Metadata v2.2.1: hand-corrected fields drop the model confidence; schema text; no label changed

metadata/v2/README.md

@@ -1,6 +1,6 @@
 # SpatialDataAgent-DB sample metadata v2
 
-Schema `sda-sample-metadata-2`, version 2.2 (2026-11-06), built from release v3 (`sda-unified-20261010-v3`, 12,163 samples).
+Schema `sda-sample-metadata-2`, version 2.2.1 (2026-11-06), built from release v3 (`sda-unified-20261010-v3`, 12,163 samples).
 No expression, coordinate or image file changes; v2 is a new metadata table that sits next to the release.
 
 ## Files
@@ -125,6 +125,10 @@ repository:
 
 ## Versions
 
+- **2.2.1** (tag `metadata-v2.2.1-20261106`): a field corrected by hand no longer carries the model's confidence or
+  low-confidence flag, so `annotation_low_confidence` filters keep human-checked samples. The schema text now lists
+  every `life_stage_source` value. No label changed.
+
 - **2.2** (tag `metadata-v2.2-20261106`): corrections from a human reader's review of the 200-sample pack.
   - Rules applied to every sample:
     - MONDO "..., non-human animal" terms are removed from human samples (16 samples).

metadata/v2/provenance.json

@@ -53,16 +53,16 @@
   "tumour_regex_only_after_xenograft": 43
  },
  "files": {
-  "README.md": "4697dfa2e1310f62c930f950103766bc015610b3404895a8e6676fa6f017fe02",
+  "README.md": "edcebb1ce6c92aefb3e7f50ff27c1155d07434fb27f7d4315f945ed7418e6ee5",
   "changes_v2.csv": "9f096e905effabc808c1b5ac142ff8cab3d9a367774ae82757b7406d23e631dc",
   "dropped_disease_terms.csv": "28412ef3f7f7660ea7a85ed46ebcfecec08728dadc549e03510d31a2cce11b80",
-  "qa_v2.json": "eed9e5ea45d33345cf16772c07e7f0adbe472b2a55d800701cdaa63402f5f4c3",
-  "samples_metadata_v2.csv": "6d2ef49baa470140d3ae5fcc621192d2422bfbca715de217efae29181fbc1804",
-  "samples_metadata_v2.parquet": "690bcd2be263396e2ce9522c543a7353915f583e56aef31a1ad0b1f2c78226b1",
-  "schema_v2.json": "df7f767bbb2914a23d9295bdc0ba4dec4fca952465e1ec3138460728db57ecbe",
+  "qa_v2.json": "43002bf2ee515e39c60b81bbd51fc5f313f2ec84a99d1a69a7a1061cf02c8466",
+  "samples_metadata_v2.csv": "16c880338828b9d05c893cde95492255840f6b7d04016e8f11fe8bb0168776b6",
+  "samples_metadata_v2.parquet": "d0be2e6b7284f662872827c767fa71c0f50535fd37b218e9793af04d29b2e5b8",
+  "schema_v2.json": "a0e90e8bf5afa33f23542f60806bf1a235cb4adb42858a4be22f6fbfbdffd05c",
   "studies_v2.csv": "47ae0513a19ebaea9282d8362164b5b898cd143ad7132310cba4d78ee5bb8150"
  },
- "version": "2.2",
+ "version": "2.2.1",
  "changes_from_2.0": "one name per assay (ASSAY_CANON, 261 rows); assay_type of 6 ISS (Cartana) samples (GSE227046) now imaging-based; um_per_unit and image_um_per_px copied exactly from the release parquet; organ, tissue, disease, life stage and other annotations unchanged",
  "sensitivity_balanced_r2_series_units": {
   "human": {
@@ -82,5 +82,6 @@
    ]
   }
  },
- "changes_from_2.1": "rules: non-human-animal MONDO terms removed from human samples (16); culture/organoid/engineered life stage = not stated; sex from male/female words in sample text (77); rodent day ages in age series; manual corrections in 10 samples (overrides_v2.csv); new column sex_source"
+ "changes_from_2.1": "rules: non-human-animal MONDO terms removed from human samples (16); culture/organoid/engineered life stage = not stated; sex from male/female words in sample text (77); rodent day ages in age series; manual corrections in 10 samples (overrides_v2.csv); new column sex_source",
+ "changes_from_2.2": "manually corrected fields: model confidence set to null and removed from annotation_low_confidence; schema text for life_stage_source; no label changed"
 }

metadata/v2/qa_v2.json

@@ -2,7 +2,7 @@
  "samples": 12163,
  "annotated": 12163,
  "flags": {
-  "low_confidence_annotation": 3119,
+  "low_confidence_annotation": 3113,
   "feature_species_differs": 47,
   "normal_but_disease_text": 17
  },

metadata/v2/samples_metadata_v2.csv

@@ -2376,13 +2376,13 @@ GSM7412879,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomic
 GSM7412881,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,,,normal,luna,WT,Mouse_Visium,adult,age rule: age with unit,adult,8mo,unknown,not stated,,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,visium,,,spot,2831,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412881,,,train,sda-all,samples/GSE233208/GSM7412881,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.96, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM7412883,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,,,disease,luna,5X,Mouse_Visium,adult,age rule: age with unit,adult,4mo,unknown,not stated,,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,visium,,,spot,2257,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412883,,,train,sda-all,samples/GSE233208/GSM7412883,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.32, ""uberon"": 0.99, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM7412885,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,,,disease,luna,5X,Mouse_Visium,adult,age rule: age with unit,adult,8mo,unknown,not stated,,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,visium,,,spot,2994,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412885,,,train,sda-all,samples/GSE233208/GSM7412885,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.2, ""uberon"": 0.99, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
-GSM7412887,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,MONDO:0004975,Alzheimer disease,disease,manual,5X,Mouse_Visium,adult,age rule: age with unit,adult,4mo,male,extracted field,M,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2805,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412887,,,train,sda-all,samples/GSE233208/GSM7412887,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.28, ""uberon"": 0.99, ""life_stage"": 0.99}",disease_status,low_confidence_annotation
+GSM7412887,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,MONDO:0004975,Alzheimer disease,disease,manual,5X,Mouse_Visium,adult,age rule: age with unit,adult,4mo,male,extracted field,M,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2805,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412887,,,train,sda-all,samples/GSE233208/GSM7412887,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": null, ""uberon"": 0.99, ""life_stage"": 0.99}",,
 GSM7412888,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,,,normal,luna,WT,Mouse_Visium,adult,age rule: age with unit,adult,4mo,male,extracted field,M,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2447,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412888,,,train,sda-all,samples/GSE233208/GSM7412888,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.96, ""uberon"": 0.99, ""life_stage"": 1.0}",,
-GSM7412889,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,MONDO:0004975,Alzheimer disease,disease,manual,5X,Mouse_Visium,adult,age rule: age with unit,adult,12mo,male,extracted field,M,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2791,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412889,,,train,sda-all,samples/GSE233208/GSM7412889,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.59, ""uberon"": 0.99, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
+GSM7412889,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,MONDO:0004975,Alzheimer disease,disease,manual,5X,Mouse_Visium,adult,age rule: age with unit,adult,12mo,male,extracted field,M,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2791,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412889,,,train,sda-all,samples/GSE233208/GSM7412889,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": null, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM7412890,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,,,normal,luna,WT,Mouse_Visium,adult,age rule: age with unit,adult,12mo,male,extracted field,M,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2676,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412890,,,train,sda-all,samples/GSE233208/GSM7412890,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.92, ""uberon"": 0.99, ""life_stage"": 1.0}",,
-GSM7412891,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,MONDO:0004975,Alzheimer disease,disease,manual,5X,Mouse_Visium,adult,age rule: age with unit,adult,6mo,female,extracted field,F,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2992,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412891,,,train,sda-all,samples/GSE233208/GSM7412891,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.19, ""uberon"": 0.98, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
+GSM7412891,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,MONDO:0004975,Alzheimer disease,disease,manual,5X,Mouse_Visium,adult,age rule: age with unit,adult,6mo,female,extracted field,F,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2992,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412891,,,train,sda-all,samples/GSE233208/GSM7412891,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": null, ""uberon"": 0.98, ""life_stage"": 1.0}",,
 GSM7412892,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,,,normal,luna,WT,Mouse_Visium,adult,age rule: age with unit,adult,6mo,female,extracted field,F,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,3009,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412892,,,train,sda-all,samples/GSE233208/GSM7412892,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.97, ""uberon"": 0.99, ""life_stage"": 1.0}",,
-GSM7412893,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,MONDO:0004975,Alzheimer disease,disease,manual,5X,Mouse_Visium,adult,age rule: age with unit,adult,8mo,female,extracted field,F,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2788,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412893,,,train,sda-all,samples/GSE233208/GSM7412893,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.21, ""uberon"": 0.99, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
+GSM7412893,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,MONDO:0004975,Alzheimer disease,disease,manual,5X,Mouse_Visium,adult,age rule: age with unit,adult,8mo,female,extracted field,F,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2788,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412893,,,train,sda-all,samples/GSE233208/GSM7412893,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": null, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM7412894,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,,,normal,luna,WT,Mouse_Visium,adult,age rule: age with unit,adult,8mo,female,extracted field,F,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2847,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412894,,,train,sda-all,samples/GSE233208/GSM7412894,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.96, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM7412895,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,,,normal,luna,WT,Mouse_Visium,adult,age rule: age with unit,adult,8mo,male,extracted field,M,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2567,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412895,,,train,sda-all,samples/GSE233208/GSM7412895,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.92, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM7412896,GSE233208,GSE233208,Single-nucleus RNA-Seq and spatial transcriptomics characterization of Alzheimer’s Disease and Down Syndrome,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,brain,luna,UBERON:0000955,brain,Brain,primary tissue,MONDO:0004975,Alzheimer disease,disease,luna,5X,Mouse_Visium,adult,age rule: age with unit,adult,12mo,male,extracted field,M,,,fresh frozen,fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2791,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,39578645,,GSM7412896,,,train,sda-all,samples/GSE233208/GSM7412896,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.99, ""life_stage"": 1.0}",,
@@ -5941,7 +5941,7 @@ GSM8674628,GSE283945,GSE283945,Spatially Resolved Insights Into Fistulating Croh
 GSM8674629,GSE283945,GSE283945,Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - Visium Spatial Transcriptomics,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,rectum,luna,UBERON:0000160,intestine,intestine,primary tissue,MONDO:0005011,Crohn disease,disease,luna,CD,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,4317,36945,counts,pixel,4.33274332068294,platform_constant,True,H&E,4.33274332068294,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41224999,,GSM8674629,,,test,hesrt,samples/GSE283945/GSM8674629,sda-tissue-disease-2.3,"{""organ"": 0.45, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.73, ""life_stage"": 1.0}",organ,low_confidence_annotation
 GSM8674630,GSE283945,GSE283945,Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - Visium Spatial Transcriptomics,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,small intestine,luna,UBERON:0000160,intestine,intestine,primary tissue,MONDO:0005011,Crohn disease,disease,luna,CD,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,2241,36945,counts,pixel,4.33274332068294,platform_constant,True,H&E,4.33274332068294,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41224999,,GSM8674630,,,test,hesrt,samples/GSE283945/GSM8674630,sda-tissue-disease-2.3,"{""organ"": 0.97, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.61, ""life_stage"": 1.0}",,
 GSM8674631,GSE283945,GSE283945,Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - Visium Spatial Transcriptomics,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,small intestine,luna,UBERON:0000160,intestine,intestine,primary tissue,MONDO:0005020,intestinal disorder,disease,mondo_predicate,NON_CD,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,4129,36945,counts,pixel,4.502876195509259,platform_constant,True,H&E,4.502876195509259,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41224999,,GSM8674631,,,test,hesrt,samples/GSE283945/GSM8674631,sda-tissue-disease-2.3,"{""organ"": 0.71, ""sample_kind"": 1.0, ""disease_status"": 0.41000000000000003, ""uberon"": 0.99, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
-GSM8674632,GSE283945,GSE283945,Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - Visium Spatial Transcriptomics,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,colon,luna,UBERON:0001155,colon,intestine,primary tissue,MONDO:0001674,diverticulitis of colon,disease,luna,DIVERTICULAR,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,2526,36945,counts,pixel,4.502654878783435,platform_constant,True,H&E,4.502654878783435,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41224999,,GSM8674632,,,test,hesrt,samples/GSE283945/GSM8674632,sda-tissue-disease-2.3,"{""organ"": 0.68, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.55, ""life_stage"": 1.0}",uberon,low_confidence_annotation
+GSM8674632,GSE283945,GSE283945,Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - Visium Spatial Transcriptomics,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,colon,luna,UBERON:0001155,colon,intestine,primary tissue,MONDO:0001674,diverticulitis of colon,disease,luna,DIVERTICULAR,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,2526,36945,counts,pixel,4.502654878783435,platform_constant,True,H&E,4.502654878783435,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41224999,,GSM8674632,,,test,hesrt,samples/GSE283945/GSM8674632,sda-tissue-disease-2.3,"{""organ"": 0.68, ""sample_kind"": 1.0, ""disease_status"": null, ""uberon"": 0.55, ""life_stage"": 1.0}",uberon,low_confidence_annotation
 GSM8674633,GSE283945,GSE283945,Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - Visium Spatial Transcriptomics,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,small intestine,luna,UBERON:0000160,intestine,intestine,primary tissue,MONDO:0005011,Crohn disease,disease,luna,CD,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,4987,36945,counts,pixel,4.091303775696442,platform_constant,True,H&E,4.091303775696442,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41224999,,GSM8674633,,,test,hesrt,samples/GSE283945/GSM8674633,sda-tissue-disease-2.3,"{""organ"": 0.91, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.65, ""life_stage"": 0.99}",,
 GSM8674634,GSE283945,GSE283945,Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - Visium Spatial Transcriptomics,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,colon,luna,UBERON:0001155,colon,intestine,primary tissue,MONDO:0005020,intestinal disorder,disease,luna,DIVERTICULAR,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,4053,36945,counts,pixel,4.1626467922476005,platform_constant,True,H&E,4.1626467922476005,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41224999,,GSM8674634,,,test,hesrt,samples/GSE283945/GSM8674634,sda-tissue-disease-2.3,"{""organ"": 0.32, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.46, ""life_stage"": 1.0}",organ;uberon,low_confidence_annotation
 GSM8674635,GSE283945,GSE283945,Spatially Resolved Insights Into Fistulating Crohn’s Disease Pathogenesis - Visium Spatial Transcriptomics,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,small intestine,luna,UBERON:0000160,intestine,intestine,primary tissue,MONDO:0005020,intestinal disorder,disease,luna,DIVERTICULAR,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,2349,36945,counts,pixel,4.5008848989510595,platform_constant,True,H&E,4.5008848989510595,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41224999,,GSM8674635,,,test,hesrt,samples/GSE283945/GSM8674635,sda-tissue-disease-2.3,"{""organ"": 0.37, ""sample_kind"": 0.99, ""disease_status"": 0.97, ""uberon"": 0.74, ""life_stage"": 1.0}",organ,low_confidence_annotation
@@ -7220,11 +7220,11 @@ GSM8921749,GSE294814,GSE294814,Spatially resolved profiling of host and bacteria
 GSM8921750,GSE294814,GSE294814,Spatially resolved profiling of host and bacteria RNAs in mammalian tissue,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,small intestine,luna,UBERON:0000160,intestine,intestine,primary tissue,,,normal,luna,,No treatment,not stated,luna,not stated,,unknown,not stated,,,,,,DBiT-seq,release v3,microDBiT,sequencing-based,microDBiT,,,spot,2500,28198,unknown,native_grid,,unresolved,False,,,,,,,,VERIFIED,,,,,,GSM8921750,,,val,sda-all,samples/GSE294814/GSM8921750,sda-tissue-disease-2.3,"{""organ"": 0.96, ""sample_kind"": 1.0, ""disease_status"": 0.92, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM8921752,GSE294814,GSE294814,Spatially resolved profiling of host and bacteria RNAs in mammalian tissue,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,colon,luna,UBERON:0001155,colon,colon,primary tissue,,,normal,luna,,No treatment,not stated,luna,not stated,,unknown,not stated,,,,,,DBiT-seq,release v3,microDBiT,sequencing-based,microDBiT,,,spot,2498,35188,unknown,native_grid,,unresolved,False,,,,,,,,VERIFIED,,,,,,GSM8921752,,,val,sda-all,samples/GSE294814/GSM8921752,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.85, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM8921753,GSE294814,GSE294814,Spatially resolved profiling of host and bacteria RNAs in mammalian tissue,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,,colon,luna,UBERON:0001155,colon,colon,primary tissue,,,normal,luna,,No treatment,not stated,luna,not stated,,unknown,not stated,,,,,,DBiT-seq,release v3,microDBiT,sequencing-based,microDBiT,,,spot,2493,44662,unknown,native_grid,,unresolved,False,,,,,,,,VERIFIED,,,,,,GSM8921753,,,val,sda-all,samples/GSE294814/GSM8921753,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.61, ""uberon"": 1.0, ""life_stage"": 1.0}",,
-GSM8925216,GSE294844,GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0005173,actinic keratosis,disease,manual,actinic keratosis,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium CytAssist,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,1435,18085,counts,pixel,4.761904761904762,platform_constant,True,H&E,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925216,,,test,hesrt,samples/GSE294844/GSM8925216,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 0.9, ""disease_status"": 0.21, ""uberon"": 0.67, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
-GSM8925217,GSE294844,GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0005173,actinic keratosis,disease,manual,,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,Visium,,,spot,1505,18085,counts,um,1.0,verified,False,,,WITHHELD,,,hesrt_review_fail,,VERIFIED,,,,,,GSM8925217,,,test,sda-all,samples/GSE294844/GSM8925217,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.21, ""uberon"": 0.49, ""life_stage"": 1.0}",disease_status;uberon,low_confidence_annotation
-GSM8925218,GSE294844,GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0005173,actinic keratosis,disease,manual,actinic keratosis,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium CytAssist,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,1706,18085,counts,pixel,4.761904761904762,platform_constant,True,H&E,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925218,,,test,hesrt,samples/GSE294844/GSM8925218,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 0.98, ""disease_status"": 0.2, ""uberon"": 0.5700000000000001, ""life_stage"": 0.99}",disease_status;uberon,low_confidence_annotation
-GSM8925219,GSE294844,GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0005173,actinic keratosis,disease,manual,actinic keratosis,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium CytAssist,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,921,18085,counts,pixel,4.761904761904762,platform_constant,True,H&E,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925219,,,test,hesrt,samples/GSE294844/GSM8925219,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 0.92, ""disease_status"": 0.28, ""uberon"": 0.54, ""life_stage"": 1.0}",disease_status;uberon,low_confidence_annotation
-GSM8925221,GSE294844,GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0005173,actinic keratosis,disease,manual,actinic keratosis,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium CytAssist,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,2289,18085,counts,pixel,4.761904761904762,platform_constant,True,H&E,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925221,,,test,hesrt,samples/GSE294844/GSM8925221,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 0.9400000000000001, ""disease_status"": 0.24, ""uberon"": 0.46, ""life_stage"": 0.99}",disease_status;uberon,low_confidence_annotation
+GSM8925216,GSE294844,GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0005173,actinic keratosis,disease,manual,actinic keratosis,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium CytAssist,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,1435,18085,counts,pixel,4.761904761904762,platform_constant,True,H&E,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925216,,,test,hesrt,samples/GSE294844/GSM8925216,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": null, ""disease_status"": null, ""uberon"": 0.67, ""life_stage"": 1.0}",,
+GSM8925217,GSE294844,GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0005173,actinic keratosis,disease,manual,,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,Visium,,,spot,1505,18085,counts,um,1.0,verified,False,,,WITHHELD,,,hesrt_review_fail,,VERIFIED,,,,,,GSM8925217,,,test,sda-all,samples/GSE294844/GSM8925217,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": null, ""disease_status"": null, ""uberon"": 0.49, ""life_stage"": 1.0}",uberon,low_confidence_annotation
+GSM8925218,GSE294844,GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0005173,actinic keratosis,disease,manual,actinic keratosis,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium CytAssist,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,1706,18085,counts,pixel,4.761904761904762,platform_constant,True,H&E,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925218,,,test,hesrt,samples/GSE294844/GSM8925218,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": null, ""disease_status"": null, ""uberon"": 0.5700000000000001, ""life_stage"": 0.99}",uberon,low_confidence_annotation
+GSM8925219,GSE294844,GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0005173,actinic keratosis,disease,manual,actinic keratosis,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium CytAssist,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,921,18085,counts,pixel,4.761904761904762,platform_constant,True,H&E,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925219,,,test,hesrt,samples/GSE294844/GSM8925219,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": null, ""disease_status"": null, ""uberon"": 0.54, ""life_stage"": 1.0}",uberon,low_confidence_annotation
+GSM8925221,GSE294844,GSE294844,Transcriptional signature for dysplastic epidermal development in human pre-malignant skin,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism is a metagenome label; host species given,human skin metagenome,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0005173,actinic keratosis,disease,manual,actinic keratosis,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium CytAssist,sequencing-based,10x Genomics Visium v2 CytAssist Spatial Gene Expression,,,spot,2289,18085,counts,pixel,4.761904761904762,platform_constant,True,H&E,4.761904761904762,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,,,GSM8925221,,,test,hesrt,samples/GSE294844/GSM8925221,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": null, ""disease_status"": null, ""uberon"": 0.46, ""life_stage"": 0.99}",uberon,low_confidence_annotation
 GSM8933087,GSE294965,GSE294965,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,kidney,luna,UBERON:0002113,kidney,kidney,primary tissue,MONDO:0005240,kidney disorder,disease,luna,,,not stated,luna,not stated,,unknown,not stated,,,,,,Xenium,release v3,Xenium,imaging-based,Xenium,hMulti_480g,xenium-1.7.1.0,cell,435381,541,counts,um,1.0,verified,True,fluorescence: DAPI,0.5000109841827768,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,40393992,,GSM8933087,,,train,sda-all,samples/GSE294965/GSM8933087,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.23, ""uberon"": 1.0, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM8933088,GSE294965,GSE294965,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,kidney,luna,UBERON:0002113,kidney,kidney,primary tissue,MONDO:0005240,kidney disorder,disease,mondo_predicate,,,not stated,luna,not stated,,unknown,not stated,,,,,,Xenium,release v3,Xenium,imaging-based,Xenium,hMulti_480g,xenium-1.7.1.0,cell,412356,541,counts,um,1.0,verified,True,fluorescence: DAPI,0.49998908138011355,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,40393992,,GSM8933088,,,train,sda-all,samples/GSE294965/GSM8933088,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.31, ""uberon"": 1.0, ""life_stage"": 0.99}",disease_status,low_confidence_annotation
 GSM8933089,GSE294965,GSE294965,Spatio-temporal interaction of immune and renal cells determines glomerular crescent formation in autoimmune kidney disease,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,kidney,luna,UBERON:0002113,kidney,kidney,primary tissue,MONDO:0005240,kidney disorder,disease,luna,,,not stated,luna,not stated,,unknown,not stated,,,,,,Xenium,release v3,Xenium,imaging-based,Xenium,hMulti_480g,xenium-1.7.1.0,cell,351827,541,counts,um,1.0,verified,True,fluorescence: DAPI,0.49999756465832157,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,40393992,,GSM8933089,,,train,sda-all,samples/GSE294965/GSM8933089,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.49, ""uberon"": 1.0, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
@@ -7519,7 +7519,7 @@ GSM8980981,GSE296975,GSE296975,Defining Cellular Diversity at the Swine Maternal
 GSM8980982,GSE296975,GSE296975,Defining Cellular Diversity at the Swine Maternal-Fetal Interface Using Spatial Transcriptomics and Organoids [MFI017_Visium],Sus scrofa,9823,pig,Sus scrofa,9823,,False,False,GEO organism field,Sus scrofa,Sus scrofa,placenta,luna,UBERON:0001987,placenta,swine placenta,primary tissue,,,normal,luna,,,fetal,luna,fetal,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,3234,22040,counts,pixel,4.30224987236243,platform_constant,True,H&E,4.30224987236243,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,40875599,,GSM8980982,,,train,hesrt,samples/GSE296975/GSM8980982,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.73, ""uberon"": 0.9500000000000001, ""life_stage"": 0.53}",life_stage,low_confidence_annotation
 GSM8980983,GSE296975,GSE296975,Defining Cellular Diversity at the Swine Maternal-Fetal Interface Using Spatial Transcriptomics and Organoids [MFI017_Visium],Sus scrofa,9823,pig,Sus scrofa,9823,,False,False,GEO organism field,Sus scrofa,Sus scrofa,placenta,luna,UBERON:0001987,placenta,swine placenta,primary tissue,,,normal,luna,,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,3679,22040,counts,pixel,4.303899673298318,platform_constant,True,H&E,4.303899673298318,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,40875599,,GSM8980983,,,train,hesrt,samples/GSE296975/GSM8980983,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.89, ""uberon"": 0.9400000000000001, ""life_stage"": 0.37}",life_stage,low_confidence_annotation
 GSM8981121,GSE296982,GSE296982,Single cell map of the adult female mouse urethra reveals epithelial and stromal macrophages with distinct functional identities,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,other,luna,UBERON:0001334,female urethra,urethra,primary tissue,,,normal,luna,,,not stated,luna,not stated,,female,extracted field,female,,,FFPE,FFPE,Xenium,release v3,Xenium,imaging-based,Xenium,,,cell,246172,541,counts,um,1.0,verified,True,fluorescence: DAPI,0.5000027250926531,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,40907791,,GSM8981121,,,train,sda-all,samples/GSE296982/GSM8981121,sda-tissue-disease-2.3,"{""organ"": 0.93, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 1.0, ""life_stage"": 0.99}",,
-GSM9232561,GSE297058,GSE297058,Hereditary Chronic Pancreatitis Induced Plasticity Cooperates with Mutant Kras in Early Pancreatic Carcinogenesis,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,pancreas,luna,UBERON:0001264,pancreas,Pancreas,primary tissue,,,normal,manual,,Cre,adult,age rule: age with unit,juvenile,7.9 wk,male,extracted field,male,,,FFPE,FFPE,Visium HD,release v3,Visium HD,sequencing-based,VisiumHD,,,bin,360769,19059,counts,um,1.0,verified,True,H&E,3.385477894863119,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,41419303,,GSM9232561,,,train,sda-all,samples/GSE297058/GSM9232561,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.41000000000000003, ""uberon"": 1.0, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
+GSM9232561,GSE297058,GSE297058,Hereditary Chronic Pancreatitis Induced Plasticity Cooperates with Mutant Kras in Early Pancreatic Carcinogenesis,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,pancreas,luna,UBERON:0001264,pancreas,Pancreas,primary tissue,,,normal,manual,,Cre,adult,age rule: age with unit,juvenile,7.9 wk,male,extracted field,male,,,FFPE,FFPE,Visium HD,release v3,Visium HD,sequencing-based,VisiumHD,,,bin,360769,19059,counts,um,1.0,verified,True,H&E,3.385477894863119,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,41419303,,GSM9232561,,,train,sda-all,samples/GSE297058/GSM9232561,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": null, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM9232562,GSE297058,GSE297058,Hereditary Chronic Pancreatitis Induced Plasticity Cooperates with Mutant Kras in Early Pancreatic Carcinogenesis,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,pancreas,luna,UBERON:0001264,pancreas,Pancreas,primary tissue,MONDO:0008185,hereditary chronic pancreatitis,disease,luna,,Cpa1,adult,age rule: age with unit,adult,8.6 wk,male,extracted field,male,,,FFPE,FFPE,Visium HD,release v3,Visium HD,sequencing-based,VisiumHD,,,bin,216977,19059,counts,um,1.0,verified,True,H&E,2.699535643921179,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,41419303,,GSM9232562,,,train,sda-all,samples/GSE297058/GSM9232562,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.89, ""uberon"": 1.0, ""life_stage"": 0.9400000000000001}",,
 GSM8983043,GSE297064,GSE297064,Targeting circulating mechanoresponsive monocytes and macrophages to reduce fibrosis,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,Human tissue section,primary tissue,,,not stated,luna,,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,2581,36601,counts,pixel,4.8044403070123325,platform_constant,True,H&E,4.8044403070123325,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41120571,,GSM8983043,,,train,hesrt,samples/GSE297064/GSM8983043,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.32, ""uberon"": 0.46, ""life_stage"": 1.0}",disease_status;uberon,low_confidence_annotation
 GSM8983044,GSE297064,GSE297064,Targeting circulating mechanoresponsive monocytes and macrophages to reduce fibrosis,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,skin,luna,UBERON:0002097,skin of body,Human tissue section,primary tissue,,,disease,luna,,,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,10x Genomics Visium,,,spot,943,36601,counts,pixel,4.806488282377554,platform_constant,True,H&E,4.806488282377554,HESRT_HUMAN_REVIEW,,,,,human_visual_review,,,,41120571,,GSM8983044,,,train,hesrt,samples/GSE297064/GSM8983044,sda-tissue-disease-2.3,"{""organ"": 0.54, ""sample_kind"": 1.0, ""disease_status"": 0.93, ""uberon"": 0.72, ""life_stage"": 1.0}",organ,low_confidence_annotation
@@ -10130,7 +10130,7 @@ GSM9429346,GSE315482,GSE315482,Single-Cell Multi-omics Profiling of Mouse Hepati
 GSM9429347,GSE315482,GSE315482,Single-Cell Multi-omics Profiling of Mouse Hepatic Immune Microenvironment Reveals Neutrophil-Kupffer Cell Crosstalk via Thrombospondin-1/CD36 after Surgical Stress,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,liver,luna,UBERON:0002107,liver,liver,primary tissue,MONDO:0005203,ischemia reperfusion injury,disease,mondo_predicate (Luna: perturbation),,ischemia-reperfusion injury (60min ischemia/6h reperfusion),not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,visium,,,spot,3438,32285,counts,um,1.0,verified,True,H&E-like (heuristic),5.222850592747951,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,check whether the stain is H&E (looks reddish),,,GSM9429347,,,train,sda-all,samples/GSE315482/GSM9429347,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.44, ""uberon"": 1.0, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM9429348,GSE315482,GSE315482,Single-Cell Multi-omics Profiling of Mouse Hepatic Immune Microenvironment Reveals Neutrophil-Kupffer Cell Crosstalk via Thrombospondin-1/CD36 after Surgical Stress,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,liver,luna,UBERON:0002107,liver,liver,primary tissue,MONDO:0005203,ischemia reperfusion injury,disease,luna,,ischemia-reperfusion injury (60min ischemia/6h reperfusion),not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,visium,,,spot,1474,32285,counts,um,1.0,verified,True,H&E-like (heuristic),5.229300808556978,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,check whether the stain is H&E (looks reddish),,,GSM9429348,,,train,sda-all,samples/GSE315482/GSM9429348,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.5700000000000001, ""uberon"": 1.0, ""life_stage"": 1.0}",disease_status,low_confidence_annotation
 GSM9429458,GSE315487,GSE315487,CD73 inhibition overcomes adaptive immune resistance to PARP inhibition in models of prostate cancer,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,prostate,uberon_chain,UBERON:0002367,prostate gland,prostate cancer,xenograft,MONDO:0008315,prostate cancer,disease,luna,,Veh,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,visium,,,spot,3729,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,,,GSM9429458,,,train,sda-all,samples/GSE315487/GSM9429458,sda-tissue-disease-2.3,"{""organ"": 0.64, ""sample_kind"": 0.65, ""disease_status"": 0.99, ""uberon"": 0.96, ""life_stage"": 0.99}",,
-GSM9429459,GSE315487,GSE315487,CD73 inhibition overcomes adaptive immune resistance to PARP inhibition in models of prostate cancer,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,other,manual,,,prostate cancer,xenograft,MONDO:0008315,prostate cancer,disease,luna,,Olaparib,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,visium,,,spot,3864,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,,,GSM9429459,,,train,sda-all,samples/GSE315487/GSM9429459,sda-tissue-disease-2.3,"{""organ"": 0.61, ""sample_kind"": 0.7000000000000001, ""disease_status"": 0.87, ""uberon"": 0.8300000000000001, ""life_stage"": 1.0}",,
+GSM9429459,GSE315487,GSE315487,CD73 inhibition overcomes adaptive immune resistance to PARP inhibition in models of prostate cancer,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,other,manual,,,prostate cancer,xenograft,MONDO:0008315,prostate cancer,disease,luna,,Olaparib,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,visium,,,spot,3864,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,,,GSM9429459,,,train,sda-all,samples/GSE315487/GSM9429459,sda-tissue-disease-2.3,"{""organ"": null, ""sample_kind"": 0.7000000000000001, ""disease_status"": 0.87, ""uberon"": null, ""life_stage"": 1.0}",,
 GSM9429460,GSE315487,GSE315487,CD73 inhibition overcomes adaptive immune resistance to PARP inhibition in models of prostate cancer,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,prostate,uberon_chain,UBERON:0002367,prostate gland,prostate cancer,xenograft,MONDO:0008315,prostate cancer,disease,luna,,a-CD73,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,visium,,,spot,1992,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,,,GSM9429460,,,train,sda-all,samples/GSE315487/GSM9429460,sda-tissue-disease-2.3,"{""organ"": 0.75, ""sample_kind"": 0.89, ""disease_status"": 0.93, ""uberon"": 0.93, ""life_stage"": 0.99}",,
 GSM9429461,GSE315487,GSE315487,CD73 inhibition overcomes adaptive immune resistance to PARP inhibition in models of prostate cancer,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,prostate,uberon_chain,UBERON:0002367,prostate gland,prostate cancer,xenograft,MONDO:0008315,prostate cancer,disease,luna,,Combination,not stated,luna,not stated,,unknown,not stated,,,,,,Visium,release v3,Visium,sequencing-based,visium,,,spot,3608,32285,counts,um,1.0,verified,False,,,,,,,,VERIFIED,,,,,,GSM9429461,,,train,sda-all,samples/GSE315487/GSM9429461,sda-tissue-disease-2.3,"{""organ"": 0.86, ""sample_kind"": 0.88, ""disease_status"": 0.97, ""uberon"": 0.9500000000000001, ""life_stage"": 0.97}",,
 GSM9431064,GSE315553,GSE315553,Spatial Transcriptomics Data from Human Choroid Plexus,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,,brain,uberon_chain,UBERON:0001886,choroid plexus,Choroid Plexus,primary tissue,,,normal,luna,,,not stated,luna,not stated,,unknown,not stated,,,,fresh frozen,OCT-embedded,Slide-seq,release v3,Slide-seq,sequencing-based,slide-seq,,,bead,21331,16662,counts,pixel,,unresolved,False,,,WITHHELD,,,hesrt_review_fail,,VERIFIED,,,,41648589,,GSM9431064,,,val,sda-all,samples/GSE315553/GSM9431064,sda-tissue-disease-2.3,"{""organ"": 0.49, ""sample_kind"": 1.0, ""disease_status"": 0.43, ""uberon"": 1.0, ""life_stage"": 1.0}",organ;disease_status,low_confidence_annotation
@@ -11681,7 +11681,7 @@ GSM9767744,GSE333529,GSE333529,A skin–kidney neutrophil axis links UV exposure
 GSM9769919,GSE333617,GSE333617,Targeting JAK1/3-STAT1 signaling attenuates cytotoxic T lymphocytes activation for the treatment in Stevens-Johnson syndrome and toxic epidermal necrolysis,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0018229,Stevens-Johnson syndrome,disease,luna,SJS/TEN,,not stated,luna,not stated,,unknown,not stated,,,,FFPE,FFPE,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2296,18085,counts,um,1.0,verified,True,H&E-like (heuristic),6.996819919949294,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9769919,,,train,sda-all,samples/GSE333617/GSM9769919,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 1.0, ""uberon"": 0.68, ""life_stage"": 1.0}",,
 GSM9769920,GSE333617,GSE333617,Targeting JAK1/3-STAT1 signaling attenuates cytotoxic T lymphocytes activation for the treatment in Stevens-Johnson syndrome and toxic epidermal necrolysis,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0018229,Stevens-Johnson syndrome,disease,luna,SJS/TEN,,not stated,luna,not stated,,unknown,not stated,,,,FFPE,FFPE,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2516,18085,counts,um,1.0,verified,True,H&E-like (heuristic),5.109669939378263,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9769920,,,train,sda-all,samples/GSE333617/GSM9769920,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.99, ""uberon"": 0.67, ""life_stage"": 1.0}",,
 GSM9769921,GSE333617,GSE333617,Targeting JAK1/3-STAT1 signaling attenuates cytotoxic T lymphocytes activation for the treatment in Stevens-Johnson syndrome and toxic epidermal necrolysis,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,MONDO:0018229,Stevens-Johnson syndrome,disease,luna,HD,,not stated,luna,not stated,,unknown,not stated,,,,FFPE,FFPE,Visium,release v3,Visium,sequencing-based,Visium,,,spot,2082,17943,counts,um,1.0,verified,True,H&E-like (heuristic),4.086611054520036,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9769921,,,train,sda-all,samples/GSE333617/GSM9769921,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.97, ""uberon"": 0.58, ""life_stage"": 1.0}",uberon,low_confidence_annotation
-GSM9769922,GSE333617,GSE333617,Targeting JAK1/3-STAT1 signaling attenuates cytotoxic T lymphocytes activation for the treatment in Stevens-Johnson syndrome and toxic epidermal necrolysis,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,,,normal,manual,HD,,not stated,luna,not stated,,unknown,not stated,,,,FFPE,FFPE,Visium,release v3,Visium,sequencing-based,Visium,,,spot,3862,18085,counts,um,1.0,verified,True,H&E-like (heuristic),10.731588419458864,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9769922,,,train,sda-all,samples/GSE333617/GSM9769922,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.88, ""uberon"": 0.47000000000000003, ""life_stage"": 1.0}",uberon,normal_but_disease_text;low_confidence_annotation
+GSM9769922,GSE333617,GSE333617,Targeting JAK1/3-STAT1 signaling attenuates cytotoxic T lymphocytes activation for the treatment in Stevens-Johnson syndrome and toxic epidermal necrolysis,Homo sapiens,9606,human,Homo sapiens,9606,,False,False,GEO organism field,Homo sapiens,Homo sapiens,skin,luna,UBERON:0000014,zone of skin,skin,primary tissue,,,normal,manual,HD,,not stated,luna,not stated,,unknown,not stated,,,,FFPE,FFPE,Visium,release v3,Visium,sequencing-based,Visium,,,spot,3862,18085,counts,um,1.0,verified,True,H&E-like (heuristic),10.731588419458864,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9769922,,,train,sda-all,samples/GSE333617/GSM9769922,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": null, ""uberon"": 0.47000000000000003, ""life_stage"": 1.0}",uberon,normal_but_disease_text;low_confidence_annotation
 GSM9457959,GSE333685,GSE333685,Vascular smooth muscle cell state trajectories mediate molecular mechanisms of coronary disease risk,Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,blood vessel,luna,UBERON:0000947,aorta,Aorta,primary tissue,MONDO:0005010,coronary artery disorder,disease,luna,,"ApoE-/-, Rosa26-Tdt+/+",not stated,luna,not stated,,unknown,not stated,,,,,,Xenium,release v3,Xenium,imaging-based,Xenium,,,cell,49909,13780,counts,um,1.0,verified,True,fluorescence: DAPI,0.499999059938332,VERIFIED,VERIFIED,VERIFIED,,,VERIFIED,PASS,,,41844614,,GSM9457959,,,train,sda-all,samples/GSE333685/GSM9457959,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.63, ""uberon"": 0.99, ""life_stage"": 1.0}",,
 GSM9770943,GSE333693,GSE333693,Rat thymic epithelium-free areas are specialized medullary niches enriched for mature thymocytes and distinct stromal subsets,Rattus norvegicus,10116,Norway rat,Rattus norvegicus,10116,,False,False,GEO organism field,Rattus norvegicus,,thymus,luna,UBERON:0002370,thymus,Thymus,primary tissue,,,normal,luna,,,not stated,luna,not stated,,unknown,not stated,,,,,,Stereo-seq,release v3,Stereo-seq,sequencing-based,Stereo-seq,,,cell,796801,38507,counts,um,1.0,verified,False,,,,,,,,VERIFIED,PASS,,,,,GSM9770943,,,train,sda-all,samples/GSE333693/GSM9770943,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.9500000000000001, ""uberon"": 1.0, ""life_stage"": 1.0}",,
 GSM9771950,GSE333735,GSE333735,TGFbeta determines epithelial tissue spacing by regulating mesenchymal condensation,Gallus gallus,9031,chicken,Gallus gallus,9031,,False,False,GEO organism field,Gallus gallus,,lung,luna,UBERON:0002048,lung,Embryonic lung,primary tissue,,,normal,luna,,WT,embryonic,luna,embryonic,,unknown,not stated,,,,,,DBiT-seq,GEO series text (assay_final.csv),DBiT-seq,sequencing-based,other,,,spot,1018,16128,unknown,unstated,,unresolved,False,,,,,,units_unstated,,VERIFIED,,,,42446999,,GSM9771950,,,train,sda-all,samples/GSE333735/GSM9771950,sda-tissue-disease-2.4,"{""organ"": 1.0, ""sample_kind"": 0.99, ""disease_status"": 0.99, ""uberon"": 0.9500000000000001, ""life_stage"": 1.0}",,
@@ -11757,7 +11757,7 @@ GSM9802657,GSE334959+GSE334960,GSE334959,Cerebellar and cerebral frontal lobe al
 GSM9802658,GSE334959+GSE334960,GSE334959,Cerebellar and cerebral frontal lobe alterations in pulmonary hypertension: Evidence of an inflammatory lung vascular-brain axis [Spatial Transcriptomics],Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,brain,luna,UBERON:0002037,cerebellum,Brain,primary tissue,MONDO:0005149,pulmonary hypertension,disease,mondo_predicate (Luna: perturbation),,,adult,luna,adult,29.14,male,extracted field,male,,,fresh frozen,Fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,7882,19465,counts,um,1.0,verified,True,H&E,4.667357369767179,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9802658,,,test,sda-all,samples/GSE334959/GSM9802658,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.39, ""uberon"": 0.92, ""life_stage"": 0.9400000000000001}",disease_status,low_confidence_annotation
 GSM9802659,GSE334959+GSE334960,GSE334959,Cerebellar and cerebral frontal lobe alterations in pulmonary hypertension: Evidence of an inflammatory lung vascular-brain axis [Spatial Transcriptomics],Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,brain,luna,UBERON:0002037,cerebellum,Brain,primary tissue,MONDO:0005149,pulmonary hypertension,disease,mondo_predicate (Luna: perturbation),,,adult,luna,adult,29.14,male,extracted field,male,,,fresh frozen,Fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,6935,19465,counts,um,1.0,verified,True,H&E,4.640340183121012,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9802659,,,test,sda-all,samples/GSE334959/GSM9802659,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.31, ""uberon"": 0.89, ""life_stage"": 0.98}",disease_status,low_confidence_annotation
 GSM9802660,GSE334959+GSE334960,GSE334959,Cerebellar and cerebral frontal lobe alterations in pulmonary hypertension: Evidence of an inflammatory lung vascular-brain axis [Spatial Transcriptomics],Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,brain,luna,UBERON:0002037,cerebellum,Brain,primary tissue,MONDO:0005149,pulmonary hypertension,disease,mondo_predicate (Luna: perturbation),,,adult,luna,adult,24,male,extracted field,male,,,fresh frozen,Fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,6477,19465,counts,um,1.0,verified,True,H&E,4.666607157480876,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9802660,,,test,sda-all,samples/GSE334959/GSM9802660,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.64, ""uberon"": 0.9500000000000001, ""life_stage"": 0.9500000000000001}",,
-GSM9802661,GSE334959+GSE334960,GSE334959,Cerebellar and cerebral frontal lobe alterations in pulmonary hypertension: Evidence of an inflammatory lung vascular-brain axis [Spatial Transcriptomics],Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,brain,luna,UBERON:0002037,cerebellum,Brain,primary tissue,,,normal,manual,,,adult,luna,adult,29,male,extracted field,male,,,fresh frozen,Fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,3480,19465,counts,um,1.0,verified,True,H&E,7.006074446876273,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9802661,,,test,sda-all,samples/GSE334959/GSM9802661,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.96, ""uberon"": 0.96, ""life_stage"": 0.97}",,
+GSM9802661,GSE334959+GSE334960,GSE334959,Cerebellar and cerebral frontal lobe alterations in pulmonary hypertension: Evidence of an inflammatory lung vascular-brain axis [Spatial Transcriptomics],Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,brain,luna,UBERON:0002037,cerebellum,Brain,primary tissue,,,normal,manual,,,adult,luna,adult,29,male,extracted field,male,,,fresh frozen,Fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,3480,19465,counts,um,1.0,verified,True,H&E,7.006074446876273,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9802661,,,test,sda-all,samples/GSE334959/GSM9802661,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": null, ""uberon"": 0.96, ""life_stage"": 0.97}",,
 GSM9802662,GSE334959+GSE334960,GSE334959,Cerebellar and cerebral frontal lobe alterations in pulmonary hypertension: Evidence of an inflammatory lung vascular-brain axis [Spatial Transcriptomics],Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,brain,luna,UBERON:0002037,cerebellum,Brain,primary tissue,MONDO:0005149,pulmonary hypertension,disease,mondo_predicate,,,adult,luna,adult,29,male,extracted field,male,,,fresh frozen,Fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,3822,19465,counts,um,1.0,verified,True,H&E,6.948191927901177,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9802662,,,test,sda-all,samples/GSE334959/GSM9802662,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.6900000000000001, ""uberon"": 0.92, ""life_stage"": 0.9400000000000001}",,
 GSM9802663,GSE334959+GSE334960,GSE334959,Cerebellar and cerebral frontal lobe alterations in pulmonary hypertension: Evidence of an inflammatory lung vascular-brain axis [Spatial Transcriptomics],Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,brain,luna,UBERON:0002037,cerebellum,Brain,primary tissue,MONDO:0005149,pulmonary hypertension,disease,mondo_predicate (Luna: perturbation),,,adult,luna,adult,29.4,male,extracted field,male,,,fresh frozen,Fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,3565,19465,counts,um,1.0,verified,True,H&E,6.997402894255731,PARTIAL,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9802663,,,test,sda-all,samples/GSE334959/GSM9802663,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.4, ""uberon"": 0.99, ""life_stage"": 0.93}",disease_status,low_confidence_annotation
 GSM9802664,GSE334959+GSE334960,GSE334959,Cerebellar and cerebral frontal lobe alterations in pulmonary hypertension: Evidence of an inflammatory lung vascular-brain axis [Spatial Transcriptomics],Mus musculus,10090,house mouse,Mus musculus,10090,,False,False,GEO organism field,Mus musculus,Mus musculus,brain,luna,UBERON:0002037,cerebellum,Brain,primary tissue,MONDO:0005149,pulmonary hypertension,disease,luna,,,adult,luna,adult,29.4,male,extracted field,male,,,fresh frozen,Fresh frozen,Visium,release v3,Visium,sequencing-based,Visium,,,spot,3481,19465,counts,um,1.0,verified,True,H&E,6.951419263808623,VERIFIED,ABSENT,ABSENT,,,VERIFIED,PASS,,,,,GSM9802664,,,test,sda-all,samples/GSE334959/GSM9802664,sda-tissue-disease-2.3,"{""organ"": 1.0, ""sample_kind"": 1.0, ""disease_status"": 0.55, ""uberon"": 0.99, ""life_stage"": 0.88}",disease_status,low_confidence_annotation

metadata/v2/samples_metadata_v2.parquet

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:690bcd2be263396e2ce9522c543a7353915f583e56aef31a1ad0b1f2c78226b1
-size 822563
+oid sha256:d0be2e6b7284f662872827c767fa71c0f50535fd37b218e9793af04d29b2e5b8
+size 822587

metadata/v2/schema_v2.json

@@ -30,7 +30,7 @@
   "disease_raw": "disease as extracted from GEO by the SDA-All agent (v3 sample.json)",
   "condition_raw": "condition as extracted from GEO by the SDA-All agent (v3 sample.json)",
   "life_stage": "embryonic / fetal / neonatal or infant / juvenile / adult / aged / not stated; from age_raw by a fixed rule where the notation is unambiguous (mouse / rat: P, E, weeks, months, years; neonatal <= P21, juvenile < 6 weeks, adult < 18 months, aged >= 18 months; ranges use their midpoint when they span two stages; human: years, post-conception weeks), else Luna",
-  "life_stage_source": "age rule: <notation> (deterministic, from age_raw) or luna (GPT-6 Luna Decisions)",
+  "life_stage_source": "age rule: <notation> (deterministic, from age_raw; includes 'age rule: days in an age series'), 'rule: culture or organoid (culture time is not a life stage)', luna (GPT-6 Luna Decisions) or manual",
   "life_stage_luna": "Luna's life-stage answer (kept when the age rule overrides it)",
   "age_raw": "age as written",
   "sex": "male / female / mixed / unknown (coded values without a stated key, e.g. 1/2, stay unknown)",
@@ -75,8 +75,8 @@
   "source_pipeline": "sda-all or hesrt",
   "sample_dir": "folder of the sample in the release",
   "annotation_version": "version of the tissue / disease / life-stage annotation (sda-tissue-disease-2.x)",
-  "annotation_confidence": "Luna Decisions confidence per annotated field",
-  "annotation_low_confidence": "fields with confidence below 0.6 (list)",
+  "annotation_confidence": "Luna Decisions confidence per annotated field; null for a field corrected by hand",
+  "annotation_low_confidence": "fields with model confidence below 0.6 (list); fields corrected by hand are not listed",
   "metadata_flags": "consistency flags for review (list): normal_but_disease_text, tumour_marked_normal, low_confidence_annotation, feature_species_differs, ..."
  }
 }