diff --git a/containers/azimuth/context/organ-metadata.json b/containers/azimuth/context/organ-metadata.json index 72d0671..813cca5 100644 --- a/containers/azimuth/context/organ-metadata.json +++ b/containers/azimuth/context/organ-metadata.json @@ -1,26 +1,32 @@ { + "UBERON:0004538": "UBERON:0002113", + "UBERON:0004539": "UBERON:0002113", "UBERON:0002113": { "model": "kidneyref", "organ_level": "Kidney_L3", "prediction_column": "annotation.l3" }, - "UBERON:0004538": "UBERON:0002113", - "UBERON:0004539": "UBERON:0002113", + "UBERON:0002168": "UBERON:0002048", + "UBERON:0002178": "UBERON:0002048", + "UBERON:0002177": "UBERON:0002048", + "UBERON:0002167": "UBERON:0002048", "UBERON:0002048": { "model": "lungref", "organ_level": "Lung_v2_finest_level", "prediction_column": "ann_finest_level" }, - "UBERON:0001004": "UBERON:0002048", + "UBERON:0000947": "UBERON:0000948", "UBERON:0000948": { "model": "heartref", "organ_level": "Heart_L2", - "prediction_column": "celltype.l2" + "prediction_column": "celltype.l2", + "comment": "Aorta (UBERON:0000947) is redirected here" }, - "UBERON:0000955": { + "UBERON:0001384": { "model": "humancortexref", "organ_level": "", - "prediction_column": "subclass" + "prediction_column": "subclass", + "comment": "Not redirecting brain (UBERON:0000955) to here as it is too broad" }, "UBERON:0001264": { "model": "pancreasref", @@ -29,7 +35,7 @@ }, "UBERON:0002373": { "model": "tonsilref", - "organ_level": "", + "organ_level": "Tonsil_v2_L2", "prediction_column": "celltype.l2" }, "UBERON:0000178": { @@ -44,7 +50,7 @@ }, "UBERON:0001013": { "model": "adiposeref", - "organ_level": "", + "organ_level": "Adipose_L2", "prediction_column": "celltype.l2" } } \ No newline at end of file diff --git a/containers/celltypist/context/organ-metadata.json b/containers/celltypist/context/organ-metadata.json index 3704c12..0b4750e 100644 --- a/containers/celltypist/context/organ-metadata.json +++ b/containers/celltypist/context/organ-metadata.json @@ -1,21 +1,37 @@ { + "UBERON:0002168": "UBERON:0002048", + "UBERON:0002178": "UBERON:0002048", + "UBERON:0002177": "UBERON:0002048", + "UBERON:0002167": "UBERON:0002048", "UBERON:0002048": { - "model": "Human_Lung_Atlas.pkl" + "model": "Human_Lung_Atlas.pkl", + "alt_model": "Cells_Lung_Airway.pkl" }, - "UBERON:0001004": "UBERON:0002048", "UBERON:0002097": { "model": "Adult_Human_Skin.pkl" }, - "UBERON:0001264": { - "model": "Adult_Human_PancreaticIslet.pkl" + "UBERON:0001264": "UBERON:0000006", + "UBERON:0000006": { + "model": "Adult_Human_PancreaticIslet.pkl", + "comment": "Pancreas (UBERON:0001264) is redirected here" }, + "UBERON:0000947": "UBERON:0000948", "UBERON:0000948": { - "model": "Healthy_Adult_Heart.pkl" + "model": "Healthy_Adult_Heart.pkl", + "comment": "Aorta (UBERON:0000947) is redirected here" }, "UBERON:0002107": { "model": "Healthy_Human_Liver.pkl" }, - "UBERON:0000955": { - "model": "Human_AdultAged_Hippocampus.pkl" + "UBERON:0002421": { + "model": "Human_AdultAged_Hippocampus.pkl", + "alt_model": "Human_Longitudinal_Hippocampus.pkl", + "comment": "Not redirecting brain (UBERON:0000955) to here as it is too broad" + }, + "UBERON:0002108": { + "model": "Cells_Intestinal_Tract.pkl" + }, + "UBERON:0000059": { + "model": "Cells_Intestinal_Tract.pkl" } -} \ No newline at end of file +} diff --git a/containers/popv/context/organ-metadata.json b/containers/popv/context/organ-metadata.json index 9be26a4..1afe08e 100644 --- a/containers/popv/context/organ-metadata.json +++ b/containers/popv/context/organ-metadata.json @@ -11,19 +11,21 @@ "model": "Bone_Marrow", "organ_level": "bone marrow" }, + "UBERON:0004548": "UBERON:0000970", + "UBERON:0004549": "UBERON:0000970", "UBERON:0000970": { "model": "Eye", "organ_level": "eye" }, - "UBERON:0004548": "UBERON:0000970", - "UBERON:0004549": "UBERON:0000970", "UBERON:0001013": { "model": "Fat", "organ_level": "adipose tissue" }, + "UBERON:0000947": "UBERON:0000948", "UBERON:0000948": { "model": "Heart", - "organ_level": "heart" + "organ_level": "heart", + "comment": "Aorta (UBERON:0000947) is redirected here" }, "UBERON:0000059": { "model": "Large_Intestine", @@ -33,25 +35,23 @@ "model": "Liver", "organ_level": "liver" }, + "UBERON:0002168": "UBERON:0002048", + "UBERON:0002178": "UBERON:0002048", + "UBERON:0002177": "UBERON:0002048", + "UBERON:0002167": "UBERON:0002048", "UBERON:0002048": { "model": "Lung", "organ_level": "lung" }, - "UBERON:0001004": { - "model": "Lung", - "organ_level": "respiratory system" - }, - "UBERON:0000029": { - "model": "Lymph_Node", - "organ_level": "lymph node" - }, "UBERON:0002509": { "model": "Lymph_Node", - "organ_level": "mesenteric lymph node" + "organ_level": "mesenteric lymph node", + "comment": "Generic lymph node (UBERON:0000029) is redirected here" }, "UBERON:0001911": { "model": "Mammary", - "organ_level": "mammary gland" + "organ_level": "mammary gland", + "comment": "Should breast (UBERON:0000310) be redirected here?" }, "UBERON:0001264": { "model": "Pancreas", @@ -61,9 +61,9 @@ "model": "Prostate", "organ_level": "prostate gland" }, - "UBERON:0000079": { - "model": "Prostate", - "organ_level": "male reproductive system" + "UBERON:0001044": { + "model": "Salivary Gland", + "organ_level": "" }, "UBERON:0002097": { "model": "Skin", @@ -81,6 +81,10 @@ "model": "Thymus", "organ_level": "thymus" }, + "UBERON:0001723": { + "model": "Tongue", + "organ_level": "" + }, "UBERON:0003126": { "model": "Trachea", "organ_level": "trachea" @@ -93,4 +97,4 @@ "model": "Vasculature", "organ_level": "blood vasculature" } -} \ No newline at end of file +}