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Problems with Chemical mentions #17

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khanspers opened this issue Nov 21, 2024 · 0 comments
Open

Problems with Chemical mentions #17

khanspers opened this issue Nov 21, 2024 · 0 comments

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@khanspers
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khanspers commented Nov 21, 2024

A couple of things about the Chemical mentions that don't seem quite right, which I've seen on several (not all) pathways. My use case is to copy the mentions from PFOCR and pasting into PathVisio for pathway curation.

  1. I don't remember where the Name column comes from in the PFOCR pipeline, but it is sometimes blank and sometimes differs from the name of the matched ChEBI id.

Example: https://pfocr.wikipathways.org/figures/PMC10953212__40001_2024_1708_Fig2_HTML.html

Name is blank for Insulin, Glycogen, SFA and MUFA.
Name is non-blank but different from name of the matched ChEBI id for acetyl-CoA and malonyl-CoA.

Example: https://pfocr.wikipathways.org/figures/PMC11347096__nihms-2007498-f0004.html

Name is blank for Glucosylceramide and Sphingomyelin
Name is non-blank but different from name of the matched ChEBI id for sphinganine, Sphingosine and Sphingosine-1-phosphate.

  1. The matched ChEBI id is sometimes different from results of a simple search for the Word at ChEBI.

Example: https://pfocr.wikipathways.org/figures/PMC10953212__40001_2024_1708_Fig2_HTML.html

Word Matched ChEBI ChEBI from website search
Insulin chebi:5931 CHEBI:145810
Glucose chebi:42758 CHEBI:17234
Pyruvate chebi:15361 CHEBI:15361
acetyl-CoA chebi:57288 CHEBI:15351
malonyl-CoA chebi:57384 CHEBI:15531
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