PMID: 24328148 Discrimination between adenocarcinoma and normal pancreatic ductal fluid by proteomic and glycomic analysis

Mindyporterfield commented 1 year ago

https://gwu0.sharepoint.com/sites/GlyGenTeam-GRP/Shared%20Documents/Forms/AllItems.aspx?csf=1&web=1&e=EACW7c&cid=aba533af%2Dff65%2D4b17%2D8c9a%2D5c21f48836db&FolderCTID=0x01200081407FA815A7124E846BD764353D93CC&id=%2Fsites%2FGlyGenTeam%2DGRP%2FShared%20Documents%2FPaper%20Curation%2FPMID%2024328148%20pancan&viewid=6ffb8fed%2D81e7%2D4af7%2Dbfcd%2Da6f29c268132

Mindyporterfield commented 11 months ago

[ ] Mindy- read paper, id data to be curated (which figures etc), draw an example structure paying attention to reducing end type (free or reduced) and modifications (permethylation). Write a ticket for Anh and link example structure.
[x] Anh-Draw assigned structures using GRITS, export as gws file and put in the corresponding folder in sharepoint, comment in github to let me know its done. @apnguyen98

Figure 7 in the paper, 6 sets

[x] S group increased
[x] S group decrease
[x] M group increased
[x] M group decreased
[x] F group increased
[x] F group decreased
[ ] Mindy-check structures, give any needed feedback

Mindy -proceed with the rest of the curation workflow

[ ] -convert structures (Sena) and get glytoucan ids
[ ] -verify structures match glytoucan structure
[ ] -Fill in remaining info for species, etc https://docs.google.com/document/d/1QPWU29l6pzo8bKIQ6epEidPDDxyp-5JQk9drhS-zJOg/edit#heading=h.urs6nll5b27n
[ ] -deposit in sharepoint and comment on ticket

apnguyen98 commented 10 months ago

@Mindyporterfield I finished drawing the structures and uploaded them here: https://gwu0.sharepoint.com/sites/GlyGenTeam-GRP/Shared%20Documents/Forms/AllItems.aspx?csf=1&web=1&e=EACW7c&cid=aba533af%2Dff65%2D4b17%2D8c9a%2D5c21f48836db&FolderCTID=0x01200081407FA815A7124E846BD764353D93CC&id=%2Fsites%2FGlyGenTeam%2DGRP%2FShared%20Documents%2FPaper%20Curation%2FPMID%2024328148%20pancan%2FGWS&viewid=6ffb8fed%2D81e7%2D4af7%2Dbfcd%2Da6f29c268132

However please double check structures 60, 68 and 74 for me as I drew them as how they were shown in the paper, but the mass didn't match up.

Mindyporterfield commented 9 months ago

@senaarpinar @ReneRanzinger how do i "draw" compositions in grits?

ReneRanzinger commented 9 months ago

You do not. For you compositions have to handled by hand. You make the spreadsheet as usual and than you have the add the compositions by hand. Look them up in GlyTouCan or GlyGen. Get their ID and add it to the spreadsheet.

Mindyporterfield commented 9 months ago

are you here?

Melody Porterfield, Ph.D. CCRC UGA Senior Research Associate @.***

From: Rene Ranzinger @.> Sent: Friday, August 25, 2023 1:41 PM To: glygener/glygen-issues @.> Cc: Melody Perlman Porterfield @.>; Mention @.> Subject: Re: [glygener/glygen-issues] PMID: 24328148 Discrimination between adenocarcinoma and normal pancreatic ductal fluid by proteomic and glycomic analysis (Issue #412)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

You do not. For you compositions have to handled by hand. You make the spreadsheet as usual and than you have the add the compositions by hand. Look them up in GlyTouCan or GlyGen. Get their ID and add it to the spreadsheet.

— Reply to this email directly, view it on GitHubhttps://github.com/glygener/glygen-issues/issues/412#issuecomment-1693721621, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A5GO7ASUWKHWWTPV3KJKY73XXDPV5ANCNFSM6AAAAAAYYVWSAU. You are receiving this because you were mentioned.Message ID: @.***>

Mindyporterfield commented 9 months ago

@senaarpinar can you re-run the gws files to add in the new columns? Thanks

senaarpinar commented 9 months ago

I ran these files but we need to wait another day and rerun to get the registered glycans

Mindyporterfield commented 9 months ago

Thank you

Mindy

On Aug 28, 2023, at 4:06 PM, Fatma Sena Arpinar @.***> wrote:

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

I ran these files but we need to wait another day and rerun to get the registered glycans

— Reply to this email directly, view it on GitHubhttps://github.com/glygener/glygen-issues/issues/412#issuecomment-1696330813, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A5GO7AVDCZKE3AY2YZ2KKWLXXT22ZANCNFSM6AAAAAAYYVWSAU. You are receiving this because you were mentioned.Message ID: @.***>

senaarpinar commented 9 months ago

I have uploaded the excel files

Mindyporterfield commented 9 months ago

I made the excel sheet manually for the compositions for the Pancreatic Cancer Paper compositionExcel If you can take a look at it @ReneRanzinger I am still working on the ones with cartoons that Sena re-ran though

glygener / glygen-issues

PMID: 24328148 Discrimination between adenocarcinoma and normal pancreatic ductal fluid by proteomic and glycomic analysis #412