cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48539/hbm957.rhvb.545
title: OMAP-11: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Spleen with IBEX, v1.0

description: OMAP-11 was designed for IBEX imaging of fixed frozen human spleen samples<br>(https://doi.org/10.1038/s41596-021-00644-9; https://doi.org/10.1073/pnas.2018488117). The panel contains 24 primary<br>antibodies, 2 secondary antibodies, and Hoechst for image alignment and nuclear segmentation. This OMAP provides a<br>spatial context for the main anatomical structures and cell types present in the ASCT+B spleen table v1.3 including<br>red pulp macrophages, splenic endothelial cells, stromal cells of the red and white pulp, B cells, T cells,<br>granulocytes, and platelets. This panel can be expanded to include more granular phenotyping of B cells (naïve,<br>memory, switched), T cells (T follicular helper cells, T regulatory cells), NK cells, dendritic cells (cDC1, cDC2,<br>plasmacytoid DCs), and lymphatic endothelial cells with the addition of appropriate markers. Several antibodies for<br>CD271, a critical splenic stromal marker (https://doi.org/10.1111/imm.12469), were tested but did not provide reliable<br>labeling in the spleen for the tissue preservation method employed for this study<br>(RRIDs AB_10982271, AB_2564818). Custom antibodies were purchased from BioLegend or conjugated in house<br>using labeling kits from Abcam (ab269820) and Thermo Fisher Scientific (A20182, A20188). A representative<br>dataset acquired using this OMAP can be found here: https://doi.org/10.5281/zenodo.5244550.
DOI: 10.48539/hbm863.mpmp.647
title: Blood Vasculature Geometry, v1.1

description: TThis table provides geometric properties (e.g., length and diameter) of selected vessels in the blood vasculature<br>Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table. The same vessel geometric property might be listed<br>multiple times with different values. These correspond to different references that reported the property.
DOI: 10.48539/hbm794.csbj.358
title: OMAP-2 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Intestine with CODEX, v1.1

description: OMAP-2 was designed for CODEX (CO Detection by IndEXing) imaging of fresh frozen human intestine<br>(https://doi.org/10.1038/s41596-021-00556-8, https://doi.org/10.1002/eji.202048891). The panel contains 54 antibodies<br>and the nuclear marker Hoechst for image alignment and nuclear segmentation. This panel provides spatial context for<br>all anatomical structures and most cell types present in the [ASCT+B intestine<br>table,v1.1](https://doi.org/10.48539/HBM325.NZPB.589). However, this panel does not include a marker for tuft cells, M<br>cells, and subsets of major cell types that are known to be present in the intestine (e.g., neuroendocrine cell<br>lineages, distinctions between alpha/beta and gamma/delta T cells, and IgA+ plasma cells). In general the panel was<br>aimed to get a broad representation of cell types found in the intestine spanning stromal, immune, and epithelial<br>origins and could be used across disease settings of the intestine. Data from this panel has been analyzed as<br>described previously (https://doi.org/10.3389/fimmu.2021.727626, https://doi.org/10.1101/2021.11.25.469203). All<br>antibodies are custom conjugated in house with oligonucleotide barcodes (no lot number available) and run using CODEX<br>imaging per previous protocols (https://doi.org/10.1038/s41596-021-00556-8).
DOI: 10.48539/hbm624.chlg.652
title: OMAP-20: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of kidney with cyclic multiplexed immunofluorescence, v1.0

description: OMAP-20 was designed for cyclic multiplexed immunofluorescence (MxIF) microscopy of fresh frozen human kidney samples<br>(dx.doi.org/10.17504/protocols.io.81wgb1m3yvpk/v3). The panel contains 10 antibodies and the nuclear marker Hoechst<br>for image alignment. This OMAP provides a spatial context for proximal tubule and glomeruli structures and cell types<br>present in the ASCT+B kidney table v1.4. Functional tissue units other than proximal tubules, glomeruli, and<br>vasculature are not targeted in the existing panel. Additional details on sample preparation and antibody validation<br>can be found here (https://www.protocols.io/workspaces/BIOMIC). Representative datasets using this OMAP can be found<br>here (https://doi.org/10.1101/2024.02.21.581450). The antibody directed against tensin (RRID: AB_10796111) is known to<br>perform better in cycle 1 than in later cycles.
DOI: 10.5281/zenodo.17100253
title: Brown-Algae.dataset

description: The dataset folder contains essential files required for the execution and testing of the iCulture pipeline. This folder includes:

1. Reference Databases:

• Pfam-A.hmm and associated index files (*.h3f, *.h3i, *.h3m, *.h3p):

• These files constitute the Pfam database used for HMMER annotation of protein sequences.

• The database enables the identification of protein domains and families within query sequences.

2. Input FASTA Files:

• brown-algae_dataset.fa:

• This FASTA file is generated from the brown algae dataset downloaded from The Phaeoexplorer Project.

• It contains protein sequences from brown algae, formatted for compatibility with the pipeline.

• This file is used as an input for clustering and annotation during the pipeline execution.

3. Sample Input Files:

• These files are provided to facilitate testing and ensure reproducibility of the pipeline results.

 

Purpose:

This directory serves as a centralized location for storing datasets and databases necessary for running the iCulture pipeline, particularly in reproducibility-focused workflows.

Note: If you wish to use the pipeline with custom datasets, replace the example files in this folder with your own, following the required format.
DOI: 10.5281/zenodo.17100254
title: Brown-Algae.dataset

description: The dataset folder contains essential files required for the execution and testing of the iCulture pipeline. This folder includes:

1. Reference Databases:

• Pfam-A.hmm and associated index files (*.h3f, *.h3i, *.h3m, *.h3p):

• These files constitute the Pfam database used for HMMER annotation of protein sequences.

• The database enables the identification of protein domains and families within query sequences.

2. Input FASTA Files:

• brown-algae_dataset.fa:

• This FASTA file is generated from the brown algae dataset downloaded from The Phaeoexplorer Project.

• It contains protein sequences from brown algae, formatted for compatibility with the pipeline.

• This file is used as an input for clustering and annotation during the pipeline execution.

3. Sample Input Files:

• These files are provided to facilitate testing and ensure reproducibility of the pipeline results.

 

Purpose:

This directory serves as a centralized location for storing datasets and databases necessary for running the iCulture pipeline, particularly in reproducibility-focused workflows.

Note: If you wish to use the pipeline with custom datasets, replace the example files in this folder with your own, following the required format.
DOI: 10.48539/hbm866.bcmc.625
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Uterus, v1.1

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim to<br>capture the nested *part_of* structure of anatomical human body parts, the typology of cells, and biomarkers used to<br>identify cell types. The tables are authored and reviewed by an international team of experts.
DOI: 10.48539/hbm787.dmfw.993
title: OMAP-6  Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX, v1.4

description: OMAP-6 was designed for CO-Detection by indEXing (CODEX) imaging of human formalin fixed paraffin embedded (FFPE)<br>pancreas samples. Following antigen retrieval (citrate buffer pH=6, heating at high pressure 114–121°C for 20<br>minutes), tissue autofluorescence was reduced using a photobleaching protocol (Du Z. et al. 2019, modified by Derek<br>Oldrige). CODEX is based on DNA-conjugated antibodies allowing the image acquisition of 3 antibodies per cycle and<br>removal of complementary fluorescently labeled DNA probes afterwards (Goltsev et al. 2018). Cell junction markers<br>(E-cadherin, Beta-catenin) and nuclear marker Hoechst are used for cell segmentation. The resulting OMAP contains 12<br>antibodies and provides a spatial context for most relevant anatomical structures and cell types in the pancreas<br>including pancreatic cells (alpha, beta, gamma, delta), ductal cells, endothelial cells, smooth muscle cells, and<br>mesenchymal cells present in the ASCT-B pancreas table, v1.3 (Campbell-Thompson, Eskaros, and Saunders 2023). Acinar<br>and epsilon cells are not targeted in the existing panel due to the complexity of finding suitable and stable<br>antibodies. A representative dataset using this OMAP can be found here: (Björklund et al. 2023). An antibody directed<br>against pancreatic polypeptide (PPY) was originally included in OMAP-5 v1.0 and v1.1, but was removed due to<br>inconsistent labeling.<br><br>**Bibliography:**<br><br>* Björklund, Frida, Anna Martinez Casals, MacDonald Patrick E., and Emma Lundberg. 2023. “Dataset: CODEX Highly Multiplexed Tissue Imaging in Pancreas.” Zenodo. https://zenodo.org/records/7742474.<br>* Campbell-Thompson, Martha, Adel Eskaros, and Diane Saunders. 2023. “Pancreas (v1.3) Graph Data, v1.3.” https://lod.humanatlas.io/asct-b/pancreas/v1.3/.<br>* Goltsev, Yury, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, and Garry P. Nolan. 2018. “Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging.” *Cell* 174 (4): 968–981.e15. https://doi.org/10.1016/j.cell.2018.07.010.
DOI: 10.48539/hbm877.btsr.898
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Heart, v1.2

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim to<br>capture the nested *part_of* structure of anatomical human body parts, the typology of cells, and biomarkers used to<br>identify cell types. The tables are authored and reviewed by an international team of experts.
DOI: 10.48539/hbm663.jjmj.628
title: OMAP-10: Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MACSima, v1.0

description: OMAP-10 was designed for MACSima (MACSima imaging cyclic staining) imaging of paraformaldehyde (PFA)-fixed human<br>tonsil samples. The MACSima technology is described in detail in the following publication<br>(https://doi.org/10.1038/s41598-022-05841-4). Most, but not all, antibodies in this panel are recombinant antibodies<br>with a mutated human IgG1 constant region. The described mutation removes the Fc receptor binding capacity of human<br>IgG1, eliminating the need for additional blocking steps and reducing non-specific binding of human antibodies on<br>human tissues. Highly multiplexed imaging is achieved through cycles of immunolabeling with FITC, PE, and APC<br>conjugated antibodies and photobleaching to eliminate fluorescence signal between imaging cycles. The panel contains<br>30 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial<br>context for all anatomical structures and most cell types present in the human palatine tonsil. OMAP-10 follows<br>closely OMAP-1 described for human lymph nodes<br>(https://cdn.humanatlas.io/hra-releases/v1.3/docs/omap/omap-1-human-lymph-node-ibex.html). All reagents were obtained<br>from Miltenyi Biotec and have been rigorously tested through an internal quality control system to have minimal<br>variation between lots. For this reason, lot information is not included in this table. Analysis was performed by an<br>accompanied software package MACSIQ View Analysis also described in the MACSima publication<br>(https://doi.org/10.1038/s41598-022-05841-4). The result of the analysis is included in the uploaded dataset. In<br>brief, the software processes the raw images of the MACSima run, generates stitched images, and then allows downstream<br>analysis including cell segmentation, cell gating, data normalization, dimension reduction plots (tSNE, UMAP), heat<br>maps, distance analyses and cluster analyses, all of which are interactively linked together. The MACSima system is<br>continuously evolving, and this is the first OMAP for the MACSima system. A representative dataset created using<br>OMAP-10 can be found here: https://doi.org/10.5281/zenodo.7875937.
DOI: 10.48539/hbm387.dsql.745
title: Musculoskeletal Crosswalk, v1.0

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim to<br>capture anatomical human body parts, the typology of cells, and biomarkers used to identify cell types. The tables are<br>authored and reviewed by an international team of experts. This table describes relationships between anatomical<br>structures in the muscular system and skeleton ASCT+B tables. This includes (1) bone “adjacent_to” bone crosswalks and<br>(2) muscle “attached_to” bone, ligament, tendon, fascia, or skin crosswalks. The bone “adjacent_to” relationships may<br>indicate a joint and joining structures. The “attached_to” relationships have a “Relationship2” value of<br>“has_muscle_origin” or “has_muscle_insertion”. The focus of this initial version of this crosswalk table is the upper<br>extremities, but it will be expanded in the future to other parts of the body.
DOI: 10.48539/hbm726.hwkt.534
title: 3D Reference Organ for Kidney, Female, Right, v1.0

description: [This reference organ](https://humanatlas.io/3d-reference-library) was created using data from the Visible Human<br>Female provided by the National Library of Medicine.
DOI: 10.48539/hbm882.lrsf.394
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Ureter, v1.0

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to capture<br>the nested ureter structure of anatomical human body parts, the typology of cells, and biomarkers used to identify<br>cell types. The tables are authored and reviewed by an international team of experts. The Ureter ASCT+B table provides<br>a comprehensive mapping of the anatomical structures, cell types, and biomarkers specific to the human ureter. This<br>table includes detailed hierarchical relationships among ureteral anatomical structures, associated cell types, and<br>their corresponding biomarkers. It serves as a valuable resource for understanding the cellular composition and<br>molecular characteristics of the ureter within the human reference atlas. A description of this Ureter ASCT+B table<br>can be found in ""Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a<br>Human Reference Atlas"" by Börner et al. 2021. The database and code used to generate the more simplified view of the<br>Ureter in these ASCT+B tables may be found here:<br>(https://github.com/hubmapconsortium/hra-vccf). <br><br>**Bibliography:**<br><br>* Börner, Katy, Sarah A. Teichmann, Ellen M. Quardokus, James C. Gee, Kristen Browne, David Osumi-Sutherland, Bruce W. Herr II, et al. 2021. “Anatomical Structures, Cell Types and Biomarkers of the Human Reference Atlas.” *Nature Cell Biology* 23 (11): 1117–28. https://doi.org/10.1038/s41556-021-00788-6.
DOI: 10.48539/hbm672.ksst.448
title: 3D Reference Organ for Pelvis, Male, v1.0

description: [This reference organ](https://humanatlas.io/3d-reference-library) was created using data from the Visible Human Male,<br>provided by the National Library of Medicine.
DOI: 10.48539/hbm389.bvpp.395
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Fallopian Tube, v1.3

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim to<br>capture the nested *part_of* structure of anatomical human body parts, the typology of cells, and biomarkers used to<br>identify cell types. The tables are authored and reviewed by an international team of experts.
DOI: 10.6084/m9.figshare.30103471
title: Data for Global hailstone under historical and future scenarios

description: This dataset accompanies the study <i>"Shifting hailstone size spectrum: Global projections of hailstorm damage potential under anthropogenic climate change</i>" under submission, and contains all data necessary to reproduce the results and analyses presented in the manuscript. The dataset is organized into three main components:<b>Hailstorm Meteorological Fields for Model Forcing (Soundings to drive model simulations)</b>Meteorological input fields computed for driving the semi–three–dimensional hail growth model.Derived from ERA5 reanalysis data and processed into the format required by the model.<b>Model Simulation Outputs (including HIST-simulation results, SSP245-simulation results, SSP370-simulation results, and SSP585-simulation results)</b>Results from hail growth model simulations, including near-surface hailstone diameter, hailstone growth duration and composite trajectory.<b>Model Validation Data (Model validations)</b>Datasets used for evaluating the performance of the hail growth model.Includes processed historical observations of hailstone size and simulated maximum hailstone diameters.<b>data_SOM5_global_after200_rightMUCAPE_mdf.nc</b>: This dataset comprises the spatiotemporal records of 14,297 major hail events analyzed in this study, their corresponding pre-storm environmental parameters, as well as the event classifications provided by Zhou et al. (2021).All data are provided in NetCDF format to ensure interoperability and ease of use in common scientific workflows. The units of all hail size data are expressed in millimeters.Zhou, Z., Q. Zhang, J. T. Allen, X. Ni, and C.-P. Ng, 2021: How Many Types of Severe Hailstorm Environments Are There Globally? Geophys. Res. Lett., 48, e2021GL095485,https://doi.org/https://doi.org/10.1029/2021GL095485.
DOI: 10.6084/m9.figshare.30103471.v1
title: Data for Global hailstone under historical and future scenarios

description: This dataset accompanies the study <i>"[Your Paper Title]"</i>, submitted to <i>Nature</i>, and contains all data necessary to reproduce the results and analyses presented in the manuscript. The dataset is organized into three main components:<b>Hailstorm Meteorological Fields for Model Forcing (Soundings to drive model simulations)</b>Meteorological input fields computed for driving the semi–three–dimensional hail growth model.Derived from ERA5 reanalysis data and processed into the format required by the model.<b>Model Simulation Outputs (including HIST-simulation results, SSP245-simulation results, SSP370-simulation results, and SSP585-simulation results)</b>Results from hail growth model simulations, including near-surface hailstone diameter, hailstone growth duration and composite trajectory.<b>Model Validation Data (Model validations)</b>Datasets used for evaluating the performance of the hail growth model.Includes processed historical observations of hailstone size and simulated maximum hailstone diameters.All data are provided in NetCDF format to ensure interoperability and ease of use in common scientific workflows.
DOI: 10.6084/m9.figshare.30103471.v2
title: Data for Global hailstone under historical and future scenarios

description: This dataset accompanies the study <i>"Shifting hailstone size spectrum: Global projections of hailstorm damage potential under anthropogenic climate change</i>" under submission, and contains all data necessary to reproduce the results and analyses presented in the manuscript. The dataset is organized into three main components:<b>Hailstorm Meteorological Fields for Model Forcing (Soundings to drive model simulations)</b>Meteorological input fields computed for driving the semi–three–dimensional hail growth model.Derived from ERA5 reanalysis data and processed into the format required by the model.<b>Model Simulation Outputs (including HIST-simulation results, SSP245-simulation results, SSP370-simulation results, and SSP585-simulation results)</b>Results from hail growth model simulations, including near-surface hailstone diameter, hailstone growth duration and composite trajectory.<b>Model Validation Data (Model validations)</b>Datasets used for evaluating the performance of the hail growth model.Includes processed historical observations of hailstone size and simulated maximum hailstone diameters.<b>data_SOM5_global_after200_rightMUCAPE_mdf.nc</b>: This dataset comprises the spatiotemporal records of 14,297 major hail events analyzed in this study, their corresponding pre-storm environmental parameters, as well as the event classifications provided by Zhou et al. (2021).All data are provided in NetCDF format to ensure interoperability and ease of use in common scientific workflows. The units of all hail size data are expressed in millimeters.Zhou, Z., Q. Zhang, J. T. Allen, X. Ni, and C.-P. Ng, 2021: How Many Types of Severe Hailstorm Environments Are There Globally? Geophys. Res. Lett., 48, e2021GL095485,https://doi.org/https://doi.org/10.1029/2021GL095485.
DOI: 10.48539/hbm934.jmvn.957
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Thymus, v1.0

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim to<br>capture the nested *part_of* structure of anatomical human body parts, the typology of cells, and biomarkers used to<br>identify cell types. The tables are authored and reviewed by an international team of experts.
DOI: 10.15468/dl.n4h4q4
title: Occurrence Download

description: A dataset containing 10623424 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "OccurrenceStatus is Present",
 "Year 2021-2021"
 ]
}

 The dataset includes 10623424 records from 6008 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053566-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3hny3e
title: Occurrence Download

description: A dataset containing 10802 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Incilius valliceps (Wiegmann, 1833)"
 ]
}

 The dataset includes 10802 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025183-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8upe9v
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cercocarpus rotundifolius Rydb."
 ]
}

 The dataset includes 5 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0146051-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.236947
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Blakea vallensis Wurdack"
 ]
}

 The dataset includes 15 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0146050-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.