turbomam
Software Developer at the Lawrence Berkeley National Laboratory. Harmonizing biomedical semantics and metadata. Microbiomes, samples, multi-omics, syn. bio.
Lawrence Berkeley National LaboratoryPhiladelphia, PA, USA
Pinned Repositories
schema-automator
Automated assistance for the schema development lifecycle
DataHarmonizer
Our dev interface is available via github pages:
biosample-basex
Using the Base-X XML database to discover structure in NCBI's Biosample database
dc_state_streets
example-runner-sandbox
A place to learn about linkml-run-examples. Brought to you by the LinkML Cookiecutter.
fastapi_docker
aggregation of nmdc-schema utilities, with fastapi interface, deployed with docker
hident
convert an unordered list of ontology terms into a ordered list, with leading whitespace to indicate heirarchy
llm-github
llm-github/
mixs-source
schemas-for-schemaless
Illustrations for ICBO 2021 submission
turbomam's Repositories
turbomam/example-runner-sandbox
A place to learn about linkml-run-examples. Brought to you by the LinkML Cookiecutter.
turbomam/biosample-basex
Using the Base-X XML database to discover structure in NCBI's Biosample database
turbomam/fastapi_docker
aggregation of nmdc-schema utilities, with fastapi interface, deployed with docker
turbomam/llm-github
llm-github/
turbomam/synbio-bestof
turbomam/bbop-helpers
Helpers for BBOP projects, esp. LinkML and NMDC
turbomam/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
turbomam/biolink-subset
turbomam/biosample-xmldb-sqldb
Tools for loading NCBI Biosample into an XML database and then transforming that into a SQL database
turbomam/ess-dive-linkml-playground
This is a collaborative repo for exploring schema creation and data validation for ESS-DIVE, using LinkML
turbomam/examples-first-cookiecutter
A cookiecutter for linkml projects which illustrates the Examples First design pattern
turbomam/exhaustion-check
Check whether an instance of a LinkML class has used all of the associated classes
turbomam/gen-pop-linkml2sheets
Single step population of linkml2sheets usage reports, with useful columns only
turbomam/hrshdhgd
turbomam/identifiers-sandbox
turbomam/linkml-gen-something-functional
Fragments of schemas including features that may not work with all genrated artifacts
turbomam/linkml-transformer
ALPHA data model mapping with linkml
turbomam/mifc
A minimum information standard checklist formalizing the description of food composition data and related metadata.
turbomam/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.
turbomam/nmdc-mixs-supplement-for-envo
turbomam/no_corners
Testing a regular expression for 96-well plates, where the corner wells must not be filled with a test sample
turbomam/obook
OBO Organized Knowledge: Training materials for becoming an OBO engineer
turbomam/ontogpt
GPT-based ontological extraction tools, including SPIRES
turbomam/reactions-for-owl
Iterative, OWL-friendly model of proteolytic reactions
turbomam/sheets-for-person-schema
Files for schemasheets exercises at ICBO 2022
turbomam/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.
turbomam/sssom
Simple Standard for Sharing Ontology Mappings
turbomam/standards-schemas
Data schema for Bridge2AI Standards.
turbomam/tank-schema
turbomam/w3id.org
Website source code for w3id.org.