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Copilot AI commented Aug 26, 2025

This PR adds CHEBI:52735 to the CHEBI OBO slim seed list as requested. The term has been inserted in the correct alphabetical position in seed.txt between CHEBI:52726 and CHEBI:5280, maintaining the required alphanumeric sorting as specified in the repository README.

Changes made:

  • Added CHEBI:52735 to seed.txt at line 8626
  • Verified proper alphabetical ordering is maintained
  • Confirmed the term appears exactly once in the file
  • Line count increased from 14,386 to 14,387 entries

The ontology files (chebi_slim.obo and chebi_slim.owl) will be automatically regenerated when maintainers run the build process (sh odk.sh make all) during the next release cycle.

Fixes #41.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

  • purl.obolibrary.org
    • Triggering command: curl -L REDACTED --create-dirs -o mirror/chebi.owl.gz --retry 4 --max-time 200 (dns block)

If you need me to access, download, or install something from one of these locations, you can either:


💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

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Copilot AI commented Aug 26, 2025

@matentzn 👋 This repository doesn't have Copilot instructions. With Copilot instructions, I can understand the repository better, work faster and produce higher quality PRs.

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Copilot AI changed the title [WIP] Add CHEBI id and update list Add CHEBI:52735 to chebi slim seed list Aug 26, 2025
Copilot AI requested a review from matentzn August 26, 2025 15:49
@matentzn
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@copilot I have updated the instructions - can you try again?

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Copilot AI commented Aug 26, 2025

@copilot I have updated the instructions - can you try again?

I've successfully added CHEBI:52735 to the seed.txt file in the correct alphabetical position. However, when attempting to run sh odk.sh make all as specified in the updated instructions to rebuild the ontology files, the build fails due to the DNS block on purl.obolibrary.org mentioned in the PR description.

The commit e8bac7f contains the required change to seed.txt. The ontology files (chebi_slim.obo and chebi_slim.owl) will need to be regenerated when maintainers run the build process in an environment with access to the required external resources, or when the necessary URLs are added to the allowlist in the repository's Copilot coding agent settings.

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

  • purl.obolibrary.org
    • Triggering command: curl -L REDACTED --create-dirs -o mirror/chebi.owl.gz --retry 4 --max-time 200 (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

@matentzn
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Experiment over/

@matentzn matentzn closed this Aug 26, 2025
@matentzn matentzn deleted the copilot/fix-41 branch August 26, 2025 16:16
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Add CHEBI id and update list

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