Added more details

README.md

@@ -60,9 +60,13 @@ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 
 ### Modifications
 
-This modified version (gg_2024_09) was created by the Systems Genomics Lab for use with DeepTaxa. The Greengenes database, downloaded from https://ftp.microbio.me/greengenes_release/2022.10/, was processed as follows:
+This modified version (gg_2024_09) was created by [the Systems Genomics Lab](https://github.com/systems-genomics-lab) for use with DeepTaxa. The Greengenes database, downloaded from https://ftp.microbio.me/greengenes_release/2022.10/, was processed as follows:
 1. The original dataset, containing 23,450,269 sequences, was downloaded.
-2. Missing taxonomic classifications were filled with "Unclassified."
+2. Missing taxonomic classifications were filled with "Unclassified" or derived labels. For each sequence, the taxonomy table's ranks (e.g., kingdom, phylum, class) were processed sequentially. If a rank was empty or contained only whitespace:
+   - If no prior rank had a valid value, the field was left empty.
+   - If the previous rank's value included "Unclassified," that value was copied to the current rank.
+   - Otherwise, the field was set to "Unclassified_" followed by the previous rank's value (e.g., "Unclassified_Proteobacteria" for a missing class after phylum "Proteobacteria").
+   This ensured hierarchical consistency in the taxonomy labels.
 3. Sequences were filtered to retain only those with at least 300 nucleotides, resulting in 354,023 sequences.
 4. Sequence IDs were extracted, and the taxonomy table was filtered to match these IDs, yielding 346,671 entries (7,352 IDs not found were noted).
 5. A clean ID list was generated from the filtered taxonomy table (346,671 IDs).