Facet vocabulary

Haplotype Resolution

3 terms

Controlled vocabulary recording the haplotype resolution of a file's content — what the values represent with respect to allele/haplotype phasing: resolved to individual alleles (allele_specific), partitioned per parental haplotype (haplotype_specific), or phase-resolved without per-haplotype splitting (phased). A small content facet — the second intrinsic-content facet after strand — that factors the resolution qualifier out of compound ENCODE output_type / DataType / FeatureType terms (e.g. "haplotype-specific contact matrix", "phased variant calls") rather than baking it into the interpretation value. It records what the values represent, not an operation applied to the data, so it lives in interpretation, not provenance. An absent value means the content is haplotype-collapsed / not phase-resolved. The vocabulary deliberately excludes three axes: the parental-origin axis (maternal/paternal), reference ploidy (diploid), and the allelic-imbalance sense of "allele-specific". Following the facet convention for axes lacking a clean ontology term for the resolution sense, the permissible values carry no meaning: CURIEs. Surfaced via the Track Interpretation schema's haplotype_resolution slot (alongside strand). Aligned with FGA-WG issue #2 (data interpretation).