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/hident
convert an unordered list of ontology terms into a ordered list, with leading whitespace to indicate heirarchy
turbomam/schemas-for-schemaless
Illustrations for ICBO 2021 submission
turbomam/synbio-alignments
turbomam/dc_state_streets
turbomam/mixs-source
turbomam/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)
turbomam/badexperiment
Convert Index of Terms to LinkML YAML. Many moving parts = bad experiment
turbomam/cogs
COGS Operates Google Sheets
turbomam/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.
turbomam/envo-robot-helpers
turbomam/linkml
Linked Open Data Modeling Language
turbomam/md2tsvs
convert all tables in a markdown document to TSV files
turbomam/sample-annotator
NMDC Sample Annotator
turbomam/scoped-mapping
when mapping strings from column/field X in some datasource, consider the values in column/field Y to determine what ontology to map to
turbomam/seq2ids
blast sequences to get ids of the taxon. gene, etc.
turbomam/shields
Concise, consistent, and legible badges in SVG and raster format
turbomam/synbio-sheets
schemasheets & cogs based synthetic biology schema
turbomam/synbio_bottomup
Dealing with one synthetic biology modeling problem at a time
turbomam/xml_splitting