Change microbial sources filter to adopt gtDB taxonomic classification tree about ampspherewebsite HOT 5 CLOSED

Solution 1

• Store raw text lineages as a column of the metadata table.
• Query GMSC genes based on string matching.
• Downside: Potential performance issue, hard to provide available options.

Solution 2

• Store taxa of each rank as an individual column of the metadata table.
• Query GMSC genes based on a rank selector and a taxon name input box (with available options provided).
• Downside: Large database size.

I think solution 2 would be the best.

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Minor points.

• The version of GTDB taxonomy database.
• Which column of the metadata table (of GTDB taxonomy database) did we use as the microbial source? I guess it's the "gtdb_taxonomy" column.
• There is a special taxon "*", which I cannot understand.

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Mapping GTDB taxonomy to NCBI taxon ids.

In the metadata table, "gtdb_taxonomy" (microbial sources) -> "ncbi_taxid" and "ncbi_taxonomy".

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Current solution: Convert Progenomes2 taxa to GTDB.

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A simple input box providing sk,k,p,c,o,f,g,s works for gtdb taxonomy tree, and move the one with rank selector to advance search

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