Merge remote-tracking branch 'origin/main' into jgadling/api-schema-v2

ingestion_tools/dataset_configs/10005.yaml

@@ -83,7 +83,7 @@ datasets:
       name: C57BI/6J
     cell_type:
       id: CL:0000019
-      name: Sperm
+      name: sperm
     cross_references:
       publications: doi:10.1101/2022.09.28.510016
     dataset_description: Cryo-electron tomograms of mouse sperm flagella from FIB-SEM

ingestion_tools/dataset_configs/10009.yaml

@@ -230,7 +230,7 @@ datasets:
       name: Benjamin D. Engel
     cell_component:
       id: GO:0005929
-      name: Cilium
+      name: cilium
     cell_strain:
       name: CC-3994
     cross_references:

ingestion_tools/dataset_configs/10010.yaml

@@ -96,10 +96,10 @@ datasets:
       primary_author_status: false
     cell_component:
       id: GO:0005741
-      name: Mitochondrial Outer Membrane
+      name: mitochondrial outer membrane
     cell_type:
       id: CL:2000042
-      name: Embryonic fibroblast
+      name: embryonic fibroblast
     cross_references:
       publications: 10.1083/jcb.202204093, 10.1101/2022.01.23.477440
       related_database_entries: EMPIAR-11370

ingestion_tools/dataset_configs/gjensen/10021.yaml

@@ -20,8 +20,8 @@ datasets:
     cross_references:
       publications: 10.1038/s41467-022-32584-7
       related_database_entries: EMD-27654, EMPIAR-11125
-    dataset_description: ' and is a part of Caltech Jensen  lab etdb. Carboxysomes
-      purified from H. Neapolitanus, WT, high resolution'
+    dataset_description: This is a single dataset studying Halothiobacillus neapolitanus
+      collected by LaurenAnn Metskas and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10021
     dataset_title: H. neapolitanus Carboxysomes
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10038.yaml

@@ -93,8 +93,8 @@ tiltseries:
     tilt_alignment_software: '{ts-tilt_alignment_software}'
     tilt_axis: 84.3
     tilt_range:
-      max: -50.0
-      min: 50.0
+      max: 50.0
+      min: -50.0
     tilt_series_quality: int {ts-tilt_series_quality}
     tilt_step: 2.0
     tilting_scheme: min to max tilt

ingestion_tools/dataset_configs/gjensen/10078.yaml

@@ -19,9 +19,9 @@ datasets:
       name: Philadelphia-1_Lp02
     cross_references:
       publications: 10.1038/s41564-019-0427-4
-    dataset_description: 'This is 21th of 41 sets of data studying Legionella pneumophila
+    dataset_description: This is 21th of 41 sets of data studying Legionella pneumophila
       collected by Debnath Ghosal and is a part of Caltech Jensen  lab etdb. JV7091
-      is a double mutant that lacks dotE and dotP (Lp02). '
+      is a double mutant that lacks dotE and dotP (Lp02).
     dataset_identifier: 10078
     dataset_title: L. pneumophila JV7091
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10099.yaml

@@ -14,8 +14,8 @@ datasets:
     - corresponding_author_status: true
       name: Grant Jensen
       primary_author_status: false
-    dataset_description: ' and is a part of Caltech Jensen  lab etdb. Archaella and
-      plate'
+    dataset_description: This is a single dataset studying Halobacterium salinarum
+      collected by Debnath Ghosal and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10099
     dataset_title: Halobacterium salinarum
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10115.yaml

@@ -14,8 +14,8 @@ datasets:
     - corresponding_author_status: true
       name: Grant Jensen
       primary_author_status: false
-    dataset_description: ' and is a part of Caltech Jensen  lab etdb. search for ESCRT
-      in dividing cells'
+    dataset_description: This is a single dataset studying Sulfolobus acidocaldarius
+      collected by Rasika Ramdasi and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10115
     dataset_title: S. acidocaldarius Sulfolobus cells synchronized fo
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10116.yaml

@@ -14,8 +14,6 @@ datasets:
     - corresponding_author_status: true
       name: Grant Jensen
       primary_author_status: false
-    cell_component:
-      id: GO:0051301,GO:0043093
     dataset_description: This is 1st of 2 sets of data studying Nitrosopumilus maritimus
       collected by Rasika Ramdasi and is a part of Caltech Jensen  lab etdb.  Looking
       for cell division related CDV proteins.

ingestion_tools/dataset_configs/gjensen/10117.yaml

@@ -14,8 +14,6 @@ datasets:
     - corresponding_author_status: true
       name: Grant Jensen
       primary_author_status: false
-    cell_component:
-      id: GO:0051301
     dataset_description: This is 2nd of 2 sets of data studying Nitrosopumilus maritimus
       collected by Rasika Ramdasi and is a part of Caltech Jensen  lab etdb.  Looking
       for cell division and ESCRt related proteins.

ingestion_tools/dataset_configs/gjensen/10122.yaml

@@ -19,9 +19,9 @@ datasets:
       name: deltaQ 167
     cross_references:
       publications: 10.1128/mBio.01898-15
-    dataset_description: 'This is 5th of 17 sets of data studying Magnetospirillum
+    dataset_description: This is 5th of 17 sets of data studying Magnetospirillum
       magneticum  collected by Poorna Subramanian and is a part of Caltech Jensen  lab
-      etdb. This is the strain in which dQ and dK have been deactivated and the '
+      etdb. This is the strain in which dQ and dK have been deactivated and the
     dataset_identifier: 10122
     dataset_title: M. magneticum dK203_3h_induced
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10125.yaml

@@ -19,9 +19,9 @@ datasets:
       name: deltaQ 167
     cross_references:
       publications: 10.1128/mBio.01898-15
-    dataset_description: 'This is 8th of 17 sets of data studying Magnetospirillum
+    dataset_description: This is 8th of 17 sets of data studying Magnetospirillum
       magneticum  collected by Poorna Subramanian and is a part of Caltech Jensen  lab
-      etdb. This is the strain in which dQ has been deactivated and an inducible '
+      etdb. This is the strain in which dQ has been deactivated and an inducible
     dataset_identifier: 10125
     dataset_title: M. magneticum dQ167_10h_induced
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10126.yaml

@@ -19,10 +19,10 @@ datasets:
       name: deltaQ 167
     cross_references:
       publications: 10.1128/mBio.01898-15
-    dataset_description: 'This is 9th of 17 sets of data studying Magnetospirillum
+    dataset_description: This is 9th of 17 sets of data studying Magnetospirillum
       magneticum  collected by Poorna Subramanian and is a part of Caltech Jensen  lab
       etdb. plasmid is present for dQdQ167 is the strain in which dQ has been mutated
-      and an inducible '
+      and an inducible
     dataset_identifier: 10126
     dataset_title: M. magneticum dQ167_14h_induced
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10159.yaml

@@ -17,7 +17,8 @@ datasets:
     cell_strain:
       id: null
       name: G27
-    dataset_description: ' and is a part of Caltech Jensen  lab etdb.'
+    dataset_description: This is a single dataset studying Helicobacter pylori collected
+      by Yi-Wei Chang and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10159
     dataset_title: Helicobacter pylori G27
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10172.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     dataset_description: This is 1st of 17 sets of data studying HUVECs collected
       by Cora Woodward and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10172

ingestion_tools/dataset_configs/gjensen/10173.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 2nd of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10174.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 3rd of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10175.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     dataset_description: This is 4th of 17 sets of data studying HUVECs collected
       by Cora Woodward and is a part of Caltech Jensen  lab etdb. HUVECs- no treatment
     dataset_identifier: 10175

ingestion_tools/dataset_configs/gjensen/10176.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 5th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10177.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 6th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10178.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 7th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10179.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     dataset_description: This is 8th of 17 sets of data studying HUVECs collected
       by Cora Woodward and is a part of Caltech Jensen  lab etdb. HUVECs transfected
       with CHMP4A+VPS4DN constructs using Nucleofector Kit. Sample# C58-2

ingestion_tools/dataset_configs/gjensen/10180.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 9th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10181.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 10th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10182.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 11th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10183.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 12th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10184.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 13th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10185.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 14th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10186.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 15th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10187.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 16th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10188.yaml

@@ -16,7 +16,7 @@ datasets:
       primary_author_status: false
     cell_type:
       id: CL:0002618
-      name: umbilical vein endothelial cell
+      name: endothelial cell of umbilical vein
     cross_references:
       publications: 10.1128/JVI.02997-14
     dataset_description: This is 17th of 17 sets of data studying HUVECs collected

ingestion_tools/dataset_configs/gjensen/10197.yaml

@@ -17,7 +17,8 @@ datasets:
     cell_strain:
       id: null
       name: 2740-80
-    dataset_description: ' and is a part of Caltech Jensen  lab etdb.'
+    dataset_description: This is a single dataset studying Vibrio cholerae collected
+      by Martin Pilhofer and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10197
     dataset_title: V. cholerae
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10242.yaml

@@ -14,8 +14,8 @@ datasets:
     - corresponding_author_status: true
       name: Grant Jensen
       primary_author_status: false
-    dataset_description: ' and is a part of Caltech Jensen  lab etdb. ribbon near
-      membrane, possibly something between ribbon and membrane'
+    dataset_description: This is a single dataset studying Spiroplasma melliferum
+      collected by Morgan Beeby and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10242
     dataset_title: Spiroplasma melliferum
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10262.yaml

@@ -17,7 +17,8 @@ datasets:
     cross_references:
       publications: 10.15252/embr.201744070
       related_database_entries: EMD-8603
-    dataset_description: ' and is a part of Caltech Jensen  lab etdb.'
+    dataset_description: This is a single dataset studying Thermococcus kodakarensis
+      collected by Ariane Briegel and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10262
     dataset_title: Thermococcus kodakarensis
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10287.yaml

@@ -17,8 +17,8 @@ datasets:
     cell_strain:
       id: null
       name: ATCC 51449
-    dataset_description: ' and is a part of Caltech Jensen  lab etdb. Helicobacter
-      hepaticus cell poles'
+    dataset_description: This is a single dataset studying Helicobacter hepaticus
+      collected by Ariane Briegel and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10287
     dataset_title: H.hepaticus
     dates: &id002

ingestion_tools/dataset_configs/gjensen/10288.yaml

@@ -16,7 +16,8 @@ datasets:
       primary_author_status: false
     cross_references:
       publications: 10.1091/mbc.E12-11-0785
-    dataset_description: ' and is a part of Caltech Jensen  lab etdb.'
+    dataset_description: This is a single dataset studying CHMP1B tubes collected
+      by Zhiheng Yu and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10288
     dataset_title: CHMP1B tubes
     dates: &id002
@@ -28,7 +29,7 @@ datasets:
       name: Homo sapiens
       taxonomy_id: 9606
     sample_preparation: null
-    sample_type: in_vitro
+    sample_type: organism
   sources:
   - literal:
       value:

ingestion_tools/dataset_configs/gjensen/10300.yaml

@@ -17,8 +17,8 @@ datasets:
     cell_strain:
       id: null
       name: NA1000
-    dataset_description: ' and is a part of Caltech Jensen  lab etdb. high-order DNA,
-      H-NS, nucleoid, asymmetric cell division'
+    dataset_description: This is a single dataset studying Caulobacter crescentus
+      collected by Jian Shi and is a part of Caltech Jensen  lab etdb.
     dataset_identifier: 10300
     dataset_title: C. crescentus Calubactor EB session22 27.5KX
     dates: &id002