search

cBioPortal / icebox

very low priority issues
0 stars 0 forks source link

Inconsistencies in using HOMDEL/DeepDel #474

Open kalletlak opened 4 years ago

kalletlak commented 4 years ago

Different naming conventions for homozygous deletion is followed in different pages. Examples

  1. In OQL -> HOMDEL
  2. Study-view CNA table -> DEL
  3. Patient-view Copy Number Alterations table -> DeepDel
  4. Results page Mutations tab -> DeepDel
  5. Patient view Mutations table -> DeepDel
  6. Comparison page copy-number tab -> DeepDel
  7. Oncoprint -> HOMODELETED (in tooltip)

For hetloss,

  1. In OQL -> HETLOSS
  2. Results page Mutations tab -> ShallowDel
  3. Patient view Mutations table -> ShallowDel
  4. Oncoprint -> ShallowDel (in tooltip)
jjgao commented 4 years ago

@cBioPortal/product Should we change everything to DeepDel? (We can support both HOMDEL and DeepDel in oql for backward compatibility.)

tmazor commented 4 years ago

Sounds good to me. But then we should also change HETLOSS in OQL (and anywhere else it might appear).

schultzn commented 4 years ago

Agreed. But it would be nice if we could still support the old terms (maybe in an undocumented way).

On Dec 16, 2019, at 1:03 PM, Tali Mazor notifications@github.com wrote:

Sounds good to me. But then we should also change HETLOSS in OQL (and anywhere else it might appear).

— You are receiving this because you are on a team that was mentioned. Reply to this email directly, view it on GitHub https://github.com/cBioPortal/icebox/issues/474?email_source=notifications&email_token=AC2XPYF7C23HTINBBO2NYL3QY67IJA5CNFSM4J3MH2D2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEG7SAYY#issuecomment-566173795, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC2XPYB4U4WKMWKLUUA2233QY67IJANCNFSM4J3MH2DQ.

jjgao commented 4 years ago

Agreed. But it would be nice if we could still support the old terms (maybe in an undocumented way).

Supporting the old terms in an undocumented way sounds good to me.

jjgao commented 4 years ago

we should also change HETLOSS in OQL (and anywhere else it might appear).

@tali Good point. @kalletlak I have updated the description to include hetloss.

@schultzn @tmazor I don't think shallowDel is a good term. This would be an opportunity to change the term to something different. But I couldn't think of better ones. Any thoughts?

stale[bot] commented 4 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

stale[bot] commented 3 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

tmazor commented 3 years ago

Maybe one of these instead of Shallow? @jjgao @schultzn Partial Moderate Intermediate

jjgao commented 3 years ago

It seems that "partial" is used to indicate "part of chromosome" in the copy number field (https://en.wikipedia.org/wiki/Aneuploidy#Partial_aneuploidy). In our case, "partial" may also be interpreted as partial deletion of a gene (e.g. c-terminal deletion).

And it looks like "Shallow deletion" is being used in the field now (maybe mainly b/c of us): https://www.google.com/search?q=shallow+deletion, including this Coursera course: https://www.coursera.org/lecture/data-genes-medicine/copy-number-alterations-1Ybdq

Maybe we can keep it? @tmazor @schultzn

tmazor commented 3 years ago

Wow, we've made an impact! I'm ok with keeping shallow - I don't feel super strongly one way or the other. If shallow has spread beyond the site, it probably does make sense to keep it.

And if we do decide to change it, good point about "partial" - definitely not a good choice for a replacement.

schultzn commented 3 years ago

Matthew Meyerson and Andy Cherniak originally proposed shallow, I believe, and they felt very strongly about this. Most of our copy-number calls at the time were based on GISTIC, and they knew that they could not be certain about the difference between heterozygous and homozygous.

I also propose that we keep the term.

On Jul 10, 2020, at 9:15 AM, Tali Mazor notifications@github.com wrote:

Wow, we've made an impact! I'm ok with keeping shallow - I don't feel super strongly one way or the other. If shallow has spread beyond the site, it probably does make sense to keep it.

And if we do decide to change it, good point about "partial" - definitely not a good choice for a replacement.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/cBioPortal/icebox/issues/474, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC2XPYA6VHL2E4MFW7MKPKTR24H7ZANCNFSM4J3MH2DQ.

jjgao commented 3 years ago

Sounds good. @kalletlak we are ready to move this forward. It's not urgent, but could you help implement this when you have the bandwidth?

stale[bot] commented 3 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

jjgao commented 3 years ago

Maybe @jtquach1 can help with this one? cc @Luke-Sikina

jtquach1 commented 3 years ago

Maybe @jtquach1 can help with this one? cc @Luke-Sikina

yes, I can help

jtquach1 commented 3 years ago

Different naming conventions for homozygous deletion is followed in different pages. Examples

  1. In OQL -> HOMDEL
  2. Study-view CNA table -> DEL
  3. Patient-view Copy Number Alterations table -> DeepDel
  4. Results page Mutations tab -> DeepDel
  5. Patient view Mutations table -> DeepDel
  6. Comparison page copy-number tab -> DeepDel
  7. Oncoprint -> HOMODELETED (in tooltip)

For hetloss,

  1. In OQL -> HETLOSS
  2. Results page Mutations tab -> ShallowDel
  3. Patient view Mutations table -> ShallowDel
  4. Oncoprint -> ShallowDel (in tooltip)

Changes documented here

stale[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

stale[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.