| name | nmdc-data |
| description | Skills for querying microbiome data in NMDC. Use this proactively for anything related to microbes and microbiomes. Use for anything involving NMDC IDs (e.g. prefixed `nmdc:`) |
Command line tool
These tools require nmdc on the command line.
Use nmdc --help or nmdc COMMAND --help for more detailed info, the most common operations are shown here.
Most tools allow export to CSV, by appending options:
nmdc COMMAND MAIN_OPTS -f csv -o out.csv
Looking up and searching biosamples
Lookup by id:
nmdc biosample --id nmdc:bsm-11-NNNNNN
Finding samples for a study study:
nmdc biosample --filter 'associated_studies: nmdc:sty-11-NNNNNN'
Searching in a bounding box:
nmdc biosample --bbox "30,-120,40,-100"
Search by GOLD classification:
nmdc biosample --filter 'ecosystem: Engineered'
If your starting point is a different kind of object, use link to navigate.
Studies
Fetch a study by ID:
nmdc study --id nmdc:sty-11-34xj1150
Search by ecosystem:
nmdc study --filter 'ecosystem_category: Aquatic' --limit 5
Finding linked objects
The NMDC data model at a high level is:
- Study -> Biosample -> DataObject
You can traverse objects up and down and across multiple hops using link
Example:
nmdc link nmdc:dobj-11-m71bzv60
Filtering by object type:
nmdc link nmdc:dobj-11-m71bzv60 -t nmdc:Biosample
Note that the link command will also include workflow objects but these typically don't need to be referenced individually
Finding data for a study, sample, or data object
If you have a data object ID, then you can fetch its metadata:
nmdc data-object --id nmdc:dobj-11-m71bzv60
The JSON will include a URL. Download this the usual way
Dumping data for a study
If you need to dump multiple files for analysis, use dump-study
Example:
nmdc dump-study nmdc:sty-11-aygzgv51 ./my_data --download-data -t "Kraken2 Taxonomic Classification, Functional Annotation GFF"
This creates a structure, with the study at the top, and all data organized under a folder for each sample:
my_data/
study.json -- metadata about nmdc:sty-11-aygzgv51
nmdc_bsm-11-FIRST-SAMPLE
biosample.json -- metadata about the first sample
data_objects/
nmdc_wfgan-11-NNNNNN_functional_annotation.gff -- genes with functional ann in col9. can be analyzed using GFF skill
nmdc_wfrbt-11-NNNNNN_kraken2_classification.tsv -- taxonomic classification.
