How does it handle scientific citations?

The skill provides patterns for citing PMIDs and DOIs in term definitions and synonyms, including capabilities to fetch full-text content to verify definitions.

Does this skill support OWL or OFN formats?

No, this skill is strictly optimized for the OBO flat-file format. It should not be used for ontologies stored in other formats like OFN or OWL.

How do I validate my OBO syntax with this skill?

The skill includes instructions for using the ROBOT tool to convert and validate OBO files, ensuring they meet the required structural standards.

What is the benefit of the checkout/checkin workflow?

Ontology files can be massive. This workflow extracts only the relevant terms into small temporary files, preventing memory issues and making edits safer and more precise.

Can I use it to create new ontology IDs?

Yes, it includes procedures for checking existing ID ranges and preventing ID clashes when generating New Term Requests (NTRs).

OBO Ontology Editor

Name: OBO Ontology Editor
Author: ai4curation

byai4curation

•

Ciencia de Datos y ML

Streamlines the editing, querying, and management of scientific ontologies in the Open Biomedical Ontologies (OBO) format.

This skill equips Claude with specialized scripts and best practices for managing complex bio-ontologies. It provides a robust workflow for querying terms with obo-grep, handling large files via a checkout/checkin system, and ensuring metadata consistency. Designed for biocurators and bioinformaticians, it automates the creation of new term requests, simplifies the process of term obsolescence, and enforces strict OBO format guidelines, including proper citation of PMIDs and DOIs to maintain scientific integrity.

Características Principales

01Automated citation formatting for scientific references (PMID/DOI)

02Optimized checkout/checkin workflow for editing individual stanzas in large files

03Efficient term searching using specialized regex-based grep tools

04Support for Dead Simple Ontology Design Patterns (DOSDP) compliance

05Guided term obsolescence with replacement and consideration logic

0614 GitHub stars

Casos de Uso

01Refactoring ontology hierarchies and obsoleting outdated term stanzas

02Batch-editing specific term properties without loading entire multi-megabyte files

03Adding new biological terms with verified definitions and literature citations

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ai4curation/curation-skills editing-obo-ontologies

For use in Claude.ai and ChatGPT

Download Skill