cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48539/hbm332.xbsp.863
title: OMAP-15 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Intestines with CODEX, v1.0

description: OMAP-15 was designed for CO-Detection by indEXing (CODEX), with the Akoya PhenoCycler system for formalin fixed<br>paraffin embedded human intestine samples (https://doi.org/10.1038/s41596-021-00556-8,<br>https://doi.org/10.1002/eji.202048891). The panel contains 54 antibodies and the nuclear marker DAPI. This OMAP<br>provides a spatial context for most anatomical structures and cell types present in the ASCT+B Large Intestine v1.3<br>and Small Intestine v1.1. This OMAP builds from OMAP-2 (https://doi.org/10.48539/HBM244.TNJG.649), adapting the<br>markers for fixed frozen tissues to formalin fixed paraffin embedded (FFPE) tissue. It excludes 19 markers originally<br>found in OMAP-2 and instead includes 22 new markers that include the following: ATP1A1, CD206, COL1A1, CTNNB1, FN1,<br>FOXP3, GP2, HLA-DRA, IGHA1, IGHM, ITGAM, KRT4/5/6a/6b/6c/8/10/13/18, MS4A1, MUC6, PDGFRA/B, POSTN, RORC, SIGLEC8,<br>SPIB, TNC, TPSAB1, and UCHL1. This panel does not contain markers for tuft cells and naive intestinal stem cells<br>(LGR5+ ASCL2+). Antibodies without carriers (BSA) are used and if the regular antibody from the supplier contains<br>carriers, custom ones are ordered without carriers . Antibodies are custom conjugated with oligonucleotide barcodes.<br>The protocols for antibody conjugation (https://doi.org//10.17504/protocols.io.4r3l2q8q4l1y/v1) and sample<br>preparation and antigen retrieval (https://doi.org/10.17504/protocols.io.n92ldm6y9l5b/v1) can be found in the<br>respective linked doi’s. Representative datasets using this OMAP can be found here:<br>https://doi.org/10.5281/zenodo.10963120.
DOI: 10.48539/hbm697.fwdq.488
title: OMAP-9: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Kidney with CODEX, v1.3

description: OMAP-9 was designed for CODEX multiplex antibody-based imaging of fresh frozen human kidney tissue<br>(dx.doi.org/10.17504/protocols.io.8epv5jdbnl1b/v1). The panel contains 41 antibodies and the nuclear marker DAPI for<br>image alignment and nuclear segmentation. OMAP-9 provides a spatial context for all anatomical structures and most<br>cell types present in the ASCT+B kidney table v1.1. This OMAP expands on OMAP-3 (10.48539/HBM373.TBKP.375), an 18-plex<br>kidney CODEX panel, by including additional markers for granular phenotyping of key cells in the kidney such as<br>structural cells (Podocalyxin, LRP2, E-cadherin, SLC12A3, Na/K ATPase and Cytokeratin 8), immune cells including T<br>cells (CD3D, CD4, CD45RO, CD8, FOXP3, GATA-3), myeloid cells (CD11c, CD68, CD206, HLA-DR, Myeloperoxidase), and B<br>cells (CD20). Antibodies directed against injury markers (KIM1, IGFBP7, Osteopontin, PLSCR1, VCAM1, MCP1, phosphor<br>c-JUN, phosphor MLKL, Fibronectin, Collagen IV, LC3, Cystatin 3, and PROM1) allows profiling of kidney disease<br>progression, prognosis, and repair. The following markers utilize different antibody clones than OMAP-3: vimentin,<br>beta-catenin, and uromodulin. Mesangial cells present in the glomerulus are not targeted in the existing panel due to<br>the absence of suitable antibodies compatible with the methodology. Additional details on sample preparation and CODEX<br>multiplexing workflow can be found on Protocols.io (dx.doi.org/10.17504/protocols.io.8epv5jdbnl1b/v1). Correction to<br>update to authors list and spelling of names appears in OMAP-9 v1.1. OMAP-9 v1.5 revises the UniProt accession number<br>for CD45RO to P08575-4 to distinguish it from CD45.
DOI: 10.48539/hbm727.fmqz.589
title: Blood Vasculature Geometry, v1.2

description: This 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 (Börner et al. 2021). The same vessel geometric<br>property might be listed multiple times with different values. These correspond to different references that reported<br>the property. This is in support of Vasculature Common Coordinate Frame (VCCF) construction (Weber, Ju, and Börner<br>2020).<br><br>**Bibliography:**<br><br>* Weber, Griffin M., Yingnan Ju, and Katy Börner. 2020. “Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body.” *Frontiers in Cardiovascular Medicine* 7 (March). https://doi.org/10.3389/fcvm.2020.00029.<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: 10.34740/kaggle/dsv/13030352
title: Maternal mortality ratio
DOI: 10.48539/hbm762.wrrq.394
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Eye, v1.2

description: The Eye ASCT+B table v1.1 focused on representing key ocular anatomical structures including the neural retina, lens,<br>cornea, iris, and ciliary body with a focus on vascular, epithelial, and neural cell types. Version 1.2 expands upon<br>v1.1 with the addition of anatomical structures including the fovea and macula and cell types such as immune and<br>endothelial.
DOI: 10.48539/hbm342.cstf.675
title: Pathway 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 provides a crosswalk between structures in the<br>blood vasculature, lymph vasculature, and peripheral nervous system (PNS) ASCT+B tables. The Relationship column<br>indicates the relationship between Structure1 and Structure2. In this version of the crosswalk, there are two types of<br>relationships: (1) “adjacent_to” is being used here for neurovascular bundles and (2) “connects_to” indicates arterial<br>vessels that connect to venous structures.
DOI: 10.48539/hbm888.mgdc.395
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Spleen, v1.4

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. The spleen ASCT+B<br>tables are derived from published literature, public datasets, unpublished studies from table authors, and input<br>provided by Dr. Birte Steiniger, an early reviewer and leader in the field of spleen anatomy. The gene biomarkers are<br>primarily derived from one landmark publication in humans: [(Madissoon et al.<br>2019)](https://doi.org/10.1186/s13059-019-1906-x). The anatomical structures and cell types of the spleen were highly<br>influenced by work from Dr. Steiniger including: [(Steiniger 2015)](https://doi.org/10.1111/imm.12469), [(Steiniger et<br>al. 2018)](https://doi.org/10.1038/s41598-018-34105-3), and [(Steiniger et al.<br>2007)](https://doi.org/10.1007/s00418-007-0320-8). Whenever possible, we used multiple sources to confirm gene and<br>protein biomarkers and united them across cell types. Cell phenotypes, especially for protein-based assays, are highly<br>granular with several markers listed at different expression levels. We anticipate further revision and refinement<br>from multimodal studies that pair sequencing and imaging studies from the same human sample. In total, this table<br>reports 37 anatomical structures, 60 cell types, and 194 biomarkers.
DOI: 10.15468/dl.rhwr2a
title: Occurrence Download

description: A dataset containing 346 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pavonia humifusa"
 ]
}

 The dataset includes 346 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053629-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nv5pp9
title: Occurrence Download

description: A dataset containing 4377 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Investigación y monitoreo de avifauna con estaciones de anillamiento permanentes en el Chocó Andino"
 ]
}

 The dataset includes 4377 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053628-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm256.hgzn.489
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Brain, 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. Only cell types and<br>biomarkers for the primary motor cortex are represented in the table currently [(Bakken et al.<br>2021)](https://doi.org/10.1038/s41586-021-03465-8.)
DOI: 10.25934/pr00011275
title: Analysis of functional data from Duchenne participants in a natural history study and the placebo control arm of an interventional clinical trial for the treatment of Duchenne in combination with other natural history data sets.

description: Duchenne muscular dystrophy (DMD) is a rare, inherited disorder that causes progressive muscle weakness, typically beginning in early childhood. It primarily affects boys and leads to loss of the ability to walk, breathing difficulties, and heart problems. Currently, there is no cure for DMD, and available treatments only slow the progression of the disease. Because of this, new treatment options are urgently needed.

This research will support a clinical trial (NCT05693142) testing a new gene therapy designed to treat DMD. Instead of using a traditional control group where some participants receive a placebo (a non-active treatment), researchers will use existing “natural history” data for comparison to our treated group with the goal of showing treatment effect of our drug. Natural history data includes information collected over time about how DMD progresses in patients who are not receiving the new therapy. 

This method of comparison to an external control group is being used because it would be unethical to deny participants access to current treatments that might help them. Also, since gene therapy can cause visible physical changes, it would be difficult to keep patients and doctors unaware of who received the real treatment (a process called “blinding”). Using natural history data allows researchers to compare treated patients with untreated ones fairly and safely. This approach will help determine whether the gene therapy improves symptoms and slows the disease, which could lead to better treatment options for people with DMD.
DOI: 10.5067/seabass/pace-pax/data001
title: PACE-PAX
DOI: 10.48539/hbm485.zcfd.459
title: OMAP-4  Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Skin with Cell DIVE, v1.3

description: OMAP-4 was designed for Cell DIVE multiplexed imaging of formalin-fixed paraffin-embedded (FFPE) human skin. Cell DIVE<br>enables highly multiplexed single cell analysis using antibody-based imaging (Gerdes, MJ. et al, 2013) The tissue<br>slides were prepared with a two-step antigen retrieval process (pH 6 and pH 9, as described<br>https://dx.doi.org/10.17504/protocols.io.bpwumpew). Antigens were detected using either primary antibodies with<br>fluorophore-labeled secondaries or fluorescent dye conjugated antibodies (protocol can be found<br>https://dx.doi.org/10.17504/protocols.io.b4kgqutw). The panel contains 18 antibodies and the nuclear marker DAPI for<br>image registration and nuclear segmentation. This OMAP provides a spatial context for most anatomical structures and<br>cell types present in the [ASCT+B skin table, v1.1](https://doi.org/10.48539/HBM423.RTRR.746). Keratinocyte<br>populations can be identified based on their spatial location, distinct morphology and, in the case of corneocytes,<br>absence of nuclei. Additionally, the inclusion of protein biomarkers DDB2 and p53 allow profiling of skin damage and<br>aging effects. The panel was designed to get a broad representation of cell types found in the skin and in the future<br>will be expanded to include dermal dendritic cell (DC) markers (e.g. Langerin, CD11c). This panel does not include<br>markers targeting several immune cell subsets including Langerhans cells, mast cells, and gamma delta T cells.<br>Representative datasets created using this OMAP are publicly available on the [HuBMAP data<br>portal.](https://portal.hubmapconsortium.org/browse/publication/e8338966c69e759157d6c6ad24847989)
DOI: 10.48539/hbm673.zzdk.622
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Kidney, 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/hbm854.cxrg.779
title: OMAP-11: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Spleen with IBEX, v1.1

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: 10.15468/dl.zs6seg
title: Occurrence Download

description: A dataset listing the 124 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-0.77758 46.81692,-0.79986 46.77901,-0.69227 46.73493,-0.65696 46.78019,-0.68753 46.80223,-0.70649 46.81977,-0.761 46.8328,-0.77758 46.81692))",
 "PublishingOrg is 1928bdf0-f5d2-11dc-8c12-b8a03c50a862",
 "TaxonKey is Aves",
 "Year 2015-2025"
 ]
}

 The dataset's 124 records were derived from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053604-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm999.lbsw.743
title: Pathway crosswalk, v1.1

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to capture<br>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 provides a crosswalk between structures in the<br>blood vasculature, lymph vasculature, and peripheral nervous system (PNS) ASCT+B tables. The Relationship column<br>indicates the relationship between Structure1 and Structure2. In this version of the crosswalk, there are three types<br>of relationships: (1) “adjacent_to” is being used here for neurovascular bundles; (2) “connects_to” indicates arterial<br>vessels that connect to venous structures; and (3) “anastomosis_to” is used for anastomoses, where vessels connect to<br>form loops.
DOI: 10.5285/3dbe7a10-c8b9-8fd9-e063-7086abc00d4e
title: Processed multibeam bathymetry grids from the Porcupine Abyssal Plain Sustained Observatory (PAP-SO) (DY116, 2020)

description: Two multibeam swath bathymetry surveys were collected using a hull-mounted Kongsberg EM122 (12 kHz) echosounder during RRS Discovery cruise DY116 in November 2020. The cruise was conducted to fill in gaps in existing maps of the area surrounding the Porcupine Abyssal Plain Sustained Observatory (PAP-SO) map in order to obtain a better insight in the biodiversity patterns, benthic habitat distributions and sediment transport processes of submarine canyons. The surveys were carried out at 6 knots. A sound velocity profile was taken from CTD cast DY116-005. The data were edited using Caris HIPS software by Catherine Wardell and gridded at 50 m spacing in a WGS84 UTM Zone 28N projection. The vertical datum of the data is matched to mean sea level (MSL). They were exported as longitude-latitude-depth triples. Funding was provided to CLASS (Climate Linked Atlantic Sector Science), the National Capability Single Sector Marine Research Programme by NERC.
DOI: 10.48539/hbm243.lzxv.772
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Small Intestine, v1.2

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to capture<br>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. The Small Intestine ASCT+B table represents terms related<br>to the adult human small intestine. These include both macroscopic and microscopic anatomical structures, major cell<br>types, and protein biomarkers specific for each cell type listed. This table was generated based on published<br>histopathologic nomenclature, as well as published literature on cell-type specific biomarkers. Most of the markers<br>listed are observed in more than one study or orthogonally validated. Note that these are predicted markers and a<br>single marker to annotate a cell type is not likely sufficient or specific. Where more refined cell types are not<br>available in the ontologies, the closest general term is used. For example, there are likely multiple types of small<br>intestine stromal cells; however, further characterization is needed to distinguish between these cell types. Where<br>cells of similar type occur in different locations, the closest and highest level of resolution available is used. For<br>example, enterocytes occur in multiple different contexts within the small intestine, including the duodenum, jejunum,<br>and ileum.<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/hbm596.sbgh.587
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Peripheral Nervous System, v1.2

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to capture<br>the nested peripheral-nervous-system structure of anatomical human body parts, the typology of cells, and biomarkers<br>used to identify cell types. The tables are authored and reviewed by an international team of experts. The peripheral<br>nervous system (PNS) ASCT+B table delineates the hierarchical organization of peripheral nerves, including cranial and<br>spinal nerves, and their associated ganglia. It maps various cell types such as Schwann cells and satellite glial<br>cells, along with relevant biomarkers, providing a comprehensive framework for understanding the PNS's structure and<br>function.
DOI: 10.48539/hbm479.xpml.677
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Mouth, v1.0

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to capture<br>the nested anatomical structure of human body parts, the typology of cells, and biomarkers used to identify cell<br>types. The tables are authored and reviewed by an international team of experts. The Mouth ASCT+B table includes<br>detailed anatomical structures such as the gingiva, tongue, buccal mucosa, hard palate, floor of mouth, and major<br>salivary ducts, along with associated epithelial, stromal, vascular, immune, and neural cell types. This comprehensive<br>mapping supports research into oral epithelial differentiation, mucosal immune regulation, salivary gland biology, and<br>related medical conditions such as periodontitis, Sjögren’s disease, and head and neck cancer.
DOI: 10.48539/hbm963.tbfp.428
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Bone Marrow and Blood/Pelvis, 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: 10.48539/hbm622.bdxn.589
title: Anatomical Structures, Cell Types and Biomarkers (ASCT+B) Tables to 3D Reference Object Library Crosswalk, v1.4

description: This lookup table maps [Anatomical Structures, Cell Types and Biomarkers (ASCT+B)<br>Table](https://humanatlas.io/asctb-tables) terms to anatomical structure terms used in the [3D Reference Object<br>Library](https://humanatlas.io/3d-reference-library).
DOI: 10.48539/hbm395.lxkx.734
title: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX, v1.0

description: The OMAP Pancreas panel was designed for CODEX (CO Detection by IndEXing) imaging of Formalin-Fixed Paraffin-Embedded<br>(FFPE) human pancreas samples.