Add BiosampleMeta_ncbi #230
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Changes to be committed: new file: data_files/biosampleMeta_ncbi.tsv
steph-sing
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Feb 27, 2023
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Correct:
- Matched the V1.2 Data Dictionary
- blank spaces instead of dashes
Changes Requested:
- Headers and subsequent cells need to be filled prior to release, either manually of via scripts (ideal): bco_id | schema_version | bioproject
- Variables in cells are not standardized and need to be addressed prior to release, either manually or via scripts (ideal): Not applicable vs. Not Applicable; unknown vs Unknown; Missing vs. missing
- some Organism names appear like this: Coprococcus eutactus ATCC 27759, where 'ATCC 27759' might affect filtering
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In addition to the comments committed during the review, action items are as follows:
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This was referenced Feb 28, 2023
[Fixes for Review](#230 (comment)) Changes to be committed: modified: data_files/biosampleMeta_ncbi.tsv
steph-sing
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Feb 28, 2023
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steph-sing
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steph-sing
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Table looks good to me. Please push to main as a .tsv, and make sure it is accessible to download so I can put it in the server.
Please also update the file name and usability domain to reflect the table updates. Once the BCO is updated, let me know and we should be good for the data release tomorrow. If BCO version changes please give me an FYI.
HadleyKing
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Apr 26, 2023
[Fixes for Review](#230 (comment)) Changes to be committed: modified: data_files/biosampleMeta_ncbi.tsv
HadleyKing
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May 2, 2023
* Add BisampleMeta_ncbi Changes to be committed: new file: data_files/biosampleMeta_ncbi.tsv * Fixes for Review [Fixes for Review](#230 (comment)) Changes to be committed: modified: data_files/biosampleMeta_ncbi.tsv * v1.3 Data data_dictionary Changes to be committed: new file: data_dictionary/v1.3/README.tsv new file: data_dictionary/v1.3/core_property_list.tsv new file: data_dictionary/v1.3/non-core_property_list.tsv new file: data_dictionary/v1.3/property_definition.tsv new file: data_dictionary/v1.3/release_notes.tsv new file: schema/v1.3/core/.json new file: schema/v1.3/core/assemblyQC.json new file: schema/v1.3/core/assemblyQC_NCBI.json new file: schema/v1.3/core/biosampleMeta.json new file: schema/v1.3/core/ngsQC.json new file: schema/v1.3/core/ngsQC_NCBI.json new file: schema/v1.3/core/siteQC.json new file: schema/v1.3/non-core/.json new file: schema/v1.3/non-core/SRA_biosample.json new file: schema/v1.3/non-core/ngs_ID_list.json new file: schema/v1.3/non-core/sars-cov-2_lineage_mutations.json new file: schema/v1.3/non-core/uniprot-proteome_*.json * After Tests Changes to be committed: new file: lib/test_file_generation.sh new file: tests/v1.3/test_files/NC_045512_SARS-CoV-2_Wuhan.fasta new file: tests/v1.3/test_files/UP000001014_99287.fasta new file: tests/v1.3/test_files/UP000001014_99287_DNA.fasta new file: tests/v1.3/test_files/UP000009255_211044.fasta new file: tests/v1.3/test_files/UP000009255_211044_DNA.fasta new file: tests/v1.3/test_files/UP000009255_proteome_genome_metadata.csv new file: tests/v1.3/test_files/UP000180448_33727.fasta new file: tests/v1.3/test_files/UP000180448_33727_DNA.fasta new file: tests/v1.3/test_files/UP000464024_2697049.fasta new file: tests/v1.3/test_files/UP000464024_2697049_DNA.fasta new file: tests/v1.3/test_files/assemblyQC_HIVE.tsv new file: tests/v1.3/test_files/assemblyQC_NCBI.tsv new file: tests/v1.3/test_files/biosampleMeta_HIVE.tsv new file: tests/v1.3/test_files/biosampleMeta_ncbi.tsv new file: tests/v1.3/test_files/core_property_list.tsv new file: tests/v1.3/test_files/ngsQC_HIVE.tsv new file: tests/v1.3/test_files/ngsQC_NCBI.tsv new file: tests/v1.3/test_files/ngsQC_PL.tsv new file: tests/v1.3/test_files/ngs_id_list.tsv new file: tests/v1.3/test_files/non-core_property_list.tsv new file: tests/v1.3/test_files/property_definition.tsv new file: tests/v1.3/test_files/reference-guided_genome_assemblies_Galaxy.fasta new file: tests/v1.3/test_files/reference-guided_genome_assemblies_HIVE-Hexagon.fasta new file: tests/v1.3/test_files/sars-cov-2_lineage_mutations.tsv new file: tests/v1.3/test_files/siteQC_HIVE.tsv new file: tests/v1.3/test_files/temp_archive new file: tests/v1.3/test_files/uniprot-proteome_UP000001014.csv new file: tests/v1.3/test_files/uniprot-proteome_UP000180448.csv new file: tests/v1.3/test_files/uniprot-proteome_UP000464024.csv new file: tests/v1.3/test_results/assemblyQC_HIVE.json new file: tests/v1.3/test_results/assemblyQC_NCBI.json new file: tests/v1.3/test_results/biosampleMeta_HIVE.json new file: tests/v1.3/test_results/biosampleMeta_ncbi.json new file: tests/v1.3/test_results/core_property_list.json * README Changes to be committed: new file: data_dictionary/README.md
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Changes to be committed:
new file: data_files/biosampleMeta_ncbi.tsv