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microbiomedata
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sample-annotator
NMDC Sample Annotator
https://microbiomedata.github.io/sample-annotator/static/intro.html
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NEON API example graphql queries
#124
sujaypatil96
opened
1 year ago
0
GOLD study ingest improvement- convert contacts to has credit associations
#123
aclum
opened
1 year ago
0
Misc updates to GOLD NMDC pipeline
#122
sujaypatil96
opened
1 year ago
0
NEON metagenomics sample metadata
#121
turbomam
opened
1 year ago
0
neon sample metadata retrieval
#120
turbomam
opened
1 year ago
0
Misc updates to GOLD NMDC pipeline
#119
sujaypatil96
closed
1 year ago
1
Submission portal metadata ingest
#118
JamesTessmer
opened
1 year ago
1
Create XML-like dict of NCBI biosample metadata from eutils; takes a GOLD Study ID as input
#117
turbomam
opened
1 year ago
0
retrieve NCBI biosample metadata with a GOLD study ID as the input
#116
turbomam
opened
1 year ago
0
Add Bioscales' biogeochemical values to data ingest process for Bioscales soil samples
#115
turbomam
closed
1 year ago
16
SSSOM mapping file between GOLD fields and NMDC slots
#114
sujaypatil96
opened
1 year ago
0
Update GOLD NMDC ingest pipeline to ingest bioscales
#113
sujaypatil96
closed
1 year ago
15
allow GOLD NMDC pipeline to filter based on biosample IDs
#112
sujaypatil96
opened
1 year ago
4
Improve logging: why don't some studies or biosamples get instantiated?
#110
turbomam
opened
2 years ago
2
Should portal submitter be included in Study instances?
#109
turbomam
opened
2 years ago
3
Better documentation for credentials required by api_or_tsv_metadata_submissions_to_json.py
#108
turbomam
opened
2 years ago
0
Deep parse when converting anything into NMDC Biosamples and Studies (at least)
#107
turbomam
opened
2 years ago
0
single codebase for converting from any source to NMDC biosamples or studies
#106
turbomam
opened
2 years ago
0
Sustainable integration of nmdc-runtime components?
#105
turbomam
opened
2 years ago
1
genericize dataset transformer method
#104
sujaypatil96
closed
1 year ago
1
add methods to filter by analysis ids
#103
sujaypatil96
closed
2 years ago
0
add gold client methods that use GOLD project and analysis ids
#102
sujaypatil96
opened
2 years ago
0
Web form that accepts dataset
#101
sujaypatil96
opened
2 years ago
3
Genericize dataset import methods
#100
sujaypatil96
closed
1 year ago
3
GROW dataset import into NMDC mongo
#99
sujaypatil96
opened
2 years ago
4
submissions_as_studies.py should keep track of whether the data came from dev or prod
#98
turbomam
opened
2 years ago
0
submissions_as_studies.py generates some empty strings in assets/out/submissions_as_studies.yaml
#97
turbomam
opened
2 years ago
1
Add credit association processing to submissions_as_studies.py
#96
turbomam
opened
2 years ago
1
submissions_as_studies.py need click CLI
#95
turbomam
opened
2 years ago
1
Add `INSDC_sample_identifiers` information to Mongo
#94
sujaypatil96
closed
2 years ago
3
Inconsistency between data in GOLD and data from bioregistry
#93
sujaypatil96
opened
2 years ago
0
pull `INSDC_sample_identifiers` information from GOLD
#92
sujaypatil96
closed
2 years ago
0
explore metadata submission API's response structure
#91
turbomam
opened
2 years ago
3
Get metadata submissions from the NMDC API & make schema compliant
#90
turbomam
opened
2 years ago
6
minimal documentation for NMDC client
#89
sujaypatil96
closed
2 years ago
1
NMDC vs INSDC id overlap
#88
turbomam
opened
2 years ago
0
find NMDC biosamples that are also present in the BBOP INSDC SQLite database
#87
turbomam
opened
2 years ago
1
uploading final .py file
#86
kristinahiraishi
closed
2 years ago
1
Add run_id to merged summaries
#85
sujaypatil96
closed
2 years ago
0
inserts one q3 parse result back into SQLite
#84
turbomam
opened
2 years ago
0
batch write quantity value reapirs to SQLite
#83
turbomam
opened
2 years ago
2
merge paired end summaries with data from GOLD API
#82
sujaypatil96
closed
2 years ago
0
integrate EMP500 paired end summary data from workflow
#81
sujaypatil96
closed
2 years ago
1
generalizable cleaning scripts (see issue #79)
#80
aarleed
closed
2 years ago
1
issue-79-Generalizable-Cleaning-Scripts
#79
aarleed
opened
2 years ago
1
inconsistent env_broad_scale #77
#78
jeaniceangelica
closed
2 years ago
0
Inconsistent env_broad_scale column
#77
jeaniceangelica
opened
2 years ago
4
handle depth and depth2 fields before populating them
#76
sujaypatil96
closed
2 years ago
1
misc fixes to `gold_nmdc.json`
#75
sujaypatil96
closed
2 years ago
0
Update part_of for omics_processing
#74
dehays
closed
2 years ago
2
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