microbiomedata Goto Github PK

archived-metadata-notebooks

attributes-of-biosamples

Vendor-neutral collection of terms for describing Environmental Biosamples

berkeley-schema-fy24

A fork of the nmdc-schema, for refactoring based on Monterey insights

binder-for-linkml-proj

research: can we expose nmdc-schema jupyter notebooks in binder? what config files are acceptable?

cleanroom-schema

Clean-room reboot of NMDC schema

cromwell_configs

dataharmonizer

Our dev interface is available via github pages:

dh_testing

Sandbox for testing the content of various minimal schemas vs DataHarmonizer

enviroms

geoloc-tools

get-neon-data-with-r

experimental repo for testing R and R package installation in GH actions

gold-ontology-translation

Translates the environmental level values in the GOLD dataset into a hierarchical ontology.

iot_to_linkml

Convert Index of Terms to LinkML YAML

issues

public repo for issues related to NMDC work

kaiko_metaproteome

Generates sample-specific protein databases from raw peptide spectra

metaassembly

Workflow for metagenome assembly

metadata-template-transformation

ETL between NMDC submission portal study records and user facility templates

metadata_converter

Conversion of schemas/templates/metadata to biolinkml

metag

End-to-end metaG workflow (WIP)

metamags

Workflow for metagenome assembled genomes generation.

metams

GC-MS Based Metabolomics Workflow

metapro

Workflow for meta-proteomics analysis

metat

Metatranscriptomics workflow

metat_assembly

workflow for metatranscriptome assembly

mg_annotation

Metagenome Annotation Workflow

minimal-metab

mixs

Minimum Information about any (X) Sequence” (MIxS) specification

mixs-6-2-release-candidate

Proposed, Harmonized MIxS 6.2

mixs-ontology-translation

mixs_fresh_start

A MIxS repo that uses LinkML cookiecutter and schemasheets from the beginning