annotations/plant/SCHEMA.md

GenBank Annotation Output Schema

Published final annotations live under:

Single-file shard output:

annotations/<division>/<shard>.parquet

Chunked shard output:

annotations/<division>/<shard>/<shard>.chunk-00000.parquet

Rows are one row per source contig segment. Most contigs have one segment; very large contigs are split to keep each Parquet row below writer limits.

Column	Type	Purpose
source_key	string	Stable local key: `
division	string	GenBank division/group used by the pipeline
record_name	string	FASTA/GenBank contig record ID
assembly_accession	string	GenBank assembly accession
organism_name	string	Assembly organism name from GenBank metadata
taxid	int64	NCBI taxonomy ID
genome_size	int64	Assembly genome size from GenBank metadata
ftp_path	string	NCBI FTP directory for the assembly; enough to recover the source FASTA path
aligned_bp_length	int64	Total number of bp represented for the source contig after 6-mer alignment
segment_start_bp	int64	0-based inclusive start coordinate of this row within the aligned source contig
segment_end_bp	int64	0-based exclusive end coordinate of this row within the aligned source contig
segment_bp_length	int64	Number of aligned bp represented by this row
segment_index	int32	0-based segment index for this source contig
segment_count	int32	Number of output rows needed to represent this source contig
annotation_run_id	string	Pipeline run identifier used when unpacking/publishing annotations
annotation_run_timestamp_utc	string	UTC timestamp associated with the annotation run
annotation_git_commit	string	Git commit of this pipeline when annotations were unpacked/submitted
manifest_id	string	Manifest/run identifier for the source assembly selection
sequence	string	Source contig sequence prefix represented by the probability arrays. Optional; omitted for Hub-scale outputs by default.
pred_prob_positive_strand_cds	list	Per-bp P(CDS) on positive strand for segment_start_bp:segment_end_bp
pred_prob_negative_strand_cds	list	Per-bp P(CDS) on negative strand for segment_start_bp:segment_end_bp

Intentionally omitted from Hub-scale final outputs:

• raw packed blocks and raw packed-block probability outputs.
• sequence, unless the run was unpacked without --omit-sequence.

Mapping back to source FASTA:

1. Use ftp_path to locate the assembly directory.
2. The FASTA file basename is the final path component of ftp_path plus _genomic.fna.gz.
3. Use record_name to find the contig in that FASTA.
4. Probability arrays cover segment_start_bp:segment_end_bp within the first aligned_bp_length bp of that contig. Concatenate rows ordered by segment_index to reconstruct full-contig arrays when segment_count > 1.