Ingalls Standards Repository

RLionheart 08/23/2022

The Ingalls Lab Standards Repository

The Ingalls_Lab_Standards.csv is the latest version of the list. Please download that version for all analysis needs.

This repository contains the most recent standards list, all previous versions, and all relational information for the standards.

Sections of the repository

Add_New_Standard.Rmd: A markdown script for creating all required columns for entering a new standard.

data_extra: This folder contains supplemental information (columns that are not part of the main standards csv but are relevant to various processes). External downloads and all alternate compound names (ChEBI, IUPAC, InCHL, SMILES, and Classyfire) can be found here. If you need to upload to CMAP or need SQL-safe names, those columns will be located here.

data_old: This folder contains information that is no longer current for the standards, such a summarized history of the 2020 standards overhaul, previous versions of the standards list (including all old columns that have been archived) and original external database downloads.

MSMS: Merged from a separate branch, this is a folder of mostly experimental information for incorporating MSMS data into the standards list in the future.

src: Mostly for archived debugging, this folder contains all of the code for editing the standards list from older versions.

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Naming Conventions for Compounds

Capitalization

• All “Acid”s changed to “acid”, in accordance with KEGG conventions
  • Example: 3-Sulfopyruvic Acid –> 3-Sulfopyruvic acid
• First appearance of compound in complete name capitalized
  • Example: 7-dehydrocholesterol –> 7-Dehydrocholesterol
  • Example: thiamine pyrophosphate –> Thiamine pyrophosphate
• “B-compoundName” changed to beta-CompoundName
  • Example: B-ionine –> beta-Ionine
• Second part of compound name lowercase
  • Example: Glutathione Disulfide –> Glutathione disulfide

Abbreviations

For shorter compound names, the column Compound_Name_Figure provides an abbreviated version of the compound name whenever possible.

• When possible, change compound names to acronyms
  • Example: S-Adenosylhomocysteine –> SAH
• Drop prefixes for compounds.
  • Example: L-Cystathionine –> Cystathionine
• Drop unnecessary commas and apostrophes.
  • Example: Guanosine monophosphate, 15N5 –> GMP 15N5

Internal Standards

• Keep internal standard names consistent with their unlabeled counterparts.
  • Example: 3-Sulfolactate, 13C3 should correspond to Sulfolactate, rather than Sulfolactic acid.

Other conventions

• Use complete descriptive names for compounds.
  • Example: All B12s –> Methylcobalamin, Hydroxocobalamin, etc.
  • All Vitamins should be listed as their descriptive name: Vitamine B1 –> Thiamine, Vitamin B2 –> Riboflavin, etc.

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History and Previous Versions

In June of 2020 and August of 2021, significant changes were made to the original Ingalls Standards sheet. Summarized changes are listed in the data_old folder, and specific changes can be viewed on the git log of this project, available at https://github.com/IngallsLabUW/Ingalls_Standards/commits/master.

This includes all previous versions of the the “original” standards list:

• Pre June 2020 (found at “data_old/Ingalls_Lab_Standards_pre2020.csv”)

• Pre August 2021 (found at “data_old/Ingalls_Lab_Standards_August2021.csv”)

• Standards with all auxilary columns that have since been dropped (found at “data_old/Ingalls_Lab_Standards_AuxColumns.csv”)