small fix

[ypriverol]

Summary by CodeRabbit

• Chores

  • Adjusted repository management to exclude additional temporary and report files.

• New Features

  • Enhanced the proteomics classification framework with refined relationships.
  • Expanded experimental categorization by adding new experiment types, quantification methods, and mass spectrometry techniques to improve data representation and analysis.

[coderabbitai]

Walkthrough

The changes update two files. In the repository's ignore settings, two new entries (/pride_tmp.owl and /report.tsv) have been added to the .gitignore. Meanwhile, the ontology file has been modified: several is_a relationships were updated from using BF:0000001 to BFO:0000001, and new experimental and quantification terms were introduced to expand the ontology.

Changes

File	Change Summary
.gitignore	Added two ignore entries: /pride_tmp.owl and /report.tsv.
pride_cv.obo	Updated ontology term relationships from BF:0000001 to BFO:0000001; added new subclasses under "Experiment Type" and new quantification/method terms.

Suggested reviewers

• deeptijk

Poem

I’m a rabbit dancing along the code trail,
New ignore paths and ontology details make me exhale.
Terms hop from BF to BFO in a neat, structured spree,
New classes and methods for all to see.
With every change my paws tap a merry jig—coding carrots make my heart big!

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between d8badb0 and 6f5b0e4.

📒 Files selected for processing (2)

• .gitignore (1 hunks)
• pride_cv.obo (6 hunks)

✅ Files skipped from review due to trivial changes (1)

• .gitignore

⏰ Context from checks skipped due to timeout of 90000ms (2)

• GitHub Check: convert_and_validate_owl
• GitHub Check: convert_and_validate_owl

🔇 Additional comments (6)

pride_cv.obo (6)

35-35: Change from BF:0000001 to BFO:0000001 is accurate
This revision properly references the Basic Formal Ontology’s top-level “entity” term.

---

71-71: Use of BFO:0000001 for the 'entity' concept is correct
No issues with referencing this well-known top-level class of Basic Formal Ontology.

---

2666-2666: Correct alignment with BFO:0000001
The update ensures consistency with Basic Formal Ontology conventions.

---

2751-2751: Reference to BFO:0000001 is valid
This change aligns the ontology term with the correct BFO entity class.

---

2841-2841: Adoption of BFO:0000001 is appropriate
This helps maintain consistency with established ontology standards.

---

3222-3222: Revising is_a relationship to BFO:0000001 is correct
Mirrors the Basic Formal Ontology’s canonical usage for high-level “entity.”

---

🪧 Tips

Chat

There are 3 ways to chat with CodeRabbit:

• Review comments: Directly reply to a review comment made by CodeRabbit. Example:
  • I pushed a fix in commit <commit_id>, please review it.
  • Generate unit testing code for this file.
  • Open a follow-up GitHub issue for this discussion.
• Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
  • @coderabbitai generate unit testing code for this file.
  • @coderabbitai modularize this function.
• PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
  • @coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
  • @coderabbitai read src/utils.ts and generate unit testing code.
  • @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
  • @coderabbitai help me debug CodeRabbit configuration file.

Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments.

CodeRabbit Commands (Invoked using PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai full review to do a full review from scratch and review all the files again.
• @coderabbitai summary to regenerate the summary of the PR.
• @coderabbitai generate docstrings to generate docstrings for this PR. (Beta)
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
• @coderabbitai help to get help.

Other keywords and placeholders

• Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
• Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
• Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (.coderabbit.yaml)

• You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
• Please see the configuration documentation for more information.
• If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

• Visit our Documentation for detailed information on how to use CodeRabbit.
• Join our Discord Community to get help, request features, and share feedback.
• Follow us on X/Twitter for updates and announcements.