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
- Pay close attention to drawing them exactly as they are presented in the paper with no assumptions from the curator including
- 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.html 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 indicates mandatory information
Keep in this order and the column names the same
Extra columns can be added to the end if needed
| GlyTouCan ID | G17689DH | From Senas spreadsheet, or manually look up |
| 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,
|
| *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/
|
| *Molecular Phenotype | Gene name
Discuss with Jeet when find example | |
| *Contributor | curatedBy:Mindy Porterfield(mindy@something.de, CCRC)|curatedBy:Name(email,institution) | Example
createdWith:GRITS Toolbox (http://www.grits-toolbox.org/) |createdWith:Software/Tool/Code Name (URL or Sourecode URL) Combined Example curatedBy:Mindy Porterfield (mindyp@ccrc.uga.edu, CCRC)|curatedBy:Anh Nyugen (anh@gwu.edu, GW)|createdWith:GRITS Toolbox (http://www.grits-toolbox.org/) The field can have multiple contribution types separated by There is no need to add a corresponding author or other author name list if curating the paper by yourself. If you are curating the paper use Example curatedBy:Mindy Porterfiel (mindy@something.de,CCRC)|curatedBy:Name (email,institution). createdWith:GRITS Toolbox (http://www.grits-toolbox.org/)|createdWith:Software/Tool/Code Name (URL or Sourecode URL) contributedBy:Bob Haltiwanger (bh@ccrc.edu,CCRC)|contributedBy:Name (email,institution) authoredBy: Daniel Williamson (daniel.williamson25@uga.edu,CCRC)|authoredBy:Name (email,instituition) createdBy:Jeet Vora (jeetvora@gwu.edu,GW)|createdBy:Name (email,instituition) |
An Asterisk * notes column can have multiple entries per line/cell: 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.
Contributor
| provenance property | Definition |
| createdBy | The creator agent participated in some activity that generated the entity. This could be someone who created the dataset or entry. |
| contributedBy | The contributor participated in some activity that generated the entity. This could be someone who provided the data and may not be the one who generated the data. The person could have have made modifications to the data. |
| authoredBy | The author participated in some activity that generated the entity. This could be someone who authored and generated the data. |
| curatedBy | The curator participated in some activity that generated the entity. This is someone who curates data from the publication or raw data. |
| importedFrom | The original resource of imported information. Import means that the content has been preserved, but transcribed somehow, for instance to fit a different representation model by converting formats or structure. The imported resource does not have to be complete but should be consistent with the knowledge conveyed by the original resource. This is the resource from where the data or dataset was downloaded and processed with modifying/transforming the original data or dataset. |
| retrievedFrom | The resource from where the URI or dataset has been retrieved from. Retrieval indicates that this resource has the same representation as the original resource. This is the resource from where the data or dataset was downloaded and processed without modifying the original data. This is the resource from where the data or dataset was downloaded and processed without modifying/ transforming the original data or dataset. |
| createdWith | The software or tool from the which the content was generated. The software is the author itself. AI machine learning tool, software suite, etc |
Curation rules
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