Use PubChem as the primary identifier for Compounds

[lparsons]

FEATURE DESCRIPTION

Feature Inspiration

HMDB is a very useful database of human metabolites, however, researchers sometimes measure or infuse compounds that are not considered naturally occurring human metabolites (e.g. ???). Using PubChem as the required, primary identification for a Compound record would allow TraceBase to handle a larger variety of compounds. Links to other databases such as HMDB can be added if available for convenience.

Feature Description

Make PubChem ID a required field for Compound. Change HMDB id to be an optional value.

Alternatives Considered

An alternative would be to use the SMILES key as the primary identifier (mostly hidden from user). Pubchem lists the SMILES id for compounds (for example: https://pubchem.ncbi.nlm.nih.gov/compound/6287#section=Canonical-SMILES).

The advantage would be that a compound not in pubchem could be integrated into the database. I doubt there are many of these. The only possibility might be pharmacologic compounds that researchers administer to animals.

Comment

Add any other context or screenshots about the feature request here.

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ISSUE OWNER SECTION

Assumptions

• List of assumptions made WRT the code
• E.g. We will assume input is correct (explaining why there is no validation)

Requirements

• List of conditions to be met for the feature
• E.g. Every column/row must display a value, i.e. cannot be empty

Limitations

• A list of things this work will specifically not do
• E.g. This feature will only handle the most frequent use case X

Affected/Changed Components

• Files
• Environment variables
• External executables
• Database tables
• Cron job settings
• Etc.

DESIGN

GUI Change description

Describe changes the user will see.

Code Change Description (Pseudocode optional)

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Tests

A test should be planned for each requirement (above), where possible.

[mneinast]

An alternative could be to use the SMILES key as the primary identifier (mostly hidden from user). https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system. Pubchem lists the SMILES id for compounds (for example: https://pubchem.ncbi.nlm.nih.gov/compound/6287#section=Canonical-SMILES).

The advantage would be that a compound not in pubchem could be integrated into the database. I doubt there are many of these. The only possibility might be pharmacologic compounds that researchers administer to animals.

I think Pubchem could be fine, but I wanted to share this idea for an alternative.

[lparsons]

From @hepcat72: Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI