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Review the classification of "cancer predisposition" #6515

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sabrinatoro opened this issue Jul 31, 2023 · 6 comments · Fixed by #7595
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Review the classification of "cancer predisposition" #6515

sabrinatoro opened this issue Jul 31, 2023 · 6 comments · Fixed by #7595
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February 2024

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sabrinatoro commented Jul 31, 2023 •
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"predisposition" to cancer is considered to be a "disease" (these diagnoses lead to specific medical actions, and have specific managed care, BEFORE one gets a cancer diagnosis).

We need to review the classification to add these predispositions terms into the disease branch
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Note: we have a 'precancerous condition' (MONDO:0021074) class in Mondo

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related issues:

@sabrinatoro sabrinatoro self-assigned this Jul 31, 2023
@sabrinatoro sabrinatoro added this to the September release milestone Aug 10, 2023
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related to #6533

@sabrinatoro sabrinatoro mentioned this issue Dec 14, 2023
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Questions to ClinGen:

  • Are the terms to be requested "cancer predisposition"? If they cover both cancer and cancer predisposition, can they be considered as "syndromic disorder of cell proliferation"?
  • Are these new terms requested intended to group diseases (specifically both cancer and cancer predisposition)?

@sagehrke sagehrke moved this to Backlog in 2024-02 Mondo Release Jan 4, 2024
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sabrinatoro commented Feb 1, 2024 •
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From meeting with ClinGen on 24-01-25:

  • "cell proliferation disorder" is problematic because some cancers are not only due to issues with cell proliferation (e.g. lack of apoptosis,...)
  • classification is also problematic (polyp are "precancer") --> note to self, check NCIT classification
  • "hereditary neoplastic syndrome" (MONDO:0015356) should be an upper class on its own

sabrinatoro added a commit that referenced this issue Feb 1, 2024
@sabrinatoro
Reverted some changes made in this release
9a6c620 
Addresses #6515
Some suggested changes have been reviewed by experts and need to be reverted (note that the changes reverted were not released yet)
- reverting label for MONDO:0045024
- remove new term 'syndromic disorder of cell proliferation' (MONDO:0700245) - only deleted since it was not in any Mondo release
@sabrinatoro sabrinatoro mentioned this issue Feb 1, 2024
Merged
sabrinatoro added a commit that referenced this issue Feb 1, 2024
@sabrinatoro
Reverted some changes made in this release (#7226)
3c6619b 
Addresses #6515
Some suggested changes have been reviewed by experts and need to be reverted (note that the changes reverted were not released yet)
- reverting label for MONDO:0045024
- remove new term 'syndromic disorder of cell proliferation' (MONDO:0700245) - only deleted since it was not in any Mondo release
@sagehrke sagehrke moved this to Backlog in 2024-03 Mondo Release Feb 22, 2024
@sabrinatoro sabrinatoro moved this to Backlog in 2024-04 Mondo Release Mar 4, 2024
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Updated spreadsheet from ClinGen: https://docs.google.com/spreadsheets/d/100Cg6PF9iFPV6AEFB2SIAlCAPRWrTJLR/edit#gid=360206974

sabrinatoro added a commit that referenced this issue Apr 15, 2024
@sabrinatoro
update cancer predisposition
930b973 
Closes #6515

This update is based on the ClinGen Hereditary Cancer Gene Curation Expert Panel
Spreadsheet: https://docs.google.com/spreadsheets/d/100Cg6PF9iFPV6AEFB2SIAlCAPRWrTJLR/edit#gid=1863365376
@sabrinatoro sabrinatoro mentioned this issue Apr 15, 2024
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nicolevasilevsky pushed a commit that referenced this issue Apr 16, 2024
@sabrinatoro
update cancer predisposition (#7595)
f2fe2c7 
* update cancer predisposition

Closes #6515

This update is based on the ClinGen Hereditary Cancer Gene Curation Expert Panel
Spreadsheet: https://docs.google.com/spreadsheets/d/100Cg6PF9iFPV6AEFB2SIAlCAPRWrTJLR/edit#gid=1863365376

* Update mondo-edit.obo

* Update mondo-edit.obo
@github-project-automation github-project-automation bot moved this from Backlog to Done in 2024-05 Mondo Release Apr 16, 2024
@sabrinatoro sabrinatoro mentioned this issue Jun 5, 2024
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2024-05 Mondo Release
Status: Done
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February 2024
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update cancer predisposition monarch-initiative/mondo
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