Generating InChIKeys for IUPAC names

[egonw]

Great! Now, to the actual tasks:

• [x] identify author
• [x] write abstract
• [ ] agree with editors on abstract
• [x] write recipe
• [ ] identify reviewer
• [ ] conduct review
• [ ] incorporate reviewer's comments
• [ ] publish recipe

[egonw]

Why this recipe?

It is a step in the larger work described in https://github.com/FAIRplus/the-fair-cookbook/issues/396

Author

Egon

Abstract

IUPAC names describe chemical structures, but one chemical compound can have multiple (equivalent) IUPAC names. That makes IUPAC names unsuited as global unique identifier. The InChIKey addresses this issue. This recipe describes how cheminformatics can be used to translate IUPAC names into unique InChIKeys. It will use the OPSIN library and show how its website can be used and how the translation can be automated with Google Colab.

[egonw]

Preview: https://egonw.github.io/cookbook-dev/content/recipes/infrastructure/iupac-names.html

[robertgiessmann]

Hi @egonw , I like it! One thing, though: InChI-Keys are not unique, either, are they? There is at least the theoretical chance of key collision. But if that is pointed out as a caveat, I am more than happy! :)

[YojanaGadiya]

Maybe this might help in getting some content or directing the readers to this resource - http://inchi.info/inchikey_overview_en.html. It would be good to highlight that differences I think.

[egonw]

@Grab(group='io.github.egonw.bacting', module='managers-inchi', version='0.0.42')
@Grab(group='io.github.egonw.bacting', module='managers-opsin', version='0.0.42')
@Grab(group='org.apache.logging.log4j', module='log4j-api', version='2.18.0')
@Grab(group='org.apache.logging.log4j', module='log4j-core', version='2.18.0')

workspaceRoot = "../ws"
opsin = new net.bioclipse.managers.OpsinManager(workspaceRoot);
inchi = new net.bioclipse.managers.InChIManager(workspaceRoot);

anInChI = inchi.generate(
  opsin.parseIUPACName("methane")
)
println "InChI: " + anInChI.value
println "InchIKey: " + anInChI.key

[egonw]

Or in Python:

[proccaserra]

@egonw @robertgiessmann @YojanaGadiya @tabbassidaloii

how far from PR?

Would you mind setting a milestone to this content and the associated isses (#396) ?

[egonw]

before the end of August.

[egonw]

My summer did not go as planned. But making the PR now.