Adding Species and Handling Genome Versions

To add a species:

1. Add species-specific genome and annotation metadata to study YAML files.
2. Add identifier maps under data/mappings/.
3. Preserve original locus, transcript, protein, and metabolite identifiers.
4. Add ortholog links only when confidence can be documented.
5. Record mapping confidence for every mapped feature.

Genome-version changes should be treated as provenance events. Do not overwrite historical standardized identifiers without recording the mapping release.

Pacific oyster reference used by the first real-study intake

Mapping release cgigas_cgi_to_ncbi_gene_rs2024_06_v1 translates selected oyster_v9 (GCA_000297895.1) features to NCBI Gene IDs confirmed in RefSeq assembly GCF_963853765.1, annotation RS_2024_06. The release table and its method, source checksums, thresholds, and unresolved cases are stored together under data/mappings/.