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abox_tbox_examples

A minimal ontology for demonstrating TBox (defining terminology, esp classes and object properties) and ABox (making instances of those classes and forming relations between the instances)

badexperiment

Convert Index of Terms to LinkML YAML. Many moving parts = bad experiment

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

biolink-subset

biosample-basex

Using the Base-X XML database to discover structure in NCBI's Biosample database

biosample-xmldb-sqldb

Tools for loading NCBI Biosample into an XML database and then transforming that into a SQL database

cogs

COGS Operates Google Sheets

dataharmonizer

A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 sampling data.

dc_state_streets

envo-robot-helpers

ess-dive-linkml-playground

This is a collaborative repo for exploring schema creation and data validation for ESS-DIVE, using LinkML

example-runner-sandbox

A place to learn about linkml-run-examples. Brought to you by the LinkML Cookiecutter.

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

fastapi_docker

aggregation of nmdc-schema utilities, with fastapi interface, deployed with docker

gen-pop-linkml2sheets

Single step population of linkml2sheets usage reports, with useful columns only

hident

convert an unordered list of ontology terms into a ordered list, with leading whitespace to indicate heirarchy

hrshdhgd

identifiers-sandbox

linkml

Linked Open Data Modeling Language

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

md2tsvs

convert all tables in a markdown document to TSV files

mifc

A minimum information standard checklist formalizing the description of food composition data and related metadata.

mixs-source

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.

nmdc-mixs-supplement-for-envo

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