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How to Contribute Tags to GNPS and Analyses Currently Supported

Pardon our dust as this is documentation is a work in progress! We also welcome your contributions.


Required Items and Summary of Steps for Contribution

  1. GNPS Tag Template
    1.1 Manual completion of the GNPS Tag Template (link here)
    1.2.a Annotation without InChi without Tags
    1.2.b Annotation without InChi with Tags
    1.2.c Annotation with InChi without Tags
    1.2.d Annotation with InChi with Tags
    1.3 Submission of the GNPS Tag Template to admin

Detailed Step-by-step Instructions for Contribution

1. GNPS Tag Template

1.1 Manual completion of the GNPS Tag Template

  • Download the "View all library hits" table from GNPS

    Notes:
    - the link is located on the results page

  • Open the "View all library hits" table in a spreadsheet program.

  • Copy and paste the tables contents (skip the headers) into the "INPUT GNPS Table" tab.

    Notes:
    - All columns in light grey are for reference only and should not be modified.
    - If done correctly, information relevant to tagging should appear in the "GNPS Tag - Batch Tag Template" tab in columns A-D.

  • IF matches are not found to the InCHI in the "GNPS Tag Master" tab, then "Check_Master" column = "No" (column E) and no tags will appear in the "Update_" columns.

  • IF matches are found to the InCHI in the "GNPS Tag Master" tab, then "Check_Master" column = "Yes" (column E) and tags will appear in the "Update_" columns.

  • Users should check that the tags present in columns F-J are accurate and appropriate for each annotation.

    Notes:
    - The InChi associated with each annotation is queried against the "GNPS Tag Master" tab which is updated by the admins and the results are displayed in the "GNPS Tag - Batch Tag Template" tab.

  • Users should then complete the "GNPS Tag - Batch Tag Template" tab in a rowwise manner to the extent possible. The following scenarios in 1.2.a - 1.2.d provide guidance.

1.2.a Complete the "GNPS Tag - Batch Tag Template" following these scenarios: Annotation without InChi without Tags

"Check_Master" column = "No" (column E) and no tags will appear in the "Update_" columns.
  • Add the InChi to the "Add_INCHI" column (column K). > Notes:
    • optional: add the common name ("Add_Name", Column L) - we suggest the use of PubChem
  • IF matches are not found to the InCHI in the "GNPS Tag Master" tab, then "Check_Added_INCHI" column = "No" (column M) and no tags will appear in the "Check_" columns (columns N-R).
  • Complete the tags using the controlled vocabulary (up to three tags can be added for each tag category) > Notes:
    • The same tag can only be applied to an InCHI once, please avoid repeated tagging.
    • If additional terms are desired, please submit an issue on GitHub - link here

1.2.b Complete the "GNPS Tag - Batch Tag Template" following these scenarios: Annotation without InChi with Tags

"Check_Master" column = "No" (column E) and no tags will appear in the "Update_" columns.
  • Add the InChi to the "Add_INCHI" column (column K). > Notes:
    • optional: add the common name ("Add_Name", Column L) - we suggest the use of PubChem
  • IF matches are found to the InCHI in the "GNPS Tag Master" tab, then "Check_Added_INCHI" column = "Yes" (column M) and tags will appear in the "Check_" columns (columns N-R).
  • Check that the tags present in columns F-J are accurate and appropriate for each annotation.
  • Complete the tags (if necessary) using the controlled vocabulary (up to three tags can be added for each tag category) > Notes:
    • The same tag can only be applied to an InCHI once, please avoid repeated tagging.
    • If additional terms are desired, please submit an issue on GitHub - link here

1.2.c Complete the "GNPS Tag - Batch Tag Template" following these scenarios: Annotation with InChi without Tags

"Check_Master" column = "Yes" (column E) and no tags will appear in the "Update_" columns.
  • Complete the tags using the controlled vocabulary (up to three tags can be added for each tag category) > Notes:
    • The same tag can only be applied to an InCHI once, please avoid repeated tagging.
    • If additional terms are desired, please submit an issue on GitHub - link here

1.2.d Complete the "GNPS Tag - Batch Tag Template" following these scenarios: Annotation with InChi with Tags

"Check_Master" column = "Yes" (column E) and no tags will appear in the "Update_" columns.
  • Check that the tags present in columns F-J are accurate and appropriate for each annotation.
  • Complete the tags using the controlled vocabulary (up to three tags can be added for each tag category) > Notes:
    • The same tag can only be applied to an InCHI once, please avoid repeated tagging.
    • If additional terms are desired, please submit an issue on GitHub - link here

1.3 Download the "GNPS Tag - Batch Tag Template"

  • Download the "GNPS Tag - Batch Tag Template" as a .tsv
  • Email file to admins:
    • Alan Jarmusch (ajarmusch@ucsd.edu)

Thank you for contributing tags to GNPS! This is a community effort and every contribution helps!

Help and Advice

  • General Questions or Advice = GNPS Forum - link here
  • New Terms, Corrections, Suggestions = GitHub - link here

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Current Analyses

  1. Summary the tags information in a GNPS molecular networking job
  2. Color an existing GNPS molecular networking using GNPS tags
  3. Coming Soon: Utilize "TagTracker" to simplify and focus the analysis of a GNPS molecular network
  4. Coming Soon: Analyze Tags using Metdata

---

1. Summary the tags information in a GNPS molecular networking job

  • Make a copy and download Master Tag Sheet (.tsv) from Google Sheets - link here
  • Download the "View all library hits" table from GNPS tag_summary
  • Run the Jupyter Notebook or Code (R) = "Tags_Summary"
    • Update the paths in the #COMMON STEPS section
    • Run the code (generates .pdf of figures, example below)
  • Modify graphs as desired
    tag_summary

2. Color an existing GNPS molecular networking using GNPS tags

  • Make a copy and download Master Tag Sheet (.tsv) from Google Sheets - link here
  • Download the Cytoscape .graphML files via the "Download Cytoscape Data" or "Direct Cytoscape Preview/Download" tag_summary
  • Download the Node Table
    • Open the molecular network in Cytoscape
    • File -> Export -> Table to File -> Select the option ending in "default node" in the dropdown -> Update Path and Save cytoscape_node
  • Run the Jupyter Notebook or Code (R) = "Tags_Cytoscape"
    • Update the paths in the #COMMON STEPS section
    • Run the code (generates and updated node table)
  • Import the Updated Node Table into Cytoscape cytoscape_node
  • Example Shown Above = Using node color to indicate chemicals tagged as "bacterial"
    • Open node fill color in cytoscape
    • Select "TAG_bacterial" and use discrete mapping
      • Value of 0.1 = no InChi and no tag information present
      • Value of 0.0 = InChi present but not tagged based on selection
      • Value of 1.0 = InChi present and tagged based on selection
    • Open node label in cytoscape
    • Select "Compound_Name" and use passthrough mapping
    • Interpretation - Molecular netowrk linked glycocholic acid, a primary bile acid conjugated to glycine, and glycodeoxycholic acid, a secondary bile acid. Glycodeoxycholic acid is known to be produced by bacteria in the human gut (and other animals) and was tagged as bacterial (green). Glycocholic acid is known to be produced by human (and other animals) and was not tagged as bacterial (red). The nodes in grey do not have tags at the time of analysis.

3. Utilize "TagTracker" to simplify and focus the analysis of a GNPS molecular network

TBD



Last update: March 10, 2020 17:31:42