cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48539/hbm848.xmnh.635
title: OMAP-7 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Lung with Cell DIVE, v1.3

description: OMAP-7 was designed for Cell DIVE imaging of Formalin-Fixed Paraffin-Embedded (FFPE) lung tissue. Cell DIVE enables<br>highly multiplexed single cell analysis using antibody-based imaging (Gerdes, MJ. et al, 2013). The tissue slides were<br>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 30 antibodies, 4 of which are used for cell<br>segmentation (Na/K ATPase, Cytokeratin, Cadherin, and S6) and the nuclear marker DAPI for image alignment and nuclear<br>segmentation. This OMAP provides a spatial context for key cell types in the[ASCT+B lung table<br>v1.1](https://doi.org/10.48539/HBM323.SGDF.945). Additionally, the inclusion of protein biomarkers such as AGTR1,<br>Cathepsin L, TMPRSS2, ICAM-1, and CD55 allow characterization of proteins relevant to SARS-CoV-2 infection and<br>profiling of the renin-angiotensin system (RAS) that may play a role in COVID-19 disease. The core and essential<br>protein biomarkers detailed here overlap (~25%) with the panel developed for multiplexed imaging of lung samples<br>established using conventional automated IHC staining for FFPE-material (Dr. Christopher Werlein, an expert lung<br>pathologist). This OMAP does not contain antibodies for typing subsets of fibroblasts, macrophages, or endothelial<br>cells. A representative dataset using this OMAP can be found here: https://zenodo.org/record/7731162#.ZBmz2nbMIuU.
DOI: 10.48539/hbm868.xltm.922
title: OMAP-6  Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX, v1.1

description: The OMAP Pancreas panel was designed for CODEX (CO Detection by IndEXing) imaging of Formalin-Fixed Paraffin-Embedded<br>(FFPE) human pancreas samples.
DOI: 10.48539/hbm874.knmc.899
title: OMAP-9: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Kidney with CODEX, v1.0

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).
DOI: 10.6084/m9.figshare.29949839
title: Appendix "New Possibilities, New Responsibilities: Ethical Challenges and Guidance for Location Tracking Device-based Research in Supply Chains"

description: Appendix of the paper "New Possibilities, New Responsibilities: Ethical Challenges and Guidance for Location Tracking Device-based Research in Supply Chains"
DOI: 10.6084/m9.figshare.29949839.v1
title: Appendix "New Possibilities, New Responsibilities: Ethical Challenges and Guidance for Location Tracking Device-based Research in Supply Chains"

description: Appendix of the paper "New Possibilities, New Responsibilities: Ethical Challenges and Guidance for Location Tracking Device-based Research in Supply Chains"
DOI: 10.48539/hbm846.xxgg.898
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Bone Marrow/Pelvis, v1.3

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to capture<br>the nested bonemarrow-pelvis 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 bone marrow table<br>reflects sampling from the iliac crest of the ilium bone within the bony pelvis. Minor updates in version 1.4<br>ensured that all cell types were mapped to the Cell Ontology (CL), and genes and proteins were linked to the Human<br>Gene Nomenclature Committee (HGNC) identifiers.
DOI: 10.48539/hbm467.lrkz.884
title: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Skin with Cell DIVE, v1.0

description: The OMAP Skin panel was designed for Cell DIVETM multiplexed imaging of formalin-fixed paraffin-embedded (FFPE) human<br>skin. The panel contains 18 antibodies and the nuclear marker DAPI for image registration and nuclear<br>segmentation. Antigens were detected using either primary antibodies with fluorophore-labelled secondary antibodies<br>or fluorescent dye conjugated antibodies. This OMAP provides a spatial context for most anatomical structures and cell<br>types present in the [ASCT+B skin table, v1.1](https://doi.org/10.48539/HBM423.RTRR.746). Additionally, the inclusion<br>of protein biomarkers DDB2 and p53 allow for profiling of skin damage and aging effects. The panel was designed to get<br>a broad representation of cell types found in the skin and in the future will be expanded to include dermal dendritic<br>cell (DC) markers (e.g. Langerin, CD11c).
DOI: 10.15468/dl.pc24yk
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Astyanax salvatoris)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053631-250827131500795/datasets/export for details.
DOI: 10.15468/dl.tdekvp
title: Occurrence Download

description: A dataset containing 2167 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Haliaeetus albicilla)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "Country is Iceland",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2167 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053632-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm447.dqmq.693
title: OMAP-4  Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Skin with Cell DIVE, v1.4

description: OMAP-4 was designed for Cell DIVE multiplexed imaging of human formalin fixed paraffin embedded (FFPE) skin. Cell DIVE<br>enables highly multiplexed single cell analysis using antibody-based imaging (Gerdes et al. 2013). The tissue slides<br>were prepared with a two-step antigen retrieval process (pH 6 and pH 9) as described here: (McDonough et al. 2020).<br>Antigens were detected using either primary antibodies with fluorophore-labeled secondaries or fluorescent dye<br>conjugated antibodies. The protocol can be found here: (Pryhuber et al. 2022). The panel contains 18 antibodies and<br>the nuclear marker DAPI for image registration and nuclear segmentation. This OMAP provides a spatial context for most<br>anatomical structures and cell types present in the ASCT+B skin table, v1.1 (Ginty, Ho, and Sunshine 2021).<br>Keratinocyte populations can be identified based on their spatial location, distinct morphology and, in the case of<br>corneocytes, absence of nuclei. Additionally, the inclusion of protein biomarkers DDB2 and p53 allow profiling of skin<br>damage and aging effects. This panel covers diverse cell types in the skin and will be further developed to include<br>markers for dermal dendritic cells (DCs) such as Langerin and CD11c. This panel does not include markers targeting<br>several immune cell subsets including Langerhans cells, mast cells, and gamma delta T cells. Representative datasets<br>created using this OMAP are publicly available on the HuBMAP data portal (Quardokus et al. 2023). This revised v1.4<br>OMAP corrects CD3D to CD3E.<br><br>**Bibliography:**<br><br>* Gerdes, Michael J., Christopher J. Sevinsky, Anup Sood, Sudeshna Adak, Musodiq O. Bello, Alexander Bordwell, Ali Can, et al. 2013. “Highly Multiplexed Single-Cell Analysis of Formalin-Fixed, Paraffin-Embedded Cancer Tissue.” *Proceedings of the National Academy of Sciences* 110 (29): 11982–87. https://doi.org/10.1073/pnas.1300136110.<br>* Ginty, Fiona, Jonhan Ho, and Joel Sunshine. 2021. “Skin (v1.1) Graph Data, v1.1.” https://lod.humanatlas.io/asct-b/skin/v1.1/.<br>* McDonough, Liz, Chrystal Chadwick, Fiona Ginty, Christine Surrette, and Anup Sood. 2020. “Cell DIVETM Platform | Slide Clearing and Antigen Retrieval,” December. https://doi.org/10.17504/protocols.io.bpwumpew.<br>* Pryhuber, Gloria, gail.deutsch, Christine Surrette, Lisa Lowery, heidie_huyck, and Cory Poole. 2022. “HuBMAP | GE/URMC/SCH Cell DIVETM Modality Overview,” February. https://doi.org/10.17504/protocols.io.b4kgqutw.<br>* Quardokus, Ellen M., Diane C. Saunders, Elizabeth McDonough, John W. Hickey, Christopher Werlein, Christine Surrette, Presha Rajbhandari, et al. 2023. “Publication Page Organ Mapping Antibody Panels: A Community Resource for Standardized Multiplexed Tissue Imaging.” *HuBMAP Data Portal*. July 19, 2023. https://portal.hubmapconsortium.org/browse/publication/e8338966c69e759157d6c6ad24847989.
DOI: 10.48539/hbm446.wglg.755
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Placenta Full Term, 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. The Placenta ASCT+B<br>table represents terms related to the full term human placenta. These include both macroscopic and microscopic<br>anatomical structures, major cell types, and protein and lipid biomarkers specific for each cell type listed. This<br>table was generated based on published placental histopathologic nomenclature, as well as published literature on<br>cell-type specific biomarkers. Most of the markers listed are observed in more than 1 study or orthogonally<br>validated. Note that these are predicted markers and a single marker to annotate a cell type is not likely sufficient<br>or specific. Where more refined cell types are not available in the ontologies, the closest general term is used. For<br>example, there are likely multiple types of placental stromal cells; however, further characterization is needed to<br>distinguish between these cell types. Where cells of similar type occur in different locations, the closest and<br>highest level of resolution available is used. For example, vascular endothelial cells (CL0000071) occur in multiple<br>different contexts within the placenta, including the umbilical vessels, chorionic plate vessels, chorionic stem<br>villous vessels and capillaries, and decidual vessels; similarly, vascular smooth muscle cells (CL0000359) occur in<br>umbilical vessels, chorionic plate vessels, and chorionic stem villous vessels.
DOI: 10.48539/hbm727.wbbf.376
title: Blood Vasculature Organ Crosswalk, v1.2

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 from vessels in the blood<br>vasculature ASCT+B table to anatomical structures in other organ ASCT+B tables. The Relationship column indicates<br>whether the vessel is “part_of”, “overlaps”, “supplies”, “drains”, “directly_supplies_drains”, “located_in”, or<br>“connected_to” the anatomical structure in the BodySubPart column.<br><br>A vessel can relate to more than one anatomical structure; and, those relationships can occur in a particular order.<br>For example, the vessel can pass through several structures along its length. The BodyPartSequence column indicates<br>the sequence of those structures, from the proximal to distal end of the vessel. <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. The FTU column indicates if the vessel is part of a functional tissue unit (the<br>smallest tissue organization that performs a unique physiologic function in an organ). The angiosome column indicates<br>if the vessel is associated with an angiosome (a region of muscle, bone, and skin supplied by a main artery).<br><br>IDs are provided for the Vessel, BodySubPart, BodySubPartSequence, BodyPart, FTU, and Angiosome columns to enable<br>linkage to other datasets and ontologies.
DOI: 10.60863/sf/1tdman
title: Policing Integrity: A Quasi-Experimental Evaluation of Varied Lockdown Browser Application Effects on Student Performance

description: The purpose of the research was to effectively collect and evaluate data for empirical evidence on the effects of a lockdown browser with video monitoring on student performance within a longitudinal trend sample of students enrolled over six semesters in a junior-level social science research methods course at a state university. The study builds on previous findings by evaluating the impact of proctoring tools based not only on their presence or absence, but also on the timing of their use within the semester. By doing so, it aims to provide nuanced insights into how digital surveillance tools affect performance, perceptions, and ethical development in higher education. The results indicate significant effects on student performance by the timing and extent of lockdown browser and monitor application in relation to test scores and completion times. Yet, they are offset by webcam observations of student behaviors. Implications for educational integrity principles and processes are evident.
DOI: 10.48539/hbm957.ckrv.896
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Blood/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/hbm835.wcgp.479
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Prostate, 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/hbm228.pzgr.344
title: Anatomical Structures, Cell Types and Biomarkers (ASCT+B) Tables to 3D Reference Object Library Crosswalk, v1.8

description: This lookup table associates anatomical structure terms used in the 3D Reference Object Library<br>(https://humanatlas.io/3d-reference-library) to Anatomical Structures, Cell Types and Biomarkers (ASCT+B) Table<br>(https://humanatlas.io/asctb-tables) (Börner et al. 2021) via ontology IDs from Uberon (Mungall et al. 2012) and<br>Foundational Model of Anatomy (Golbreich, Grosjean, and Darmoni 2013; Rosse and Mejino 2003).<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.<br>* Golbreich, Christine, Julien Grosjean, and Stefan Jacques Darmoni. 2013. “The Foundational Model of Anatomy in OWL 2 and Its Use.” *Artificial Intelligence in Medicine* 57 (2): 119–32. https://doi.org/10.1016/j.artmed.2012.11.002.<br>* Rosse, Cornelius, and José L.V. Mejino. 2003. “A Reference Ontology for Biomedical Informatics: The Foundational Model of Anatomy.” *Journal of Biomedical Informatics* 36 (6): 478–500. https://doi.org/10.1016/j.jbi.2003.11.007.<br>* Mungall, C. J., C. Torniai, G. V. Gkoutos, S. E. Lewis, and M. A. Haendel. 2012. “Uberon, an Integrative Multi-Species Anatomy Ontology.” *Genome Biol* 13 (1): R5. https://doi.org/10.1186/gb-2012-13-1-r5.
DOI: 10.48539/hbm469.lhtb.255
title: OMAP-19: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Palatine Tonsil with IBEX, v1.0

description: OMAP-19 was designed for IBEX (Iterative Bleaching Extends multi-pleXity) imaging of human FFPE tonsil samples<br>sectioned onto glass slides (https://doi.org/10.1038/s41596-021-00644-9). The panel consists of 6 cycles of 20 primary<br>antibodies, 5 secondary antibodies, and the nuclear label Hoechst for image alignment and nuclear segmentation. This<br>OMAP provides a spatial context for 10 anatomical structures and at least 16 cell types present in the ASCT+B tonsil<br>table. OMAP-19 was designed to examine myeloid subsets (CD11b, CD11c, CD14, CD15, HLA-DR) and angiogenesis (VEGF-A and<br>VEGF-C) in human ovarian cancer biopsies. The human tonsil was used as a positive control for antibody validation and<br>panel development. OMAP-19 has 11 markers in common with the tonsil MICS panel (OMAP-10,<br>https://doi.org/10.48539/HBM663.JJMJ.628); however, there is no overlap between the antibodies used across the tonsil<br>OMAPs. This panel does not allow for visualization of the mantle zone, naive B cells, plasma cells, or cycling B cells<br>enriched in the dark zone of the germinal center. Prior to immunolabeling, antigen retrieval was performed using a<br>pressure cooker (Borg Decloaker BD1000, 110°C for 15 minutes) and a tris-based buffer (pH 9.5). Several custom<br>antibodies were created using commercial labeling kits as indicated in the associated RRID entries for these<br>antibodies (AB_3095771, RRID:AB_3095773, and RRID:AB_3095774). More details on the antigen retrieval protocol and<br>step-by-step application of antibodies can be found on the [IBEX Imaging Community<br>site](https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/). A representative dataset and associated<br>channel metadata has been uploaded to Zenodo (https://zenodo.org/records/11222093).
DOI: 10.48539/hbm245.pwlj.489
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Trachea, v1.0

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to capture<br>the nested trachea 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 Trachea ASCT+B table v1.0<br>was developed following the revisions of the Lung ASCT+B tables (v1.2–1.3), during which the Trachea and Main Bronchus<br>were delineated into separate tables. This table focuses on the anatomical structures, cell types, and biomarkers<br>specific to the human trachea. With the assistance of Joshua Fortriede, Ellen Quardokus, and Aleix Puig Barbe (EBI),<br>updates were made to Uberon and the Cell Ontology, including the addition and revision of terms as necessary.<br>Relationships among anatomical structures (AS-AS), anatomical structures and cell types (AS-CT), and among cell types<br>(CT-CT) were corrected and verified. Gene markers were reviewed and updated based on recent single-cell RNA sequencing<br>(scRNAseq) lung cell type references. A description of this Trachea ASCT+B table can be found in "Anatomical<br>Structures, Cell Types, and Biomarkers Tables Plus 3D Reference Organs in Support of a Human Reference Atlas" by<br>(Börner et al. 2021). The database and code used to generate the more simplified view of the Trachea in these ASCT+B<br>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/hbm785.xbpb.444
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Skin, 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: 10.15468/dl.xuqrww
title: Occurrence Download

description: A dataset containing 885 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Main components of radiolarian assemblage at Site 177-1092"
 ]
}

 The dataset includes 885 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053634-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm673.rkqv.672
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Main Bronchus, v1.2
DOI: 10.48539/hbm699.ptnx.744
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Kidney, v1.6

description: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables aim to capture the nested kidney 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 kidney ASCT+B tables are generated from a variety of<br>publicly available human kidney datasets and from data generated by HuBMAP and KPMP consortia. 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. Therefore, these are just a guide; more<br>accurate annotation should be done using the entire set of enriched genes in a cluster. The cell types shown here are<br>at much higher granularity, although general markers for many of the structures are also shown. There is a tradeoff in<br>uncertainty of cell type annotation with higher granularity, and as spatial validation approaches become more robust,<br>we will be accordingly revising these.