From 1241724ae8d86cc9dc78f21f5492250de5f189e1 Mon Sep 17 00:00:00 2001 From: "Bruce W. Herr II" Date: Fri, 13 Dec 2024 12:53:21 -0500 Subject: [PATCH] Update OMAPs data and page --- .../src/assets/content/pages/omap.yaml | 3 +++ .../src/assets/table-data/omaps_release7.csv | 6 ++--- .../src/assets/table-data/omaps_release8.csv | 24 +++++++++++++++++++ 3 files changed, 30 insertions(+), 3 deletions(-) create mode 100644 apps/humanatlas.io/src/assets/table-data/omaps_release8.csv diff --git a/apps/humanatlas.io/src/assets/content/pages/omap.yaml b/apps/humanatlas.io/src/assets/content/pages/omap.yaml index 2412d9d5e..58d790f3d 100644 --- a/apps/humanatlas.io/src/assets/content/pages/omap.yaml +++ b/apps/humanatlas.io/src/assets/content/pages/omap.yaml @@ -92,6 +92,9 @@ versionData: # SOURCE: https://github.com/x-atlas-consortia/hra-dashboard-data/blob/main/data/humanatlas.io/omaps-release.csv # and have Ellen fill in the blanks + - release: '8th HRA Release (v2.2), December 2024' + file: omaps_release8.csv + version: '2.1' - release: '7th HRA Release (v2.1), June 2024' file: omaps_release7.csv version: '2.1' diff --git a/apps/humanatlas.io/src/assets/table-data/omaps_release7.csv b/apps/humanatlas.io/src/assets/table-data/omaps_release7.csv index 8fabfa240..a2e00d305 100644 --- a/apps/humanatlas.io/src/assets/table-data/omaps_release7.csv +++ b/apps/humanatlas.io/src/assets/table-data/omaps_release7.csv @@ -15,8 +15,8 @@ OMAP-13,https://purl.humanatlas.io/omap/13-pancreas-codex/v1.1,pancreas,4% PFA f OMAP-14,https://purl.humanatlas.io/omap/14-kidney-cycif/v1.0,kidney,Fresh frozen,CyCIF,https://cdn.humanatlas.io/digital-objects/omap/14-kidney-cycif/v1.0/assets/omap-14-kidney-cycif.csv,https://cdn.humanatlas.io/digital-objects/omap/14-kidney-cycif/v1.0/assets/omap-14-kidney-cycif.xlsx,https://doi.org/10.5281/zenodo.10445538,8,9,17 OMAP-15,https://purl.humanatlas.io/omap/15-intestine-codex/v1.0,intestine,FFPE,CODEX,https://cdn.humanatlas.io/digital-objects/omap/15-intestine-codex/v1.0/assets/omap-15-intestine-codex.csv,https://cdn.humanatlas.io/digital-objects/omap/15-intestine-codex/v1.0/assets/omap-15-intestine-codex.xlsx,https://doi.org/10.5281/zenodo.10963121,30,38,54 OMAP-16,https://purl.humanatlas.io/omap/16-lung-codex/v1.0,lung,FFPE,CODEX,https://cdn.humanatlas.io/digital-objects/omap/16-lung-codex/v1.0/assets/omap-16-lung-cell-codex.csv,https://cdn.humanatlas.io/digital-objects/omap/16-lung-codex/v1.0/assets/omap-16-lung-cell-codex.xlsx,,3,35,34 -OMAP-17,https://purl.humanatlas.io/omap/17-thymus-ibex/v1.0,thymus,1% PFA Fixed Frozen,IBEX,https://cdn.humanatlas.io/digital-objects/omap/17-thymus-ibex/v1.0/assets/omap-17-thymus-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/17-thymus-ibex/v1.0/assets/omap-17-thymus-ibex.xlsx,,7,30,43 -OMAP-18,https://purl.humanatlas.io/omap/18-lymph-node-cell-dive-ibex/v1.0,lymph node,FFPE,Cell DIVE-IBEX,https://cdn.humanatlas.io/digital-objects/omap/18-lymph-node-cell-dive-ibex/v1.0/assets/omap-18-lymph-node-cell-dive-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/18-lymph-node-cell-dive-ibex/v1.0/assets/omap-18-lymph-node-cell-dive-ibex.xlsx,,15,11,11 +OMAP-17,https://purl.humanatlas.io/omap/17-thymus-ibex/v1.0,thymus,1% PFA Fixed Frozen,IBEX,https://cdn.humanatlas.io/digital-objects/omap/17-thymus-ibex/v1.0/assets/omap-17-thymus-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/17-thymus-ibex/v1.0/assets/omap-17-thymus-ibex.xlsx,https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1257,7,30,43 +OMAP-18,https://purl.humanatlas.io/omap/18-lymph-node-cell-dive-ibex/v1.0,lymph node,FFPE,Cell DIVE-IBEX,https://cdn.humanatlas.io/digital-objects/omap/18-lymph-node-cell-dive-ibex/v1.0/assets/omap-18-lymph-node-cell-dive-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/18-lymph-node-cell-dive-ibex/v1.0/assets/omap-18-lymph-node-cell-dive-ibex.xlsx,https://idr.openmicroscopy.org/webclient/?show=project-3001,15,11,11 OMAP-19,https://purl.humanatlas.io/omap/19-palatine-tonsil-ibex/v1.0,palatine tonsil,FFPE,IBEX,https://cdn.humanatlas.io/digital-objects/omap/19-palatine-tonsil-ibex/v1.0/assets/omap-19-palatine-tonsil-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/19-palatine-tonsil-ibex/v1.0/assets/omap-19-palatine-tonsil-ibex.xlsx,https://doi.org/10.5281/zenodo.11222093,10,16,20 -OMAP-20,https://purl.humanatlas.io/omap/20-kidney-ims-cycif/v1.0,kidney,Fresh frozen,CyCIF,https://cdn.humanatlas.io/digital-objects/omap/20-kidney-ims-cycif/v1.0/assets/omap-20-kidney-ims-cycif.csv,https://cdn.humanatlas.io/digital-objects/omap/20-kidney-ims-cycif/v1.0/assets/omap-20-kidney-ims-cycif.xlsx,https://doi.org/10.1101/2024.02.21.581450,3,4,10 +OMAP-20,https://purl.humanatlas.io/omap/20-kidney-ims-cycif/v1.0,kidney,Fresh frozen,IMS-CyCIF,https://cdn.humanatlas.io/digital-objects/omap/20-kidney-ims-cycif/v1.0/assets/omap-20-kidney-ims-cycif.csv,https://cdn.humanatlas.io/digital-objects/omap/20-kidney-ims-cycif/v1.0/assets/omap-20-kidney-ims-cycif.xlsx,https://doi.org/10.1101/2024.02.21.581450,3,4,10 OMAP-21,https://purl.humanatlas.io/omap/21-palatine-tonsil-mics/v1.0,palatine tonsil,FFPE,MICS,https://cdn.humanatlas.io/digital-objects/omap/21-palatine-tonsil-mics/v1.0/assets/omap-21-palatine-tonsil-mics.csv,https://cdn.humanatlas.io/digital-objects/omap/21-palatine-tonsil-mics/v1.0/assets/omap-21-palatine-tonsil-mics.xlsx,https://doi.org/10.5281/zenodo.11286187,12,16,46 \ No newline at end of file diff --git a/apps/humanatlas.io/src/assets/table-data/omaps_release8.csv b/apps/humanatlas.io/src/assets/table-data/omaps_release8.csv new file mode 100644 index 000000000..8ba0932e8 --- /dev/null +++ b/apps/humanatlas.io/src/assets/table-data/omaps_release8.csv @@ -0,0 +1,24 @@ +omapId,url,organ,tissuePreservationMethod,imagingMethod,csv,xlsx,representativeDataset,as,ct,bp +OMAP-1,https://purl.humanatlas.io/omap/1-human-lymph-node-ibex/v1.4,lymph node,1% PFA fixed frozen,IBEX,https://cdn.humanatlas.io/digital-objects/omap/1-human-lymph-node-ibex/v1.4/assets/omap-1-human-lymph-node-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/1-human-lymph-node-ibex/v1.4/assets/omap-1-human-lymph-node-ibex.xlsx,https://zenodo.org/record/5244551#.Y8SRcnbMIuU,28,32,39 +OMAP-2,https://purl.humanatlas.io/omap/2-intestine-codex/v1.5,intestine,Fresh frozen,CODEX,https://cdn.humanatlas.io/digital-objects/omap/2-intestine-codex/v1.4/assets/omap-2-intestine-codex.csv,https://cdn.humanatlas.io/digital-objects/omap/2-intestine-codex/v1.5/assets/omap-2-intestine-codex.xlsx,https://doi.org/10.5061/dryad.pk0p2ngrf,30,33,54 +OMAP-3,https://purl.humanatlas.io/omap/3-kidney-codex/v1.3,kidney,Fresh frozen,CODEX,https://cdn.humanatlas.io/digital-objects/omap/3-kidney-codex/v1.3/assets/omap-3-kidney-codex.csv,https://cdn.humanatlas.io/digital-objects/omap/3-kidney-codex/v1.3/assets/omap-3-kidney-codex.xlsx,https://zenodo.org/record/8082943,28,38,24 +OMAP-4,https://purl.humanatlas.io/omap/4-skin-cell-dive/v1.3,skin of body,FFPE,Cell DIVE,https://cdn.humanatlas.io/digital-objects/omap/4-skin-cell-dive/v1.3/assets/omap-4-skin-cell-dive.csv,https://cdn.humanatlas.io/digital-objects/omap/4-skin-cell-dive/v1.3/assets/omap-4-skin-cell-dive.xlsx,https://portal.hubmapconsortium.org/browse/publication/e8338966c69e759157d6c6ad24847989,22,13,18 +OMAP-5,https://purl.humanatlas.io/omap/5-liver-sims/v1.3,liver,Fresh frozen,SIMS,https://cdn.humanatlas.io/digital-objects/omap/5-liver-sims/v1.3/assets/omap-5-liver-sims.csv,https://cdn.humanatlas.io/digital-objects/omap/5-liver-sims/v1.3/assets/omap-5-liver-sims.xlsx,https://zenodo.org/record/8084259,24,14,19 +OMAP-6,https://purl.humanatlas.io/omap/6-pancreas-codex/v1.3,pancreas,FFPE,CODEX,https://cdn.humanatlas.io/digital-objects/omap/6-pancreas-codex/v1.3/assets/omap-6-pancreas-codex.csv,https://cdn.humanatlas.io/digital-objects/omap/6-pancreas-codex/v1.3/assets/omap-6-pancreas-codex.xlsx,https://zenodo.org/record/7742474,10,10,11 +OMAP-7,https://purl.humanatlas.io/omap/7-lung-cell-dive/v1.3,lung,FFPE,Cell DIVE,https://cdn.humanatlas.io/digital-objects/omap/7-lung-cell-dive/v1.3/assets/omap-7-lung-cell-dive.csv,https://cdn.humanatlas.io/digital-objects/omap/7-lung-cell-dive/v1.3/assets/omap-7-lung-cell-dive.xlsx,https://zenodo.org/record/7731162#.ZBmz2nbMIuU,28,36,30 +OMAP-8,https://purl.humanatlas.io/omap/8-placenta-full-term-imc/v1.1,placenta,FFPE,IMC,https://cdn.humanatlas.io/digital-objects/omap/8-placenta-full-term-imc/v1.1/assets/omap-8-placenta-full-term-imc.csv,https://cdn.humanatlas.io/digital-objects/omap/8-placenta-full-term-imc/v1.1/assets/omap-8-placenta-full-term-imc.xlsx,https://zenodo.org/records/10406597,8,15,26 +OMAP-9,https://purl.humanatlas.io/omap/9-kidney-codex/v1.3,kidney,Fresh Frozen,CODEX,https://cdn.humanatlas.io/digital-objects/omap/9-kidney-codex/v1.2/assets/omap-9-kidney-codex.csv,https://cdn.humanatlas.io/digital-objects/omap/9-kidney-codex/v1.3/assets/omap-9-kidney-codex.xlsx,,29,33,41 +OMAP-10,https://purl.humanatlas.io/omap/10-palatine-tonsil-mics/v1.1,palatine tonsil,1% PFA fixed frozen,MICS,https://cdn.humanatlas.io/digital-objects/omap/10-palatine-tonsil-mics/v1.1/assets/omap-10-palatine-tonsil-mics.csv,https://cdn.humanatlas.io/digital-objects/omap/10-palatine-tonsil-mics/v1.1/assets/omap-10-palatine-tonsil-mics.xlsx,https://doi.org/10.5281/zenodo.7875937,12,16,30 +OMAP-11,https://purl.humanatlas.io/omap/11-spleen-ibex/v1.1,spleen,1% PFA fixed frozen,IBEX,https://cdn.humanatlas.io/digital-objects/omap/11-spleen-ibex/v1.1/assets/omap-11-spleen-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/11-spleen-ibex/v1.1/assets/omap-11-spleen-ibex.xlsx,https://doi.org/10.5281/zenodo.5244550,23,23,24 +OMAP-12,https://purl.humanatlas.io/omap/12-eye-retina-ibex/v1.1,retina,1% PFA Fixed Frozen,IBEX,https://cdn.humanatlas.io/digital-objects/omap/12-eye-retina-ibex/v1.1/assets/omap-12-eye-retina-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/12-eye-retina-ibex/v1.1/assets/omap-12-eye-retina-ibex.xlsx,https://doi.org/10.5281/zenodo.7777285,4,7,14 +OMAP-13,https://purl.humanatlas.io/omap/13-pancreas-codex/v1.1,pancreas,4% PFA fixed frozen,CODEX,https://cdn.humanatlas.io/digital-objects/omap/13-pancreas-codex/v1.1/assets/omap-13-pancreas-codex.csv,https://cdn.humanatlas.io/digital-objects/omap/13-pancreas-codex/v1.1/assets/omap-13-pancreas-codex.xlsx,https://doi.org/10.5281/zenodo.7916783,13,21,27 +OMAP-14,https://purl.humanatlas.io/omap/14-kidney-cycif/v1.0,kidney,Fresh frozen,CyCIF,https://cdn.humanatlas.io/digital-objects/omap/14-kidney-cycif/v1.0/assets/omap-14-kidney-cycif.csv,https://cdn.humanatlas.io/digital-objects/omap/14-kidney-cycif/v1.0/assets/omap-14-kidney-cycif.xlsx,https://doi.org/10.5281/zenodo.10445538,8,9,17 +OMAP-15,https://purl.humanatlas.io/omap/15-intestine-codex/v1.0,intestine,FFPE,CODEX,https://cdn.humanatlas.io/digital-objects/omap/15-intestine-codex/v1.0/assets/omap-15-intestine-codex.csv,https://cdn.humanatlas.io/digital-objects/omap/15-intestine-codex/v1.0/assets/omap-15-intestine-codex.xlsx,https://doi.org/10.5281/zenodo.10963121,30,38,54 +OMAP-16,https://purl.humanatlas.io/omap/16-lung-codex/v1.0,lung,FFPE,CODEX,https://cdn.humanatlas.io/digital-objects/omap/16-lung-codex/v1.0/assets/omap-16-lung-cell-codex.csv,https://cdn.humanatlas.io/digital-objects/omap/16-lung-codex/v1.0/assets/omap-16-lung-cell-codex.xlsx,,3,35,34 +OMAP-17,https://purl.humanatlas.io/omap/17-thymus-ibex/v1.0,thymus,1% PFA Fixed Frozen,IBEX,https://cdn.humanatlas.io/digital-objects/omap/17-thymus-ibex/v1.0/assets/omap-17-thymus-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/17-thymus-ibex/v1.0/assets/omap-17-thymus-ibex.xlsx,https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1257,7,30,43 +OMAP-18,https://purl.humanatlas.io/omap/18-lymph-node-cell-dive-ibex/v1.0,lymph node,FFPE,Cell DIVE-IBEX,https://cdn.humanatlas.io/digital-objects/omap/18-lymph-node-cell-dive-ibex/v1.0/assets/omap-18-lymph-node-cell-dive-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/18-lymph-node-cell-dive-ibex/v1.0/assets/omap-18-lymph-node-cell-dive-ibex.xlsx,https://idr.openmicroscopy.org/webclient/?show=project-3001,15,11,11 +OMAP-19,https://purl.humanatlas.io/omap/19-palatine-tonsil-ibex/v1.0,palatine tonsil,FFPE,IBEX,https://cdn.humanatlas.io/digital-objects/omap/19-palatine-tonsil-ibex/v1.0/assets/omap-19-palatine-tonsil-ibex.csv,https://cdn.humanatlas.io/digital-objects/omap/19-palatine-tonsil-ibex/v1.0/assets/omap-19-palatine-tonsil-ibex.xlsx,https://doi.org/10.5281/zenodo.11222093,10,16,20 +OMAP-20,https://purl.humanatlas.io/omap/20-kidney-ims-cycif/v1.0,kidney,Fresh frozen,IMS-CyCIF,https://cdn.humanatlas.io/digital-objects/omap/20-kidney-ims-cycif/v1.0/assets/omap-20-kidney-ims-cycif.csv,https://cdn.humanatlas.io/digital-objects/omap/20-kidney-ims-cycif/v1.0/assets/omap-20-kidney-ims-cycif.xlsx,https://doi.org/10.1101/2024.02.21.581450,3,4,10 +OMAP-21,https://purl.humanatlas.io/omap/21-palatine-tonsil-mics/v1.1,palatine tonsil,FFPE,MICS,https://cdn.humanatlas.io/digital-objects/omap/21-palatine-tonsil-mics/v1.1/assets/omap-21-palatine-tonsil-mics.csv,https://cdn.humanatlas.io/digital-objects/omap/21-palatine-tonsil-mics/v1.1/assets/omap-21-palatine-tonsil-mics.xlsx,https://doi.org/10.5281/zenodo.11286187,12,16,46 +OMAP-22,https://purl.humanatlas.io/omap/22-skin-cell-dive/v1.0,skin of body,FFPE,Cell DIVE,https://cdn.humanatlas.io/digital-objects/omap/22-skin-cell-dive/v1.0/assets/omap-22-skin-cell-dive.csv,https://cdn.humanatlas.io/digital-objects/omap/22-skin-cell-dive/v1.0/assets/omap-22-skin-cell-dive.xlsx,,19,20,34 +OMAP-23,https://purl.humanatlas.io/omap/23-vermiform-appendix-mics/v1.0,vermiform appendix,FFPE,MICS,https://cdn.humanatlas.io/digital-objects/omap/23-vermiform-appendix-mics/v1.0/assets/omap-23-vermiform-appendix-mics.csv,https://cdn.humanatlas.io/digital-objects/omap/23-vermiform-appendix-mics/v1.0/assets/omap-23-vermiform-appendix-mics.xlsx,https://zenodo.org/records/14008816,6,21,28 \ No newline at end of file