From df2ac74ee2fe57254938afdc8c90094162f7dfc1 Mon Sep 17 00:00:00 2001
From: Bento007 <trent.smith007@gmail.com>
Date: Tue, 20 Feb 2024 16:03:44 -0800
Subject: [PATCH] remove orphans

---
 tools/ontology-builder/src/curated_lists.py | 78 ---------------------
 1 file changed, 78 deletions(-)
 delete mode 100644 tools/ontology-builder/src/curated_lists.py

diff --git a/tools/ontology-builder/src/curated_lists.py b/tools/ontology-builder/src/curated_lists.py
deleted file mode 100644
index d59d7909..00000000
--- a/tools/ontology-builder/src/curated_lists.py
+++ /dev/null
@@ -1,78 +0,0 @@
-# Production tissues with no corresponding hand-curated system; required so
-# that they are explicitly added to the generated subgraph.
-# TODO generate using https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/gh/chanzuckerberg
-#  /single-cell-data-portal/6227
-ORPHAN_TISSUES = [
-    "UBERON_0001013",  # adipose tissue
-    "UBERON_0009472",  # axilla
-    "UBERON_0018707",  # bladder organ
-    "UBERON_0000310",  # breast
-    "UBERON_0001348",  # brown adipose
-    "UBERON_0007106",  # chorionic villus
-    "UBERON_0000030",  # lamina propria
-    "UBERON_0015143",  # mesenteric fat pad
-    "UBERON_0000344",  # mucosa
-    "UBERON_0003688",  # omentum
-    "UBERON_0001264",  # pancreas
-    "UBERON_0000175",  # pleural effusion
-    "UBERON_0000403",  # scalp
-    "UBERON_0001836",  # saliva
-    "UBERON_0001416",  # skin of abdomen
-    "UBERON_0002097",  # skin of body
-    "UBERON_0001868",  # skin of chest
-    "UBERON_0001511",  # skin of leg
-    "UBERON_0002190",  # subcutaneous adipose tissue
-    "UBERON_0002100",  # trunk
-    "UBERON_0035328",  # upper outer quadrant of breast
-    "UBERON_0001040",  # yolk sac
-    "UBERON_0000014",  # zone of skin
-]
-
-# Production cell types with no corresponding hand-curated cell class; required
-# so that they are explicitly added to the generated subgraph.
-# TODO check if this can be generated as part of
-#  https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/gh/chanzuckerberg/single-cell-data
-#  -portal/6227
-ORPHAN_CELL_TYPES = [
-    "CL_0000003",
-    "CL_0009012",
-    "CL_0000064",
-    "CL_0000548",
-    "CL_0000677",
-    "CL_0000186",
-    "CL_0009011",
-    "CL_1001319",
-    "CL_0000188",
-    "CL_1000497",
-    "CL_0008019",
-    "CL_1000597",
-    "CL_1000500",
-    "CL_1000271",
-    "CL_0000663",
-    "CL_0000255",
-    "CL_0001034",
-    "CL_0001063",
-    "CL_0011101",
-    "CL_0008036",
-    "CL_0000525",
-    "CL_0002488",
-    "CL_0000148",
-    "CL_0001064",
-    "CL_0002092",
-    "CL_0002371",
-    "CL_0009005",
-    "CL_0000019",
-    "CL_0000114",
-    "CL_0000630",
-    "CL_0008034",
-    "CL_0000010",
-    "CL_0009002",
-    "CL_0000670",
-    "CL_0000222",
-    "CL_0009010",
-    "CL_0000001",
-    "CL_0000183",
-    "CL_1000458",
-    "CL_2000021",
-    "CL_0001061",
-]