registry.yml

mapping_registry_id: https://w3id.org/sssom/commons/monarch
mapping_registry_title: Monarch Mapping Commons
mapping_registry_description: A collection of the SSSOM-format mappings used for the Monarch Initiative knowledge graph
homepage: https://github.com/monarch-initiative/monarch-mapping-commons

mapping_set_references:
  # MONDO disease mappings
  - mapping_set_id: http://purl.obolibrary.org/obo/mondo/mappings/mondo.sssom.tsv
    mapping_set_group: disease_mappings
    local_name: mondo.sssom.tsv
    mapping_set_confidence: "0.99"
    other:
      local_id: mondo

  # Biomappings for CTD
  - mapping_set_id: http://w3id.org/sssom/commons/monarch/mesh_chebi_biomappings.sssom.tsv
    mapping_set_group: chemical_mappings
    local_name: mesh_chebi_biomappings.sssom.tsv
    mirror_from: https://raw.githubusercontent.com/biopragmatics/biomappings/master/docs/_data/sssom/biomappings.sssom.tsv
    mapping_set_confidence: "0.9"

  # Monarch Gene Mappings
  - mapping_set_id: http://w3id.org/sssom/commons/monarch/gene_mappings.sssom.tsv
    mapping_set_group: gene_mappings
    local_name: gene_mappings.sssom.tsv
    mirror_from: https://data.monarchinitiative.org/monarch-gene-mapping/latest/gene_mappings.sssom.tsv
    mapping_set_confidence: "0.9"

  # HP-Mesh Mappings
  - mapping_set_id: http://w3id.org/sssom/commons/monarch/hp_mesh.sssom.tsv
    mapping_set_group: phenotype
    local_name: hp_mesh.sssom.tsv
    mirror_from: https://raw.githubusercontent.com/monarch-initiative/umls-ingest/main/src/umls_ingest/mappings/hp_mesh.sssom.tsv
    mapping_set_confidence: "0.9"

  # UMLS-HP Mappings
  - mapping_set_id: http://w3id.org/sssom/commons/monarch/umls_hp.sssom.tsv
    mapping_set_group: phenotype
    local_name: umls_hp.sssom.tsv
    mirror_from: https://raw.githubusercontent.com/monarch-initiative/umls-ingest/main/src/umls_ingest/mappings/umls_hp.sssom.tsv
    mapping_set_confidence: "0.9"

  # uPheno Custom Mappings (byproduct of current uPheno2 pipeline)
  - mapping_set_id: http://w3id.org/sssom/commons/monarch/upheno_custom.sssom.tsv
    mapping_set_group: phenotype
    local_name: upheno_custom.sssom.tsv
    mapping_set_confidence: "1"

  # uPheno species independent mappings
  - mapping_set_id: https://data.monarchinitiative.org/mappings/upheno/upheno-species-independent.sssom.tsv
    mapping_set_group: phenotype
    local_name: upheno-species-independent.sssom.tsv
    mapping_set_confidence: "1"