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

[NTR] New lung terms - from Mattias and Christina #5261

Open
nicolevasilevsky opened this issue Aug 10, 2022 · 11 comments
Open

[NTR] New lung terms - from Mattias and Christina #5261

nicolevasilevsky opened this issue Aug 10, 2022 · 11 comments
Assignees
@twhetzel
Labels
New term request user request A request from an external user
Milestone
[obsolete] Novemb...

Comments

@nicolevasilevsky
Copy link
Member

nicolevasilevsky commented Aug 10, 2022 •
edited
Loading

Peter and I met with pulmonary experts Mattias and Christina. We'll add new lung terms from this spreadsheet.

Related to #3026

cc @pnrobinson
@nicolevasilevsky nicolevasilevsky self-assigned this Aug 10, 2022
@nicolevasilevsky nicolevasilevsky added this to the September release milestone Aug 10, 2022
This was referenced Aug 10, 2022
Closed
Closed
nicolevasilevsky added a commit that referenced this issue Aug 10, 2022
@nicolevasilevsky
add synonyms and definitions to lung terms
98e5c35 
address #5261
@nicolevasilevsky nicolevasilevsky mentioned this issue Aug 10, 2022
Closed
@nicolevasilevsky
Copy link
Member Author

@pnrobinson
is pulmonary hypoplasia the same as MONDO:0020419 'pulmonary artery hypoplasia'?

@pnrobinson
Copy link
Member

pulmonary hypoplasia means undergrowth of the lung, so it is different!

@nicolevasilevsky
Copy link
Member Author

Thanks @pnrobinson!

nicolevasilevsky added a commit that referenced this issue Aug 10, 2022
@nicolevasilevsky
add new lung terms (Mattias and Christina)
76ea89f 
address #5261
@nicolevasilevsky nicolevasilevsky mentioned this issue Aug 10, 2022
Closed
nicolevasilevsky added a commit that referenced this issue Aug 11, 2022
@nicolevasilevsky
Lung terms (3/3): add new terms associated with genes
8899b89 
close #5261
@nicolevasilevsky nicolevasilevsky mentioned this issue Aug 11, 2022
Closed
nicolevasilevsky added a commit that referenced this issue Aug 11, 2022
@nicolevasilevsky
Lung terms (3/3): add new terms associated with genes
1f491fb 
Note: one term was added as a synonym for an existing term:
Immunodeficiency, autosomal recessive due to ZNFX1 deficiency, I believe is equivalent to OMIM:619644

close #5261
@nicolevasilevsky nicolevasilevsky mentioned this issue Aug 11, 2022
Closed
@nicolevasilevsky
Copy link
Member Author

From Christina:
Immunodeficiency, autosomal recessive, due to ZNFX1 deficiency: same as in OMIM 619644; citation: PMID: 33872655. I will add this as a synonym to MONDO:0030491

nicolevasilevsky added a commit that referenced this issue Aug 16, 2022
@nicolevasilevsky
add synonym to 'immunodeficiency 91 and hyperinflammation'
2c87d8f 
address #5261
@nicolevasilevsky nicolevasilevsky mentioned this issue Aug 16, 2022
Merged
@nicolevasilevsky
Copy link
Member Author

From Christina:
immunodeficiency, due to IKZF3 deficiency: Has also an OMIM ID: 619437; citation: PMID: 34155405. i added this a synonym of MONDO:0030333 'immunodeficiency 84'

nicolevasilevsky added a commit that referenced this issue Aug 16, 2022
@nicolevasilevsky
add synonym to 'immunodeficiency 91 and hyperinflammation' (#5278)
86e5821 
* add synonym to 'immunodeficiency 91 and hyperinflammation'

address #5261

* add synonym to MONDO:0030491 'immunodeficiency 91 and hyperinflammation
@nicolevasilevsky
Copy link
Member Author

talked to Ada on 09/21/22- I will send PMIDs to her for any terms that are not in OMIM and they will consider adding them and then we can map them in Mondo

nicolevasilevsky added a commit that referenced this issue Sep 21, 2022
@nicolevasilevsky
add new lung terms
3518ebc 
ROBOT gene
address #5261
@nicolevasilevsky nicolevasilevsky mentioned this issue Sep 21, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Sep 22, 2022
@nicolevasilevsky
add new lung terms (#5407)
4e04743 
* add new lung terms

ROBOT gene
address #5261

* remove term

* add def and xrefs to MONDO:0009842

* add syn

* remove dup term

* fix xref

* relabel non-severe combined immunodeficiency due to polymerase delta deficiency

* fix seeAlso
nicolevasilevsky added a commit that referenced this issue Sep 23, 2022
@nicolevasilevsky
add defs, syns to lung terms
18e89f3 
address #5261
@nicolevasilevsky nicolevasilevsky mentioned this issue Sep 23, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Sep 24, 2022
@nicolevasilevsky
add inheritance to lung terms
db03b58 
address #5261
@nicolevasilevsky nicolevasilevsky mentioned this issue Sep 24, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Sep 24, 2022
@nicolevasilevsky
add new lung terms
c5fff2d 
ROBOT Add new term
ROBOT add subclass
address #5261
@nicolevasilevsky nicolevasilevsky mentioned this issue Sep 24, 2022
Merged
nicolevasilevsky added a commit that referenced this issue Oct 3, 2022
@nicolevasilevsky
add defs, syns to lung terms (#5412)
8099017 
* add defs, syns to lung terms

address #5261

* fix xref
nicolevasilevsky added a commit that referenced this issue Oct 3, 2022
@nicolevasilevsky
add inheritance to lung terms (#5413)
7c43512 
* add inheritance to lung terms

address #5261

* remove term
nicolevasilevsky added a commit that referenced this issue Oct 3, 2022
@nicolevasilevsky
add new lung terms (#5414)
bd1afc4 
* add new lung terms

ROBOT Add new term
ROBOT add subclass
address #5261

* fix errors

* exclude from QC
@nicolevasilevsky
Copy link
Member Author

this is done, will be available in the November release

@cmungall
Copy link
Member

It looks like the genes were not added? E.g.

id: MONDO:0800136
name: non-severe combined immunodeficiency due to COPG1 deficiency
def: "Any non-severe combined immunodeficiency caused by a deficiency in the COPG1 gene." [PMID:33529166]
subset: gard_rare {source="MONDO:GARD"}
subset: nord_rare {source="MONDO:NORD"}
subset: rare
is_a: MONDO:0018814 {source="https://orcid.org/0000-0002-7371-8158", source="https://orcid.org/0000-0003-0113-912X"} ! non-SCID combined immunodeficiency
relationship: RO:0002573 HP:0000007 {source="https://orcid.org/0000-0002-7371-8158", source="https://orcid.org/0000-0003-0113-912X"} ! has modifier Autosomal recessive inheritance
property_value: IAO:0000233 "#5261" xsd:anyURI

But no link to COPG1?

@cmungall cmungall mentioned this issue Aug 21, 2024
Open
@nicolevasilevsky nicolevasilevsky removed their assignment Aug 21, 2024
@nicolevasilevsky
Copy link
Member Author

nicolevasilevsky commented Aug 21, 2024 •
edited by twhetzel
Loading

to do:

  • import COPG1 gene
  • add axiom to MONDO:0800136 non-severe combined immunodeficiency due to COPG1 deficiency

@twhetzel can you take care of this?

@twhetzel
Copy link
Collaborator

twhetzel commented Nov 4, 2024

Sorry, I missed this one! Yes, I can do that. I'll add this to the Nov board so it's tracked in a release board, but will be in Dec release.

There is now a gSheet to add any imports needed when we do this step for the Mondo Release SOP.

@twhetzel
Copy link
Collaborator

twhetzel commented Nov 6, 2024

Importing the gene is blocked by an issue where the refresh-merged is running out of memory.

@sabrinatoro sabrinatoro added the user request A request from an external user label Nov 6, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@twhetzel twhetzel

Labels
New term request user request A request from an external user
Projects
None yet
Milestone
[obsolete] November release
5 participants
@cmungall @twhetzel @pnrobinson @nicolevasilevsky @sabrinatoro