Fixing term classification for EFO 3

[zoependlington]

• [x] EFO:EDIT1 retinoblastoma (Orphaner:790)
  • Align term with Orphanet
    • Remove as subclass of genetic eye tumor and genetic vitreous-retinal disease
    • Child of eye neoplasm (neoplasm and (has_disease_location some eye))
    • Child of retinopathy

More may be added according to this spreadsheet.

[zoependlington]

• [x] Ovarian carcinoma a child of malignant epithelial tumor of ovary
• [x] Malignant tumor of ovary child of ovarian neoplasm

[zoependlington]

Terms still requiring a decision to fix:

• [x] Primary lymphedema (Orphanet_77240)

  • Problem: Is equivalent to lymphedema and hereditary lymphedema
  • Follows the Orphanet classification.

• [x] Isolated aniridia (Orphanet_250923)

  • Problem: Is equivalent to Aniridia and Syndromic aniridia
  • Aniridia has inherited the isolated disease connection through Iridogoniodysgenesis (seems to stem from Hereditary glaucoma)
  • All classifications match or are similar to ORDO classification
    • The discrepancies/equivalence comes from MONDO's extra axiomatisation and equivalence definition axioms.

• [x] Syndromic aniridia (Orphanet_98557)

  • Problem: Is equivalent to Aniridia and Isolated aniridia
  • Aniridia has inherited the syndromic disease through syndromic cataracts.
  • All classifications match or are similar to ORDO classification
    • The discrepancies/equivalence comes from MONDO's extra axiomatisation and equivalence definition axioms.
  • Also seems to be connected to isolated disease through Iridogoniodysgenesis.

[zoependlington]

• [x] OBSOLETE Congenital primary lymphedema (Orphanet_2416)
  • Replaced by Milroy disease (Orphanet_79452) in accordance with ORDO classification
  • Also OBSOLETE Non-hereditary congenital primary lymphedema with same replacement.
  • Check Milroy disease classification against ORDO.

[zoependlington]

• [x] eccrine acrospiroma
  • reclassify as neoplasm and has_disease_location some eccrine sweat gland

[zoependlington]

Remaining terms have been submitted as issues to ORDO (https://github.com/Orphanet/ORDO/issues/18) and MONDO (https://github.com/monarch-initiative/mondo/issues/334).

[zoependlington]

• [x] EFO:EDIT Sphingolipidosis (Orphanet:79225)
  • Reclassified to child of Lipid storage disease (Orphanet:79204)
• [x] EFO:EDIT Lipid storage disease (Orphanet:79204)
  • Reclassified as child of Lysosomal disease (Orphanet:68366)
• [x] EFO:EDIT Niemann-Pick disease type C (Orphanet:646)
  • Reclassified as child of Sphingolipidosis