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Issue #84 - add links for downloading data collections to README #85

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merged 9 commits into from
Jul 1, 2021
Merged

Issue #84 - add links for downloading data collections to README #85

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ea4431e
creating local folder
turbomam Jun 28, 2021
247f2e4
added collections table
turbomam Jun 28, 2021
4489110
added download links to collections table
turbomam Jun 28, 2021
7f628b8
Added download notes for collections table
turbomam Jun 28, 2021
3d9dc21
spelling must -> most
turbomam Jun 28, 2021
d7508d5
column alignment
turbomam Jun 28, 2021
0880d61
ignore /local
turbomam Jun 28, 2021
e1bdc1a
Merge branch 'issue-84' of github.com:microbiomedata/nmdc-schema into…
turbomam Jun 28, 2021
881371b
Merge branch 'main' into issue-84
wdduncan Jul 1, 2021
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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