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Repo Creation

LinkML was installed within a conda env to work with locally.

LinkML-OWL extension downloaded via pip:

pip install linkml-owl

  1. Create cookie cutter template repo from LinkML & new GitHub repo in GitHub GUI (https://github.com/new).

https://github.com/linkml/linkml-project-cookiecutter

  1. Cruft: used to take a template repo and customize through interactive questions

Cruft Version: 2.15.0 (installed via pipx) Poetry Version 1.8.3 (installed via pipx)

cruft create https://github.com/linkml/linkml-project-cookiecutter

Accept all defaults past entries through email

  1. cd into NIST-GEC_Lexicon/ and set up vm, install dependencies, etc.

make setup

  1. Push to GitHub

git remote add origin https://github.com/usnistgov/NIST-GEC_Lexicon.git git branch -M main git push -u origin main

  1. Change settings in GitHub GUI to allow pages documentation workflows

Publish schema documentation - For the documentation tool, set up Pages in GitHub: From your repo's page - go to (repo) > Settings > Pages Branch: gh-pages (branch exists from setup, automatically)

ISSUE Do not have a gh-pages branch so can't automatically generate documentation (have message on linkml slack)

Schema Dev

/src/nist_gec_lexicon/schema/nist_gec_lexicon.yaml

Boilerplate:

id: https://w3id.org/NIST/NIST-GEC_Lexicon
name: NIST-GEC_Lexicon
title: NIST-GEC_Lexicon
description: |-
  NIST Genome Editing Lexicon ontology repo with LinkML
license: MIT
see_also:
  - https://NIST.github.io/NIST-GEC_Lexicon

prefixes

How to map shorter URIs to longer form URIs Allows us to map to other ontologies

prefixes:
  nist_gec_lexicon: https://w3id.org/NIST/NIST-GEC_Lexicon/
  linkml: https://w3id.org/linkml/
  biolink: https://w3id.org/biolink/
  schema: http://schema.org/
  PATO: http://purl.obolibrary.org/obo/PATO_
  example: https://example.org/
default_prefix: nist_gec_lexicon
default_range: string

Mapping to OWL

Each LinkML class maps to an OWL class

Each LinkML slot maps to an OWL property

https://linkml.io/linkml/generators/owl.html

Generate OWL

note every time I ran poetry I was getting a 'The virtual environment found in [path] seems to be broken.'

To resolve:

poetry shell poetry env use python3.10 poetry install

--add-root-classes