Mark Andrew Miller's repositories
example-runner-sandbox
A place to learn about linkml-run-examples. Brought to you by the LinkML Cookiecutter.
biosample-basex
Using the Base-X XML database to discover structure in NCBI's Biosample database
fastapi_docker
aggregation of nmdc-schema utilities, with fastapi interface, deployed with docker
llm-github
llm-github/
bbop-helpers
Helpers for BBOP projects, esp. LinkML and NMDC
biocore-data-model-linkml-template
LinkML model for the Data Biosphere project, migrated from https://github.com/DataBiosphere/biocore-data-model/tree/main/content/linkml into a LinkML cookie cutter template
biosample-xmldb-sqldb
Tools for loading NCBI Biosample into an XML database and then transforming that into a SQL database
ess-dive-linkml-playground
This is a collaborative repo for exploring schema creation and data validation for ESS-DIVE, using LinkML
examples-first-cookiecutter
A cookiecutter for linkml projects which illustrates the Examples First design pattern
exhaustion-check
Check whether an instance of a LinkML class has used all of the associated classes
gen-pop-linkml2sheets
Single step population of linkml2sheets usage reports, with useful columns only
linkml-gen-something-functional
Fragments of schemas including features that may not work with all genrated artifacts
linkml-transformer
ALPHA data model mapping with linkml
mifc
A minimum information standard checklist formalizing the description of food composition data and related metadata.
mixs-subset-examples-first
A subset of the MIxS specification that's self-documenting and DataHarmonizer compatible. Comes with valid and invalid data examples. Subset = all checklists and all environmental packages, but partial combinations.
no_corners
Testing a regular expression for 96-well plates, where the corner wells must not be filled with a test sample
obook
OBO Organized Knowledge: Training materials for becoming an OBO engineer
ontogpt
GPT-based ontological extraction tools, including SPIRES
reactions-for-owl
Iterative, OWL-friendly model of proteolytic reactions
sheets-for-person-schema
Files for schemasheets exercises at ICBO 2022
split-pool-mod-schema
A Schema with processes for splitting, pooling and modifying material entities. Intended to illustrate solutions for NMDC modeling of NEON metadata and metabolomics data. Based on https://github.com/turbomam/examples-first-cookiecutter.
sssom
Simple Standard for Sharing Ontology Mappings
standards-schemas
Data schema for Bridge2AI Standards.