Name: Mark Andrew Miller
Type: User
Company: Lawrence Berkeley National Laboratory
Bio: Software Developer at the Lawrence Berkeley National Laboratory. Harmonizing biomedical semantics and metadata. Microbiomes, samples, multi-omics.
Location: Philadelphia, PA, USA
Blog: https://berkeleybop.github.io/people/mark-a-miller/
Mark Andrew Miller's Projects
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)
Convert Index of Terms to LinkML YAML. Many moving parts = bad experiment
Helpers for BBOP projects, esp. LinkML and NMDC
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
Convert NCBI Bioproject to MongoDB in Python
Using the Base-X XML database to discover structure in NCBI's Biosample database
Tools for loading NCBI Biosample into an XML database and then transforming that into a SQL database
COGS Operates Google Sheets
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.
This is a collaborative repo for exploring schema creation and data validation for ESS-DIVE, using LinkML
A place to learn about linkml-run-examples. Brought to you by the LinkML Cookiecutter.
A cookiecutter for linkml projects which illustrates the Examples First design pattern
Check whether an instance of a LinkML class has used all of the associated classes
aggregation of nmdc-schema utilities, with fastapi interface, deployed with docker
Single step population of linkml2sheets usage reports, with useful columns only
convert an unordered list of ontology terms into a ordered list, with leading whitespace to indicate heirarchy
Linked Open Data Modeling Language
Fragments of schemas including features that may not work with all genrated artifacts
ALPHA data model mapping with linkml
llm-github/
just enough to experiment with OAK and llm
convert all tables in a markdown document to TSV files
A minimum information standard checklist formalizing the description of food composition data and related metadata.
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.