Read a reviewed SSSOM mapping set — read_sssom_mapping

Reads the SSSOM 1.1 embedded-TSV serialization used by Salmon Data Packages. The reader enforces UTF-8 without a byte-order mark, LF line endings, tab delimiters, declared CURIE prefixes, and the package's alignment-only profile. In particular, decomposition fields and raw literal assignments are refused because they belong in separate SDP semantic artifacts.

Usage

read_sssom_mapping_set(path, validate = TRUE)

Arguments

path: Path to one .sssom.tsv file.
validate: Logical; validate metadata, CURIEs, mappings, and no-match cardinalities after parsing. The byte and table structure is always checked.

Value

A metasalmon_sssom_mapping_set list containing metadata, a mappings tibble, and the normalized source path.

Details

CURIE prefixes in identifier/reference fields must be declared in curie_map except the SSSOM built-in prefixes (owl, rdf, rdfs, semapv, skos, sssom, xsd and linkml), which the SSSOM specification lets a file omit, so a canonical SSSOM/TSV file that leaves them out is read. A curie_map that does declare a built-in prefix must give it the expansion the specification fixes for it (for example http://www.w3.org/2004/02/skos/core# for skos); any other expansion is refused.

predicate_type uses SSSOM's entity-type enum, excluding the values the specification forbids for predicates. subject_category, object_category and similarity_measure are text, so their values need no CURIE declaration.

Examples

# Illustrative mapping only; curate real assertions before publication.
mapping_file <- tempfile(fileext = ".sssom.tsv")
writeLines(c(
  '#sssom_version: "1.1"',
  "#curie_map:",
  "#  exa: https://example.org/ontology-a/",
  "#  exb: https://example.org/ontology-b/",
  "#mapping_set_id: https://example.org/mappings/demo",
  "#mapping_set_version: 1",
  "#license: https://creativecommons.org/licenses/by/4.0/",
  "#subject_source: https://example.org/ontology-a/",
  "#subject_source_version: 1",
  "#object_source: https://example.org/ontology-b/",
  "#object_source_version: 1",
  paste("subject_id", "subject_label", "predicate_id", "object_id",
        "object_label", "mapping_justification", sep = "\t"),
  paste("exa:spawner-count", "Spawner count", "skos:exactMatch",
        "exb:spawner-count", "Spawner count",
        "semapv:ManualMappingCuration", sep = "\t")
), mapping_file, useBytes = TRUE)
mapping_set <- read_sssom_mapping_set(mapping_file)
mapping_set$metadata$mapping_set_id
#> [1] "https://example.org/mappings/demo"
unlink(mapping_file)