microbiomedata/sample-annotator

Issues

• Determine if and how `rel_to_oxygen` will be used in the submission schema

  #58 opened 10 months ago by turbomam
  21

• Get metadata submissions from the NMDC API & make schema compliant

  #90 opened 2 years ago by turbomam
  6

• Add Bioscales' biogeochemical values to data ingest process for Bioscales soil samples

  #115 opened a year ago by turbomam
  16

• GOLD study ingest improvement- convert contacts to has credit associations

  #123 opened 2 years ago by aclum
  0

• neon sample metadata retrieval

  #120 opened 2 years ago by turbomam
  0

• retrieve NCBI biosample metadata with a GOLD study ID as the input

  #116 opened 2 years ago by turbomam
  0

• SSSOM mapping file between GOLD fields and NMDC slots

  #114 opened 2 years ago by sujaypatil96
  0

• convert kristinahiraishi/sample-annotator from notebook to script

  #68 opened 2 years ago by turbomam
  4

• mark get spin access

  #61 opened 2 years ago by turbomam
  3

• Genericize dataset import methods

  #100 opened 2 years ago by sujaypatil96
  3

• allow GOLD NMDC pipeline to filter based on biosample IDs

  #112 opened 2 years ago by sujaypatil96
  4

• GROW dataset import into NMDC mongo

  #99 opened 2 years ago by sujaypatil96
  4

• Web form that accepts dataset

  #101 opened 2 years ago by sujaypatil96
  3

• Should portal submitter be included in Study instances?

  #109 opened 2 years ago by turbomam
  3

• Improve logging: why don't some studies or biosamples get instantiated?

  #110 opened 2 years ago by turbomam
  2

• Better documentation for credentials required by api_or_tsv_metadata_submissions_to_json.py

  #108 opened 2 years ago by turbomam
  0

• single codebase for converting from any source to NMDC biosamples or studies

  #106 opened 2 years ago by turbomam
  0

• Deep parse when converting anything into NMDC Biosamples and Studies (at least)

  #107 opened 2 years ago by turbomam
  0

• Sustainable integration of nmdc-runtime components?

  #105 opened 2 years ago by turbomam
  1

• Add `INSDC_sample_identifiers` information to Mongo

  #94 opened 2 years ago by sujaypatil96
  3

• submissions_as_studies.py need click CLI

  #95 opened 2 years ago by turbomam
  1

• Add credit association processing to submissions_as_studies.py

  #96 opened 2 years ago by turbomam
  1

• submissions_as_studies.py generates some empty strings in assets/out/submissions_as_studies.yaml

  #97 opened 2 years ago by turbomam
  1

• submissions_as_studies.py should keep track of whether the data came from dev or prod

  #98 opened 2 years ago by turbomam
  0

• Inconsistency between data in GOLD and data from bioregistry

  #93 opened 2 years ago by sujaypatil96
  0

• cache Pipfile.lock in github action

  #41 opened 2 years ago by wdduncan
  1

• find NMDC biosamples that are also present in the BBOP INSDC SQLite database

  #87 opened 2 years ago by turbomam
  1

• Removal of unnecessary folders

  #71 opened 3 years ago by sujaypatil96
  1

• batch write quantity value reapirs to SQLite

  #83 opened 2 years ago by turbomam
  2

• issue-79-Generalizable-Cleaning-Scripts

  #79 opened 3 years ago by aarleed
  1

• Inconsistent env_broad_scale column

  #77 opened 3 years ago by jeaniceangelica
  4

• Fix double prefixed GOLD study ID references produced for omics_processing

  #72 opened 3 years ago by dehays
  0

• Change form of biosample EnvO term values in gold_client_wrapper

  #73 opened 3 years ago by dehays
  0

• changes to gold_nmdc.json

  #70 opened 3 years ago by dehays
  1

• FAO soil group to OBO term mapping by @turbomam and DataGood? (microbiomedata/nmdc-schema #113)

  #64 opened 3 years ago by turbomam
  0

• Example Makefile entry

  #62 opened 3 years ago by turbomam
  2

• create bin directory

  #60 opened 3 years ago by turbomam
  0

• Where to put repaired output?

  #57 opened 3 years ago by turbomam
  0

• Missing values repair/normalization

  #56 opened 3 years ago by turbomam
  0

• add DataGood team members as explicit contributors

  #55 opened 3 years ago by turbomam
  0

• make @turbomam and admin or maintainer in this repo

  #54 opened 3 years ago by turbomam
  0

• create tsv illegal relationship_to_oxygen values flagged

  #49 opened 3 years ago by turbomam
  0

• did somebody say poetry?

  #47 opened 3 years ago by turbomam
  0

• reconcile recent branches

  #52 opened 3 years ago by turbomam
  5

• capitalize a string to learn the infrastructure

  #31 opened 3 years ago by turbomam
  0

• implement get_elevation

  #35 opened 3 years ago by cmungall
  1

• modify hardcoded URLs in get_fao_soil_type

  #42 opened 3 years ago by wdduncan
  0

• modify make test so the lock file isn't recreated every time

  #39 opened 3 years ago by wdduncan
  0

• get_fao_soil_class assumes a file path

  #34 opened 3 years ago by cmungall
  0

• move imports from method to header and add to pipenv dependencies

  #36 opened 3 years ago by cmungall
  0