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Merge pull request #85 from microbiomedata/issue-84
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Issue #84 - add links for downloading data collections to README
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@wdduncan
wdduncan committed Jul 1, 2021
2 parents 2d82955 + 881371b commit b18bb2c
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38 changes: 38 additions & 0 deletions README.md
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Expand Up @@ -24,3 +24,41 @@ The NMDC [Introduction to metadata and ontologies](https://microbiomedata.org/in

See also [these slides](https://microbiomedata.github.io/nmdc-metadata/docs/schema-slides) describing the schema

## Collections within the schema

_If some colelctions are reported to contain 0 documents, it could be that the MongoDB is being repopulated based on new data or a new schema._

**These colelction downloads are compressed in the `.bz2` format. If you click the links, most browsers will display binary garbage on your screen. Right-click "save as" will work better in most cases.**


| Collection Name | Documents | Avg. Document Size | Total Document Size | Notes |
|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------:|-------------------:|--------------------:|--------------------------------------------------------------------|
| [activity_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/activity_set.json.bz2) | 0 | | 0.0 B | |
| [biosample_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/biosample_set.json.bz2) | 716 | 1.2 KB | 835.1 KB | |
| [capabilities](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/capabilities.json.bz2) | 9 | 120.1 B | 1.1 KB | |
| [data_object_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/data_object_set.json.bz2) | 12,455 | 294.0 B | 3.5 MB | |
| [date_created](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/date_created.json.bz2) | 0 | | 0.0 B | |
| [etl_software_version](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/etl_software_version.json.bz2) | 0 | | 0.0 B | |
| [functional_annotation_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/functional_annotation_set.json.bz2) | 0 | | 0.0 B | |
| [genome_feature_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/genome_feature_set.json.bz2) | 0 | | 0.0 B | |
| [ids](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/ids.json.bz2) | 12 | 29.0 B | 348.0 B | |
| [mags_activity_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/mags_activity_set.json.bz2) | 114 | 5.2 KB | 597.7 KB | |
| [metabolomics_analysis_activity_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/metabolomics_analysis_activity_set.json.bz2) | 209 | 72.6 KB | 14.8 MB | |
| [metagenome_annotation_activity_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/metagenome_annotation_activity_set.json.bz2) | 156 | 649.0 B | 98.9 KB | |
| [metagenome_assembly_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/metagenome_assembly_set.json.bz2) | 403 | 1.1 KB | 427.2 KB | |
| [metaproteomics_analysis_activity_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/metaproteomics_analysis_activity_set.json.bz2) | 33 | 3.6 MB | 120.1 MB | |
| [nmdc_schema_version](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/nmdc_schema_version.json.bz2) | 0 | | 0.0 B | |
| [nom_analysis_activity_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/nom_analysis_activity_set.json.bz2) | 788 | 431.0 B | 331.7 KB | |
| [notes](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/notes.json.bz2) | 0 | | 0.0 B | |
| [object_types](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/object_types.json.bz2) | 1 | 141.0 B | 141.0 B | |
| [objects](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/objects.json.bz2) | 2 | 412.0 B | 824.0 B | |
| [omics_processing_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/omics_processing_set.json.bz2) | 2,716 | 478.5 B | 1.2 MB | |
| [operations](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/operations.json.bz2) | 4 | 585.0 B | 2.3 KB | |
| [raw.functional_annotation_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/raw.functional_annotation_set.json.bz2) | 0 | | 0.0 B | "raw" means this collection hasn't been run through any validation |
| [read_QC_analysis_activity_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/read_QC_analysis_activity_set.json.bz2) | 405 | 611.9 B | 242.0 KB | |
| [read_based_analysis_activity_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/read_based_analysis_activity_set.json.bz2) | 274 | 904.0 B | 241.9 KB | |
| [sites](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/sites.json.bz2) | 1 | 187.0 B | 187.0 B | |
| [study_set](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/study_set.json.bz2) | 8 | 1.2 KB | 9.6 KB | |
| [triggers](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/triggers.json.bz2) | 1 | 146.0 B | 146.0 B | |
| [users](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/users.json.bz2) | 1 | 124.0 B | 124.0 B | |
| [workflows](https://polyneme.nyc3.cdn.digitaloceanspaces.com/nmdc/mongo/export/dwinston_share/workflows.json.bz2) | 9 | 161.3 B | 1.4 KB | |
4 changes: 4 additions & 0 deletions local/README.md
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## this is a placeholder for creating the parent folder

This folder will be gitignored

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