PMID: 17264077 Dynamic developmental elaboration of N-linked glycan complexity in the Drosophila melanogaster embryo

Mindyporterfield commented 1 year ago

Fly-N-paper

Tasks for Anh

414

Tasks for Sena

Tasks for Mindy

Mindyporterfield commented 1 year ago

[x] 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.
[x] Mindy-check structures, give any needed feedback
Mindy -proceed with the rest of the curation workflow
@senaarpinar [ ] -convert structures (Sena) and get glytoucan ids Fly-GWS
[x] -verify structures match glytoucan structure
[x] -Fill in remaining info for species, etc https://docs.google.com/document/d/1QPWU29l6pzo8bKIQ6epEidPDDxyp-5JQk9drhS-zJOg/edit#heading=h.urs6nll5b27n
[x] -deposit in sharepoint and comment on ticket

senaarpinar commented 1 year ago

generated the excel sheet with glytoucan ids

senaarpinar commented 1 year ago

uploaded a new version of the excel file (after rerunning with Rene's changes to handle structures with brackets)

Mindyporterfield commented 1 year ago

reviewed structures and filled in remaining columns on spreadsheet (separate tab) complete except no functional annotations found,

@mtiemeyer0919 what functional annotation do you suggest for the fly N-linked paper? here is the current list, you can add terms if needed

For Functional annotation use the following (non-comprehensive) dictionary:

adhesion 
homing 
inflammation 
protein targeting 
protein secretion 
protein stability 
protein folding 
ER stress 
protein degradation 
circulating half-life 
clearance 
internalization 
metastasis 
shielding 
recognition 
toxin receptor 
viral receptor 
microbial receptor 
receptor signaling 
sperm maturation

Added terms (Mike) differentiation biomarker

Mindyporterfield commented 1 year ago

data is in sharepoint folder excel sheet

I will go over with @mtiemeyer0919 and then let @ReneRanzinger know its ready use the tab 3-Final Glygen for data upload

Mindyporterfield commented 1 year ago

@ReneRanzinger The fly n linked excel is ready in sharepoint. there are 4 sets of data (4 tabs that are named 3-final glygen...) The only thing is there is a duplicate column that needs to be removed once jeet replies about where he wants it (he accidentally left 2 copies of 1 column) see #622

ReneRanzinger commented 1 year ago

@Mindyporterfield we talked about having a single sheet that my program can detect with a fixed name. That is missing. I also noticed that in the tollo sheet it has "tollo-" in the Variant column. Is that a typo? Also the contributor column only has you mentioned. Was that done without Ain?

Mindyporterfield commented 1 year ago

I will fix it tollo- is how tollo minus is written as a gene that is missing as stated in the paper, let me check with mike if I can write as tollo, does - cause a problem? i couls also spell it out if so i will combine the tabs or make separate files and add anh (i totally missed that)

thanks

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

From: Rene Ranzinger @.> Sent: Friday, August 25, 2023 5:51 PM To: glygener/glygen-issues @.> Cc: Melody Perlman Porterfield @.>; Mention @.> Subject: Re: [glygener/glygen-issues] PMID: 17264077 Dynamic developmental elaboration of N-linked glycan complexity in the Drosophila melanogaster embryo (Issue #399)

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@Mindyporterfieldhttps://github.com/Mindyporterfield we talked about having a single sheet that my program can detect with a fixed name. That is missing. I also noticed that in the tollo sheet it has "tollo-" in the Variant column. Is that a typo? Also the contributor column only has you mentioned. Was that done without Ain?

— Reply to this email directly, view it on GitHubhttps://github.com/glygener/glygen-issues/issues/399#issuecomment-1693972175, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A5GO7AQ34GE3DDAOVR3KLTLXXEM6BANCNFSM6AAAAAAYVR63SY. You are receiving this because you were mentioned.Message ID: @.***>

Mindyporterfield commented 1 year ago

@ReneRanzinger I am still not sure about the contributor column, we will need to see what come out of the meeting wednesday. otherwise you can give it a try. The tab name is Final-GlyGen

Mindyporterfield commented 1 year ago

the fly n-linked structures excel ready @ReneRanzinger The tab name is Final-GlyGen

Mindyporterfield commented 6 months ago

the fly n-linked structures excel ready @ReneRanzinger The tab name is Final-GlyGen

glygener / glygen-issues

PMID: 17264077 Dynamic developmental elaboration of N-linked glycan complexity in the Drosophila melanogaster embryo #399

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