Ontology Mapper Agent Skill
> Map materials science terms, crystal structures, and sample descriptions to standardized ontology classes and properties — resolve natural-language concepts to ontology entries with confidence scores, translate Bravais lattice types, space groups, and lattice constants into ontology-compliant annotations, and produce full sample metadata from structured descriptions. Supports any ontology in ontology_registry.json (CMSO, ASMO, etc.). Use when annotating simulation inputs with FAIR metadata, translating "BCC iron" or "FCC copper" into formal ontology terms, preparing machine- readable sample descriptions, or bridging between lab vocabulary and ontology vocabulary, even if the user only says "what CMSO terms describe my material" or "annotate this sample for me."
Install
one command, takes just this skill from the repositorynpx skills add https://github.com/HeshamFS/materials-simulation-skills --skill ontology-mapperOther skills for the same job
different authors, same section of the catalogue
Guide users through a structured workflow for co-authoring documentation. Use when user wants to write documentation, proposals, technical specs, decision docs, or similar structured content. This workflow helps users efficiently transfer context, refine content through iteration, and verify the doc works for readers. Trigger when user mentions writing docs, creating proposals, drafting specs, or similar documentation tasks.
Automatically creates user-facing changelogs from git commits by analyzing commit history, categorizing changes, and transforming technical commits into clear, customer-friendly release notes. Turns hours of manual changelog writing into minutes of automated generation.
Use when implementing any feature or bugfix, before writing implementation code
Use when you have a spec or requirements for a multi-step task, before touching code
Use when creating new skills, editing existing skills, or verifying skills work before deployment
Use when writing or improving README files. Not all READMEs are the same — provides templates and guidance matched to your audience and project type.
| Remove signs of AI-generated writing from text. Use when editing or reviewing text to make it sound more natural and human-written. Based on Wikipedia's inflated symbolism, promotional language, superficial -ing analyses, vague attributions, em dash overuse, rule of three, AI vocabulary words, negative parallelisms, and excessive conjunctive phrases.
Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons protocols, official API compatibility. For multi-vendor automation or broader equipment control use pylabrobot.
How to use it
Take heshamfs/ontology-mapper from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.