cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48539/hbm899.qtjc.265
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Skeleton, 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. This ASCT+B table contains a hierarchical “partonomy” of<br>the human skeleton. The top-level anatomical structure (“AS/1”) is “skeleton” for all structures. The second level<br>(“AS/2”) divides the skeleton into “appendicular skeleton” and “axial skeleton”. The third (“AS/3”) and fourth<br>(“AS/4”) levels further divide the skeleton by body region and sub-region, respectively. The fifth level (“AS/5”)<br>lists individual bones. Finally, the sixth level (“AS/6”) contains bony landmarks and parts of bones. Note that the<br>main purpose of this table is to provide a comprehensive list of bones and their location in the body. Individual<br>bones, bone tissues, and joints might have their own ASCT+B table, which provides more detail about its anatomical<br>structure, cell types, and biomarkers.<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/hbm656.vqrd.249
title: OMAP-1 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Lymph Node with IBEX, v1.4

description: OMAP-1 was designed for IBEX (Iterative Bleaching Extends multi-pleXity) imaging of fixed frozen human lymph nodes<br>(https://doi.org/10.1038/s41596-021-00644-9; https://doi.org/10.1073/pnas.2018488117). The panel contains 39<br>antibodies and the nuclear marker Hoechst 33342 for image alignment and nuclear segmentation. his OMAP provides a<br>spatial context for all anatomical structures and most cell types present in the [ASCT+B lymph node table,<br>v1.1](https://doi.org/10.48539/HBM573.SHCQ.259). Additionally, the inclusion of protein biomarkers BCL2, CD10, CD138,<br>and CD44 allow profiling of lymph node disease states, e.g. follicular lymphoma and metastasis. The core and<br>prioritized OMAP targets detailed here overlap (~50-85%) with panels developed for multiplexed imaging of lymphoid<br>samples using other technologies and sample preparations (https://doi.org/10.7554/eLife.31657,<br>https://doi.org/10.1002/eji.202048891). This OMAP does not contain antibodies for typing pericytes, plasmacytoid<br>dendritic cells, or different T helper lineages (Th1, Th2, Th17). Beyond spatial mapping of healthy human lymph nodes,<br>this OMAP was used to characterize the tissue microenvironment of follicular lymphoma lymph nodes. For this study,<br>object-based cellular segmentation was performed using a convolutional neural network (CNN)-based approach with Mask<br>R-CNN architecture and ResNet-50 as a backbone. As an input three channels were used: Hoechst for nuclei, CD45 as a<br>base membrane, and composite of several other membrane markers (CD138, CD163, CD94, CD69, CD8, CD4). More details and<br>accompanying datasets associated with OMAP-1 can be found here (https://doi.org/10.1101/2022.06.03.494716,<br>https://doi.org/10.5281/zenodo.5244550). Several antibodies required custom conjugation by commercial suppliers or<br>antibody conjugation kits (e.g., AF532, Thermo A20182).
DOI: 10.48539/hbm682.dvwx.968
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Thymus, v1.5

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to capture<br>the nested thymus 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 thymus ASCT+B table provides<br>a comprehensive mapping of the anatomical structures, cell types, and biomarkers associated with the human thymus. It<br>includes detailed information on thymic epithelial cells (TECs), such as cortical (cTECs) and medullary (mTECs)<br>subtypes, which play crucial roles in T cell development and selection. The table also encompasses various stages of<br>thymocyte maturation and associated biomarkers, facilitating a deeper understanding of thymic function and its role in<br>the immune system. A description of this thymus ASCT+B table can be found in ""Anatomical Structures, Cell Types, and<br>Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas"" by Börner et al. 2021. The database<br>and code used to generate the more simplified view of the thymus 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/hbm539.rrdb.894
title: 3D Reference Organ for Pelvis, Female, 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/hbm622.pdvs.333
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Lymph Vasculature, v1.5

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to capture<br>the nested lymph-vasculature 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 lymph vasculature<br>table focuses on major central lymphatic structures. The primary source is *Rouvière H. Anatomie des Lymphatiques de<br>l'Homme. Masson et Cie: Paris, 1932*. This release extends lymphatic structures of the arm and hand. Currently,<br>“lymphatic endothelial cell” and “FLT4 (VEGFR-3)” are the only cell types and biomarkers included in the table.
DOI: 10.48539/hbm257.rsrq.666
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Muscular System, v1.1

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 ASCT+B table contains a hierarchical “partonomy” of<br>the muscular system. The top level anatomical structure (“AS/1”) is “muscular system” for all structures. The second<br>level (“AS/2”) divides the musculature into body regions. The third level (“AS/3”) lists muscle groups; and, the<br>fourth level (“AS/4”) lists individual muscles. Finally, the fifth level (“AS/5”) contains parts of muscles. This<br>version of the muscular system ASCT+B table only contains skeletal muscles. Future versions will add cardiac and<br>smooth muscles. Note that the main purpose of this table is to provide a comprehensive list of muscles and their<br>location in the body. Individual muscles might have their own ASCT+B table, which provides more detail about its<br>anatomical structure, cell types and biomarkers.
DOI: 10.48539/hbm736.pjqv.368
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Small Intestine, 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/hbm954.tgng.395
title: OMAP-9: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Kidney with CODEX, v1.2

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.
DOI: 10.48539/hbm692.wvqx.752
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Bone Marrow/Pelvis, 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/hbm496.mnth.952
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Lung, v1.3

description: This is a revision of the “Single Lung Lobe” table that simplified the ASCT+B table from Lung v1.1, to consider the<br>anatomical and cellular composition of the lower respiratory tract of one lung lobe as representative of the five<br>human lung lobes, reducing table redundancies in structure and cell nomenclature and to improve visualization by the<br>ASCT+B Reporter.
DOI: 10.48539/hbm522.svhm.477
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Fallopian Tube, 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/hbm446.zzzn.837
title: Peripheral Nervous System Organ Crosswalk, v1.0

description: [Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables](https://humanatlas.io/asctb-tables) aim 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 from structures in the<br>peripheral nervous system (PNS) ASCT+B table to anatomical structures in other organ ASCT+B tables. The Relationship<br>column indicates that the nerve “innervates” the anatomical structure in the BodySubPart column.<br><br>The BodySubPart structure is contained within the anatomical structure listed in the BodyPart column. The BodyPart is<br>typically an organ or organ system.<br><br>IDs are provided for the Nerve, BodySubPart, BodySubPartSequence, BodyPart, FTU, and Angiosome columns to enable<br>linkage to other datasets and ontologies.<br><br>NOTE: In this version 1.0 crosswalk file, there is no BodySubPartSequence, FTU or Angiosome information. These are<br>placeholders for future versions of this crosswalk.
DOI: 10.48539/hbm934.njhf.526
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Small Intestine, 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/hbm564.vpjv.699
title: OMAP-28: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based  Imaging of Heart with CODEX, v1.0

description: OMAP-28 was developed for CO-Detection by indEXing (CODEX) imaging using the Akoya Biosciences PhenoCycler system on<br>human formalin fixed paraffin embedded (FFPE) heart samples. Antigen retrieval was performed by heating the samples in<br>Dako Target Retrieval Solution (pH 9) in a high-pressure cooker for 20 minutes. To reduce tissue autofluorescence,<br>slides were treated with a solution of 4.5% hydrogen peroxide (H₂O₂) and 20 mM sodium hydroxide (NaOH) in PBS,<br>followed by photoirradiation using broad-spectrum LED light sources for two 45-minute cycles. Full protocol details<br>are provided in Ahn et al. 2024. The antibody panel includes 38 antibodies and the nuclear marker DAPI for image<br>registration and cell segmentation. Cell membrane markers such as Sodium-Potassium ATPase, CD45, and vimentin, along<br>with DAPI, were used for segmentation and annotation of individual cells. This OMAP provides spatial context for 26<br>anatomical structures and 14 cell types as listed in the ASCT+B Heart table v1.5 (Lin, Halushka, and Boppana 2024). It<br>captures all major cardiac cell types including atrial and ventricular cardiomyocytes, vascular and lymphatic<br>endothelial cells, vascular smooth muscle cells, pericytes, lymphocytes, macrophages, fibroblasts, adipocytes,<br>mesothelial cells, and Schwann cells. Markers for specialized pacemaking regions (sinoatrial and atrioventricular<br>nodes) are also included. Although subtypes of immune cells and cell states are not fully represented, future updates<br>may expand on these components.<br><br>**Bibliography:**<br><br>* Ahn, Kyung J., Shovik Bandyopadhyay, Anusha Thadi, and Kai Tan. 2024. “Phenocycler-Fusion Staining Protocol For FFPE Tissue,” January. https://www.protocols.io/view/phenocycler-fusion-staining-protocol-for-ffpe-tiss-c8cyzsxw.<br>* Lin, Shin, Marc Halushka, and Avinash Boppana. 2024. “Heart (v1.5) Graph Data, v1.5.” https://lod.humanatlas.io/asct-b/heart/v1.5/.
DOI: 10.48539/hbm373.tbkp.375
title: Organ Mapping Antibody Panel (OMAP)  for Multiplexed Antibody-Based Imaging of Kidney with CODEX, v1.0

description: The OMAP kidney panel was designed for CODEX (CO Detection by IndEXing) of fresh frozen human kidney samples. The<br>panel contains 24 antibodies and the nuclear marker Hoechst 33342 or DAPI for image alignment and nuclear<br>segmentation. This OMAP provides a spatial context for all anatomical structures and most cell types present in the<br>[ASCT+B kidney table v1.1](https://doi.org/10.48539/HBM673.ZZDK.622). Additionally, the inclusion of protein<br>biomarkers tryptase and MARCKS allow profiling of different regions in glomeruli that are often affected by disease<br>as well as several immune cell markers that are indicative of health. The core and essential protein biomarkers<br>detailed here overlap with panels developed for multiplexed imaging of kidney samples using other technologies, such<br>as cyTOF and cyclic multiplexed immunofluorescence.
DOI: 10.48539/hbm668.jvlm.333
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Liver, v1.4

description: ​Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables aim to capture the nested liver structure of<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 Liver ASCT+B table includes detailed anatomical<br>structures such as the hepatic lobule, portal triad, and central vein, along with associated cell types like<br>hepatocytes, Kupffer cells, and hepatic stellate cells.This comprehensive mapping supports research into hepatic<br>biology and related medical<br>conditions. <br><br>**Bibliography:** <br><br>* James, Kylie R., Tomas Gomes, Rasa Elmentaite, Nitin Kumar, Emily L. Gulliver, Hamish W. King, Mark D. Stares, et al. 2020. “Distinct Microbial and Immune Niches of the Human Colon.” *Nature Immunology* 21 (3): 343–53. https://doi.org/10.1038/s41590-020-0602-z.<br>* Rodda, Lauren B., Erick Lu, Mariko L. Bennett, Caroline L. Sokol, Xiaoming Wang, Sanjiv A. Luther, Ben A. Barres, Andrew D. Luster, Chun Jimmie Ye, and Jason G. Cyster. 2018. “Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity.” *Immunity* 48 (5): 1014-1028.e6. https://doi.org/10.1016/j.immuni.2018.04.006.<br>* Szabo, Peter A., Hanna Mendes Levitin, Michelle Miron, Mark E. Snyder, Takashi Senda, Jinzhou Yuan, Yim Ling Cheng, et al. 2019. “Single-Cell Transcriptomics of Human T Cells Reveals Tissue and Activation Signatures in Health and Disease.” *Nature Communications* 10 (1): 4706. https://doi.org/10.1038/s41467-019-12464-3. <br>* Willard-Mack, Cynthia L. 2006. “Normal Structure, Function, and Histology of Lymph Nodes.” *Toxicologic Pathology* 34 (5): 409–24. https://doi.org/10.1080/01926230600867727.<br>* Xiang, Menglan, Rubén Adrián Grosso, Akira Takeda, Junliang Pan, Tove Bekkhus, Kevin Brulois, Denis Dermadi, et al. 2020. “A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature.” *Frontiers in Cardiovascular Medicine* 7 (April). https://doi.org/10.3389/fcvm.2020.00052.
DOI: 10.48539/hbm944.clld.594
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Muscular System, 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 ASCT+B table contains a hierarchical “partonomy” of<br>the muscular system. The top level anatomical structure (“AS/1”) is “muscular system” for all structures. The second<br>level (“AS/2”) divides the musculature into body regions. The third level (“AS/3”) lists muscle groups; and, the<br>fourth level (“AS/4”) lists individual muscles. Finally, the fifth level (“AS/5”) contains parts of muscles. This<br>version of the muscular system ASCT+B table only contains skeletal muscles. Future versions will add cardiac and<br>smooth muscles. Note that the main purpose of this table is to provide a comprehensive list of muscles and their<br>location in the body. Individual muscles might have their own ASCT+B table, which provides more detail about its<br>anatomical structure, cell types and biomarkers.
DOI: 10.57745/vbshuo
title: AquaEcOmics meeting: exploring aquatic ecology through omics. March 17-20, 2025. Program and abstracts booklet

description: A meeting to explore aquatic ecosystems biodiversity, functionning and monitoring with eDNA and multi-Omics methods
DOI: 10.48539/hbm325.zpww.358
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Large Intestine, v1.4

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to capture<br>the nested large-intestine 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 Large Intestine<br>ASCT+B table includes detailed anatomical structures such as the cecum, ascending colon, transverse colon, descending<br>colon, sigmoid colon, rectum, and anal canal. Associated cell types, including various epithelial and immune cells,<br>are mapped alongside relevant biomarkers. This comprehensive mapping supports research into gastrointestinal biology<br>and related medical conditions.
DOI: 10.5281/zenodo.17096249
title: Towards constraining ocean estimates in ice-covered regions using sea level altimetry data

description: This folder contains data generated for the manuscript "Towards constraining ocean estimates in ice-covered regions using sea level altimetry data". It contains the following datasets:

[1] lat_Arc_IS2grids.npy, lon_Arc_IS2grids.npy, lat_Ant_IS2grids.npy, lon_Ant_IS2grids.npy: latitudes and longitudes for the sea surface data on polar stereographic projection of 25 km resolution.

[2] ssha_ATL21_IS2grid_Ant_toFeb25.npy, ssha_ATL21_IS2grid_Arc_toFeb25.npy: sea surface height anomaly data from ICESat-2 ATL21 productson polar stereographic projection of 25 km resolution.

[3] sla_aviso_Ant_IS2grid.npy, sla_aviso_Arctic_IS2grid.npy: sea level anomaly from AVISO on polar stereographic projection of 25 km resolution.

[4] ssh_ECCO_ISgrids_Ant.npy, ssh_ECCO_ISgrids_Arc.npy: sea surface height from ECCO on polar stereographic projection of 25 km resolution.

[5] pb_GRACE_noglob_ISgrids_Ant_toMay25.npy, pb_GRACE_noglob_ISgrids_Arc_toMay25.npy: GRACE ocean bottom pressure on polar stereographic projection of 25 km resolution.
DOI: 10.48539/hbm637.pwpq.773
title: Anatomical Structures, Cell Types and Biomarkers (ASCT+B) Tables to 2D Functional Tissue Unit (FTU) Reference Object Library Crosswalk, v1.3

description: This lookup table maps [Anatomical Structures, Cell Types and Biomarkers (ASCT+B)<br>Table](https://humanatlas.io/asctb-tables) terms to anatomical structure and cell type terms used in the<br>[CCF-2D-reference-object-library](https://humanatlas.io/2d-ftu-illustrations).
DOI: 10.48539/hbm423.rtrr.746
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Skin, 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: 10.5066/p13nmpsn
title: Campaign GNSS measurements on the Island of Hawaiʻi collected by the Hawaiian Volcano Observatory in 2024

description: This release includes data collected during campaign GNSS surveys at Kīlauea, Mauna Loa, and Hualālai volcanoes on the Island of Hawaiʻi in 2024. It includes data from a total of 63 sites occupied from January 1 to December 31, 2024. For each site, we include its measured raw data in daily files, Receiver INdependent EXchange (RINEX) files for each day, field log sheet(s), and associated metadata information. The authors thank USGS Hawaiian Volcano Observatory staff, volunteers, and collaborators for helping collect these data.
DOI: 10.34847/nkl.d8aa4766
title: Χίος - Σκοποί της Χίου - Γιάννης Βούκουνας, Δημήτρης Κοντός, Πέτρος Μαθιούδης, Σάκης Πιππίδης, Θωμάς Παραδείσης - Συρτός Στην Αγιά Μαρκέλλα