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

context-collaboration

Resources for data-driven and collaboratively refined mappings between ontology classes like ENVO:00002259 ‘agricultural soil’ to MIxS environmental context questions like env_medium, subsetted according to MIxS environmental extensions like Agriculture.

cromwell_configs

dataharmonizer

Our dev interface is available via github pages:

dh_testing

Sandbox for testing the content of various minimal schemas vs DataHarmonizer

docs

User-facing, web-based documentation about the NMDC

enviroms

external-metadata-awareness

Tools for fetching and processing external schemas, ontologies and metadata records. Includes value set maintenance and some GitHub org exploration.

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-for-user-facility-template-transformations

CLI tool to convert metadata submissions from the NMDC submission portal to user facility Excel 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

metat_readcounts

metat_readsqc

Workflow for metatranscriptome quality control

mg_annotation

Metagenome Annotation Workflow