevsky mentioned this issue Jul 6, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Jul 7, 2022
@nicolevasilevsky
revise superclasses for ORDO only is_a supported classes (#5143)
ab24003 
* revise superclasses for ORDO only is_a supported classes

address #5114

* exclude superclasses

* exclude superclass for 'erythrokeratodermia variabilis'

add defs
@nicolevasilevsky
Copy link
Member Author

nicolevasilevsky commented Jul 7, 2022 •
edited

@ErinRiggs I spoke to our team on the curation call today and we do prefer to consider obsoleting the term "syndromic intellectual disability" (MONDO:0000508), as it is a grouping class that is currently grouping together disorders that have a feature of intellectual disability but not necessarily terms that are types of a syndromic intellectual disability. In addition, the grouping is incomplete, there may be additional terms that should be grouped under this term.

Could you let us know how you are using this term in your curations, and if there is another term that could be used from Mondo instead?

We're not determined to obsolete it, but if we do keep it, we'll need to thoroughly review this branch and make sure the grouping class is being used properly.

Thank you!

nicolevasilevsky added a commit that referenced this issue Jul 7, 2022
@nicolevasilevsky
revise def and add seeAlso for 'Batten-Turner congenital myopathy'
4138106 
address #5114
@nicolevasilevsky nicolevasilevsky mentioned this issue Jul 7, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Jul 7, 2022
@nicolevasilevsky
revise def and add seeAlso for 'Batten-Turner congenital myopathy' (#…
bcfde2b 
…5152)

address #5114
@nicolevasilevsky nicolevasilevsky added the effort-XL Ticket may take more than 2 hours complete label Aug 2, 2022
nicolevasilevsky added a commit that referenced this issue Aug 2, 2022
@nicolevasilevsky
obsolete ORDO grouping classes
23b0c53 
address #5114
@nicolevasilevsky nicolevasilevsky mentioned this issue Aug 2, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Aug 3, 2022
@nicolevasilevsky
reclassify terms whose parent will be obsoleted
c7fdb02 
address #5114
@nicolevasilevsky nicolevasilevsky mentioned this issue Aug 3, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Aug 3, 2022
@nicolevasilevsky
obsolete ORDO grouping classes (#5225)
d23eff9 
* obsolete ORDO grouping classes

address #5114

* 'obsolete neurometabolic disease'

* remove axiom from genetic skin disease

* remove axioms from genetic hair anomaly, genetic nail anomaly

* add consider

* remove superclasses

* remove superclasses

* obsolete terms

MONDO:0015163	primary glomerular disease
MONDO:0016139	qualitative or quantitative protein defects in neuromuscular diseases
MONDO:0016193	qualitative or quantitative defects of alpha-actin
MONDO:0018282	qualitative or quantitative defects of alpha-dystroglycan
MONDO:0016195	qualitative or quantitative defects of beta-myosin heavy chain (MYH7)
MONDO:0016152	qualitative or quantitative defects of calpain
MONDO:0016145	qualitative or quantitative defects of dysferlin
MONDO:0016147	qualitative or quantitative defects of dystrophin
MONDO:0016196	qualitative or quantitative defects of emerin
MONDO:0016200	qualitative or quantitative defects of glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase -
MONDO:0016150	qualitative or quantitative defects of integrin alpha-7
MONDO:0016149	qualitative or quantitative defects of merosin
MONDO:0016186	qualitative or quantitative defects of myofibrillar proteins
MONDO:0016201	qualitative or quantitative defects of myotilin
MONDO:0016154	qualitative or quantitative defects of myotubularin
MONDO:0016194	qualitative or quantitative defects of nebulin

* remove parents

* obsolete terms

MONDO:0024255
MONDO:0019282
MONDO:0018609
MONDO:0020208
MONDO:0021027
MONDO:0021028
MONDO:0018529
MONDO:0017303
MONDO:0017302
MONDO:0016197
MONDO:0016192
MONDO:0016191
MONDO:0016153
MONDO:0016144
MONDO:0016143
MONDO:0016142
MONDO:0016141

* fix source

* obsolete syndromic nail anomaly

* obsolete terms

MONDO:0043008
MONDO:0018283
MONDO:0016188
MONDO:0016189
MONDO:0016155
MONDO:0016190

* reclassify 'Behr syndrome'

* remove superclasses

* obsolete terms

MONDO:0016156
MONDO:0016183
MONDO:0016182
MONDO:0016184
MONDO:0016185

* save as
nicolevasilevsky added a commit that referenced this issue Aug 3, 2022
@nicolevasilevsky
revise parents and defs for ORDO grouping classes
4aac439 
address #5114
@nicolevasilevsky nicolevasilevsky mentioned this issue Aug 3, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Aug 3, 2022
@nicolevasilevsky
reclassify terms whose parent will be obsoleted (#5226)
df3ed32 
* reclassify terms whose parent will be obsoleted

address #5114

* reclassify children

* reclassify terms

* reclassify parents

* reclassify term

* remove superclass

* remove axioms

* obsolete terms

* exclude

* fix qc-deprecated-class-reference
nicolevasilevsky added a commit that referenced this issue Aug 3, 2022
@nicolevasilevsky
revise parents and defs for ORDO grouping classes (#5227)
b9bb58a 
* revise parents and defs for ORDO grouping classes

address #5114

* obsolete terms

MONDO:0019833
MONDO:0019721
MONDO:0019601
MONDO:0019589
MONDO:0017143

* fix synonym

* fix errors
@nicolevasilevsky nicolevasilevsky mentioned this issue Apr 8, 2023
Merged
nicolevasilevsky added a commit that referenced this issue Apr 8, 2023
@nicolevasilevsky
obsolete genetic hypertension (#6174)
02cfd0d 
address #5114
address #5952
@madysoncbrown
Copy link

The parent term for Fuhrmann Syndrome non-syndromic limb reduction defect (MONDO:0019713) is being obsoleted. What is the new term to which Fuhrmann Syndrome is going to be anchored? The ClinGen Dosage Sensitivity WG specifically picked non-syndromic limb reduction defect because it is the parent term for Fuhrmann Syndrome. The WG would want to consider using the new parent term for Fuhrmann Syndrome.

@nicolevasilevsky
Copy link
Member Author

Hi @madysoncbrown - thanks for your comment. Looking at this term, I think it should not be obsoleted.

This term is included in this paper PMID:31633310 (related ticket: #4948), so it should remain in Mondo.

cc @sabrinatoro

nicolevasilevsky added a commit that referenced this issue Sep 20, 2023
@nicolevasilevsky
remove non-syndromic limb reduction defect as a obs candidate
39de335 
address #5114
@nicolevasilevsky nicolevasilevsky mentioned this issue Sep 20, 2023
Merged
nicolevasilevsky added a commit that referenced this issue Sep 20, 2023
@nicolevasilevsky
remove non-syndromic limb reduction defect as a obs candidate (#6683)
c1d19f5 
address #5114
@nicolevasilevsky nicolevasilevsky removed their assignment Dec 8, 2023
@nicolevasilevsky nicolevasilevsky removed this from the January release milestone Dec 15, 2023
@nicolevasilevsky nicolevasilevsky mentioned this issue Feb 26, 2024
Closed
@sabrinatoro
Copy link
Collaborator

@nicolevasilevsky
I think this issue can be closed. If we want to do another round of review, we can create a new issue.
Do you agree?

@nicolevasilevsky
Copy link
Member Author

YES!

@nicolevasilevsky nicolevasilevsky mentioned this issue Apr 19, 2024
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
effort-XL Ticket may take more than 2 hours complete mass obsoletion obsolete This includes both obsolete and merge requests ordo-project
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
5 participants
@larrybabb @nicolevasilevsky @sabrinatoro @ErinRiggs @madysoncbrown