Annotated Genome Data

Overview

Generate JSON-LD files for annotated genes from a given GFF3 file. Currently GFF3 files from ENSEMBL and NCBI are supported.

Each JSON-LD file will contain:

  • GeneAnnotation objects

  • 1 GenomeAnnotation object

  • 1 GenomeAssembly object

  • 1 OrganismTaxon object

  • 1 Checksum object

NCBI Taxonomy Data

No setup is required before running bkbit gff2jsonld. A taxonomy subset covering every organism with a GenBank common name ships inside the bkbit package, so organism names resolve offline for all supported species.

If a GFF3 file references a taxon outside that subset, bkbit downloads the full NCBI taxonomy once and caches it in a per-user cache directory. To do that download up front instead of mid-run - for example when building a container image or running air-gapped - use the optional command:

$ bkbit download-ncbi-taxonomy

Set BKBIT_DATA_DIR to control where the cache is stored, or BKBIT_NO_DOWNLOAD to make an out-of-subset lookup raise an error instead of downloading.

Command Line

bkbit gff2jsonld

$ bkbit gff2jsonld [OPTIONS] GFF3_URL

Options

-a, --assembly_accession <assembly_accession>

ID assigned to the genomic assembly used in the GFF3 file.

Note

Must be provided when using ENSEMBL GFF3 files

-s, --assembly_strain <assembly_strain>

Specific strain of the organism associated with the GFF3 file.

-l, --log_level <log_level>

Logging level.

Default:

WARNING

Options:

DEBUG | INFO | WARNING | ERROR | CRITICAL

-f, --log_to_file

Log to a file instead of the console.

Default:

False

-o, --output_format <output_format>

Output format for the serialized data.

Default:

jsonld

Options:

jsonld | turtle

Arguments

GFF3_URL

Required argument

Examples

Example 1: NCBI GFF3 file

# Run gff2jsonld command
$ bkbit gff2jsonld 'https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9823/106/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.gff.gz' > output.jsonld

Example 2: ENSEMBL GFF3 file

# Run gff2jsonld command
$ bkbit gff2jsonld -a 'GCF_003339765.1' 'https://ftp.ensembl.org/pub/release-104/gff3/macaca_mulatta/Macaca_mulatta.Mmul_10.104.gff3.gz' > output.jsonld