JSON Import Format

See here for discussion: https://github.com/pombase/canto/issues/1779

"notes"

Text to store in the session that will be displayed on the front page / publication summary page in Canto.

"genes"

The IDs of the genes mentioned in the publication.

"alleles"

A map of allele IDs to allele details.

"gene"

The gene ID from the "genes" list. This field is required except for allele with type "abberation". The gene ID must appear in the "genes" list.

"type"

The allele type which must match an allele type in the allele_type_list configuration

"name"

The display name of the allele.

"description"

An internal description or note to make available to the curator via the "View/edit notes" menu item in the genotype list.

Example file:

{
  "PMID:2120045": {
    "genes": [
      "FBgn0004107", "FBgn0016131"
    ],
    "alleles": {
      "FBal0119310": {
        "gene": "FBgn0004107",
        "type": "other",
        "name": "Dmel\\Cdk2_UAS.Tag:MYC",
        "description": null
      },
      "FBal0064432": {
        "gene": "FBgn0016131",
        "type": "other",
        "name": "Dmel\\Cdk4_k06503",
        "description": null
      },
      "FBab0036462": {
        "type": "aberration",
        "name": "Df(3R)ED5223"
      }
    },
    "genotypes": {
      "FB<something>": {
        "taxon_id": 7227,
        "genotype_name": "...",
        "background": "...",
        "comment": "...",
        "alleles": [
          {
            "uniquename": "FBal0119310"
          },
          {
            "uniquename": "FBal0064432"
          }
        ]
      }
    }
  }
}

Possible new format including diploids:

{
  "PMID:2120045": {
    "genes": [
      "FBgn0004107", "FBgn0016131"
    ],
    "alleles": {
      "FBal0119310": {
        "gene": "FBgn0004107",
        "type": "other",
        "name": "Dmel\\Cdk2_UAS.Tag:MYC",
        "description": null
      },
      "FBal0064432": {
        "gene": "FBgn0016131",
        "type": "other",
        "name": "Dmel\\Cdk4_k06503",
        "description": null
      },
      "FBab0036462": {
        "type": "aberration",
        "name": "Df(3R)ED5223"
      }
    },
    "genotypes": {
      "FB<something_else>": {
        "taxon_id": 7227,
        "genotype_name": "...",
        "background": "...",
        "comment": "...",
        "diploids": {
          "FBsome_diploid_name": [
            {
              "uniquename": "FBal0119310"
            },
            {
              "uniquename": "FBal0064432"
            }
          ]
        }
      },
      "FB<something>": {
        "taxon_id": 7227,
        "genotype_name": "...",
        "background": "...",
        "comment": "...",
        "alleles": [
          {
            "uniquename": "FBal0119310"
          },
          {
            "uniquename": "FBal0064432"
          }
        ]
      }
    }
  }
}