ncbi taxonomy data cleaning #1014
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fill in missing subsections
spiekos
reviewed
Jun 25, 2024
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Great start to documenting the import!
- I filled out the README.md further, but there are still a couple of subsections that need to be added - please finish.
- Currently this does not run as intended by the prescribed import procedure. Please make sure that files are stored and callable properly in the scripts/, import/, and output/ subdirectories. Currently everything needs to be stored, called, and written to the same head directory
- There are multiple formatting errors in the generated "ncbi_taxonomy_schem_enum.mcf" file - please update your script to fix this
- The taxonRank is not processed as part of the nodes.dmp file - this is column 3 (rank) of the file. Please add the two prescribed two lines of code to the function at line 514 to fix this.
- Please include the java test tool in the test script including downloading it as part of the script. These lines that need to be added to tests.sh are in the comments.
scripts/biomedical/NCBI_Taxonomy/schema_mfc/ncbi_taxonomy_schema.mcf
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scripts/biomedical/NCBI_Taxonomy/test_data/division_enum_expected.mcf
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scripts/biomedical/NCBI_Taxonomy/scripts/format_ncbi_taxonomy.py
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add schema documentation on edges
update script
add json tool test
Add documentation around new schema added as part of this import
Fix typo in subdirectory name
add missing enumeration generated by script to the appropriate subsection of the New Schema section
add quotes around name for generated enum
revert back to original test script
spiekos
requested changes
Jul 4, 2024
scripts/biomedical/NCBI_Taxonomy/test_data/division_enum_expected.mcf
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scripts/biomedical/NCBI_Taxonomy/test_data/host_enum_expected.mcf
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scripts/biomedical/NCBI_Taxonomy/test_data/nodes_enum_expected.mcf
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ajaits
reviewed
Aug 27, 2024
update the properties subsection to describe all properties included in the import
update notes and caveat subsection
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