Glycomics paper curation

This article describes the curation of glycomics papers as part of the GlyGen project.

Curation workflow

• Identify a paper of interest, and look for glycan structures being reported in both primary and supplemental data sections.
• Draw the glycans represented by cartoons in Grits Toolbox,
  • Pay close attention to drawing them exactly as they are presented in the paper with no assumptions from the curator including
    • Reducing end type (reduced, free etc)
    • Derivitization status (permethylated C12, native, etc)
    • Topology (which arm monosaccharides are placed on)
    • Linkages
    • only draw cartoons if they are drawn in the paper, draw compositions as compositions, may have multiple representations for ex a spectra with cartoons and a table with compositions, make both
• Export the glycan drawings to gws format and put in a folder in SharePoint
• Request the gws file to be processed (by Sena) into an excel sheet and glytoucan id's added. Structures without glytoucan ids are submitted to glytoucan and registered. The finished excel is placed in Sharepoint and notification is given.
• Once this is complete, retrieve the excel file from SharePoint
• Check that the glytoucan structure matches the structure you submitted.
• Add meta info using the specified format (see curation table section) and fill in those columns.
• Make a copy as a new tab and delete columns not specified in the Curation table (ex file name, row number, both cartoons, status, error). The column format must be the same, same order, same column name.
• Save a tab as Final-GlyGen to designate which tab to be used in downstream processing
• For structures that are compositions only you must Look up GlyToucan ID's manually and create the same table as for cartoons.
  • by going to https://gnome.glyomics.org/CompositionBrowser.htm and selecting the appropriate # of each residue. Select double ?? forms (Top ? means ring size, bottom ? means anomere)
  • or searching by mass in glygen

Curation table

Table structure for glycomics information

The file will be a CSV file using “,” as cell delimiter and all cells will be quoted.

List of columns in the curation file that needs to be filled for glycomics information.  

Bold Red indicates mandatory information

Keep in this order

Extra columns can be added to the end if needed

GlyTouCan ID	G17689DH	From Senas spreadsheet
Paper Evidence	PMID:25753706 DOI:10.1007/978-1-4939-2343-4_8	PMID or DOI
Species	9606	From NCBI Taxonomy browser
Strain	Oregon-R	(Model organisms fly, yeast, mouse)   Add species number to Uniprotlink and get text name from there (in column on rt) https://www.uniprot.org/taxonomy/<taxID> Look for the strain on the right side. Find the strain you are looking for. Sometimes synonymes are given in parenthesis. Use the term in the beginning of the line.   If no match is found => Audio meeting
Tissue	UBERON:0002107	From Uberon, if it can not be found we will discuss.
Cell line ID	Cellosaurus:CVCL_A4VI	From Cellosaurus
Disease	DOID:3571	From Human Disease Ontology
Glycan dictionary term ID	GSD000011
has_abundance	yes no	Are there Numbers associated with the amount present in a sample
has_expression	yes no	Don't use for now until talk with Karina
Functional annotation/Keyword	<term1>|<term2>	Mike will provide a dictionary (~15 terms) that Mindy will use. See list end of sheet
Experimental technique	LC-MS|MS profile	Free text, we create dictionary to avoid things like LC/MS LC-MS,   MS MS/MS LC-MS/MS LC-MS CE-MS CE-MS/MS CE HPLC GC GC-MS
Glycan dictionary term ID	GSD000011	From the Glycan structure dictionary.
Variant (Fly, yeast, mouse)	Wild Type, Tollo395,	Gene name and position (if known) as text
Organismal/cellular Phenotype	HP:0012373	HPO (human) https://hpo.jax.org/app/ If no match is found => Audio meeting
Molecular Phenotype		Gene name Discuss with Jeet when find example
Contributor	createdBy:Mindy Porterfield(mindy@something.de, CCRC)|createdBy:Name(email,institution)	From ticket 42

The following columns can have multiple entries per line/cell:

• Disease  
• Functional annotation
• Keywords

• Glycan dictionary term ID
• Contributor
• Experimental technique

The following format will be used for these cells: <term1>|<term2>

For experimental techniques the following (non-comprehensive) dictionary will be used:

• MS
• MS/MS
• LC-MS/MS

• LC-MS
• CE-MS
• CE-MS/MS
• CE
• HPLC

• GC
• GC-MS

This list will be extended if new experimental techniques are detected in the papers.

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

This list will be extended if new function annotation terms are detected in the papers.