cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.48577/jpl.kij821
title: OPERA 2024 SCEC Community Models for Seismic Hazard Assessments

description: No abstract available.
DOI: 10.15468/dl.7nyhp3
title: Occurrence Download

description: A dataset containing 6492 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1822-2020",
 "HasCoordinate is true",
 "TaxonKey is Erigeron strigosus Muhl. ex Willd.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6492 records from 131 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012418-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dc4sqt
title: Occurrence Download

description: A dataset containing 700 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "Country is Cocos (Keeling) Islands",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 700 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009387-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tab6th
title: Occurrence Download

description: A dataset containing 163 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Anastomus oscitans (Boddaert, 1783)",
 "Country is Thailand",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "Year is 2012"
 ]
}

 The dataset includes 163 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083435-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zva4up
title: Occurrence Download

description: A dataset containing 6179503 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Living Specimen",
 "BasisOfRecord is Unknown evidence"
 ]
 },
 {
 "or" : [
 "Continent is Europe",
 "Continent is Africa",
 "Continent is Oceania",
 "Continent is Asia"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Muscicapidae"
 ]
}

 The dataset includes 6179503 records from 152 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028526-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4msrwo
title: Occurrence Download

description: A dataset containing 6295 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "TaxonKey is Helianthemum violaceum (Cav.) Pers."
 ]
}

 The dataset includes 6295 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009391-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3njnuf
title: Occurrence Download

description: A dataset containing 1410 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-102.5354 18.4671,-99.40649 18.4004,-99.42407 21.4408,-102.5354 21.4408,-102.5354 18.4671))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Elanus leucurus (Vieillot, 1818)"
 ]
}

 The dataset includes 1410 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083453-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48577/jpl.5t4ayb
title: Reconstruction of Sea Surface Temperature Under Clouds Using Masked Autoencoders

description: This paper presents a methodology for reconstructing high- spatial-resolution sea surface temperature (SST) fields under cloud cover using masked autoencoders (MAE). The MAE model is trained on high-resolution SST maps from the ECCO forward simulation, LLC4320, and reconstructs missing data by masking out a portion of the input pixels. The impact of masking ratios and methods, as well as network architecture variations, is investigated. Preliminary results demonstrate the promise of the MAE approach in reconstructing SST un- der cloud cover. Applying this methodology to SST data with significant cloud contamination can enhance dataset quality, uncovering details hidden by clouds and expanding the use of high-resolution SST images.
DOI: 10.15468/dl.albvlk
title: Occurrence Download

description: A dataset containing 2330125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "Year 2017-2020",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 2330125 records from 120 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009380-200127171203522/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dxe86m
title: Occurrence Download

description: A dataset containing 389 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-180 -11,180 -11,180 -9,-180 -9,-180 -11))",
 "HasCoordinate is true",
 "TaxonKey is Cycadopsida",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 389 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031655-190918142434337/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tkzm8g
title: Occurrence Download

description: A dataset containing 617 species occurrences available in GBIF matching the query:
{
 "or" : [
 "TaxonKey is Didymodon giganteus (Funck) Jur.",
 "TaxonKey is Didymodon japonicus (Broth.) K.Saito",
 "TaxonKey is Didymodon michiganensis (Steere) K.Saito"
 ]
}

 The dataset includes 617 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028542-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5064/f6mfn8d4
title: Data for: Exposure to trade and postcolonial divergence on the island of Hispaniola
title: Hispaniola Archival Research

description: &lt;h3&gt;Data Overview&lt;/h3&gt;

These documents focus on political, economic and social development processes in Haiti and the Dominican Republic during the post-colonial period. In particular, they provide a window into the diverging trajectories of trade integration, industrialization, and long-run economic development. They were collected in public and non-profit archives located in Santo Domingo, DR and Port-au-Prince, Haiti. They were captured primarily using a digital camera placed on a tripod over a period beginning in the summer of 2009 through the summer of 2012.
DOI: 10.48539/hbm975.bbtf.393
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Pancreas, 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/hbm948.xlmz.833
title: OMAP-6  Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX, v1.2

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/hbm375.bjgd.993
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Thymus, 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: 10.48539/hbm847.dnhp.222
title: OMAP-6  Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX, v1.3

description: The OMAP Pancreas panel was designed for CODEX (CO Detection by IndEXing) imaging of Formalin-Fixed Paraffin-Embedded<br>(FFPE) human pancreas samples. Following antigen retrieval (citrate buffer pH=6, heating at high pressure 114-121°C<br>for 20 minutes), tissue autofluorescence was reduced using a photobleaching protocol (Du Z. et al, 2019, modified by<br>Derek Oldrige). CODEX is based on DNA-conjugated antibodies allowing the image acquisition of 3 antibodies per cycle<br>and removal of complementary fluorescently labeled DNA probes afterwards Goltsev, Y. et al, 2018. Cell junction<br>markers (E-cadherin,Beta-catenin) and nuclear marker Hoechst are used for cell segmentation. The resulting OMAP<br>contains 12 antibodies and provides a spatial context for most relevant anatomical structures and cell types in the<br>pancreas including pancreatic cells (alpha, beta, gamma, delta), ductal cells, endothelial cells,smooth muscle and<br>mesenchymal cells present in the ASCT-B pancreas table, v1.0. Acinar and epsilon cells are not targeted in the<br>existing panel due to the complexity of finding suitable and stable antibodies. A representative dataset using this<br>OMAP can be found here: https://zenodo.org/record/7742474. An antibody directed against pancreatic polypeptide (PPY)<br>was originally included in OMAP-5 v1.0 and v1.1, but was removed due to inconsistent labeling.
DOI: 10.15468/dl.xgpjyz
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Angostura quinquefolia)"
 ]
}

 The dataset includes 27 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053637-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm397.phbh.975
title: OMAP-16 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Lung with CODEX, v1.1

description: OMAP-16 was developed for Multiplexed Immunofluorescent (MxIF) imaging of formalin-fixed paraffin-embedded (FFPE)<br>human lung sections using the Akoya Biosciences Phenocycler-Fusion platform (Purkerson, Pryhuber, Colon, et al. 2023).<br>This panel includes 34 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. OMAP-16<br>provides spatial context for airway, vasculature, and alveolar features, and detects 35 of 72 epithelial, endothelial,<br>and immune cell types listed in the ASCT+B Lung v1.2 table (Pryhuber 2021). It does not capture Cap1 and Cap2<br>endothelial cells, eosinophils/basophils, fibroblasts/pericytes, neuroendocrine cells, ciliated cells, chondrocytes,<br>or NK cells, though antibody barcode conjugates for these are under development. Cell segmentation was performed using<br>the StarDist extension in QuPATH 0.3.2, based on DAPI-stained nuclei. Vascular smooth muscle and airway epithelial<br>structures were annotated using thresholded ACTA2 and PanCK signals with the Pixel Classifier in QuPATH, with<br>resulting object data exported as GeoJSON files. Antigen retrieval was carried out using AR9 Buffer (Akoya<br>Biosciences) at 110°C for 20 minutes. Barcode-conjugated antibodies were sourced from Akoya Biosciences or created<br>through custom conjugation using their antibody conjugation kit (Cat# 232195). For optimal preservation of structural<br>features, antibodies targeting extracellular matrix and vascular smooth muscle should be imaged early (within the<br>first five imaging cycles). The antibody validation protocol and full imaging workflow are documented in the<br>referenced protocols.<br><br>**Bibliography:**<br><br>* Pryhuber, Gloria. 2021. “Lung (v1.2) Graph Data, v1.2.” https://lod.humanatlas.io/asct-b/lung/v1.2/.<br>* Purkerson, Jeffrey, Gloria S. Pryhuber, Luis Colon, and Heidie Huyck. 2023. “813.1 Multiplexed Immunofluorescence Phenocycler-Fusion® Imaging of FFPE Lung Sections.” https://www.protocols.io/view/813-1-multiplexed-immunofluorescence-phenocycler-f-c4f5ytq6.<br>* Purkerson, Jeffrey, Gloria S. Pryhuber, Heidie Huyck, and Gail Deutsch. 2023. “812.1 Lung FFPE OMAP Multiplexed Immunofluorescence Phenocycler-Fusion® Antibody Validation Protocol.” https://www.protocols.io/view/812-1-lung-ffpe-omap-multiplexed-immunofluorescenc-c32ayqae.
DOI: 10.48539/hbm493.tbms.423
title: Peripheral Nervous System Organ 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 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.The BodySubPart<br>structure is contained within the anatomical structure listed in the BodyPart column. The BodyPart is typically an<br>organ or organ system. IDs are provided for the Nerve, BodySubPart, BodySubPartSequence, BodyPart, FTU, and Angiosome<br>columns to enable linkage to other datasets and ontologies.Version 1.1 adds support for the pelvis, abdomen, back, and<br>lower limb. NOTE: In this version 1.0 crosswalk file, there is no BodySubPartSequence, FTU or Angiosome information.<br>These are placeholders for future versions of this crosswalk.
DOI: 10.15468/dl.rxbbrg
title: Occurrence Download

description: A dataset containing 19085 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Información florística del Proyecto Mapa de Vegetación para la Clasificación de Ecosistemas del Ecuador Continental"
 ]
}

 The dataset includes 19085 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053638-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm287.tjzd.872
title: 3D Reference Organ for Skin, Female, v1.0

description: [This reference organ](https://humanatlas.io/3d-reference-library) was created with the Open Source modelling tool<br>MakeHuman; screenshots of Visible Human Female provided by the National Library of Medicine were used to model<br>dimensions. The head and neck regions were replaced with custom models and the bodies were further adjusted using<br>Pixelogic Zbrush.
DOI: 10.48539/hbm972.whpw.455
title: OMAP-7 Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Lung with Cell DIVE, v1.1

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.
DOI: 10.15468/dl.8v7evd
title: Occurrence Download

description: A dataset containing 436 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pereskia bahiensis"
 ]
}

 The dataset includes 436 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053639-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6cgncb
title: Occurrence Download

description: A dataset containing 1136 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pereskia grandifolia"
 ]
}

 The dataset includes 1136 records from 179 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053640-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm872.rnsg.734
title: OMAP-14: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Kidney with CyCIF, v1.0

description: OMAP-14 was designed for CyCIF imaging of unfixed frozen human kidney samples<br>(https://dx.doi.org/10.17504/protocols.io.81wgb1m3yvpk/v3). The panel contains 17 antibodies, 1 lectin, and Hoechst<br>33342 for image alignment and nuclear segmentation. The OMAP provides a spatial context for the main anatomical<br>structures and key cell types present in the healthy human kidney. These include markers for podocytes, mesangial and<br>endothelial cells, glomerular basement membrane, mesangial matrix in glomeruli, endothelial and vascular smooth<br>muscle cells in the renal vasculature, renal tubular segments including proximal tubular epithelial cells, loops of<br>Henle (including descending thin limb and thick ascending limb), distal convoluted tubules, connecting segment,<br>cortical and medullary collecting duct principal cells and intercalated cells, myofibroblasts and peritubular<br>extracellular matrix. A polyclonal antibody recognizing Zonula occludens-1 ZO-1, also known as Tight junction<br>protein-1, antibodies, which detect tight junctions, were used to segment podocyte plasma membranes as well as<br>basolateral plasma membranes in all tubular epithelium distal to proximal tubules. Lotus Tetragonolobus Lectin (LTL)<br>was used to visualize proximal tubular epithelial cells, collecting duct intercalated cells, and inner medullary<br>collecting duct principal cells. LTL is visualized in the accompanying datasets but not included in the OMAP because<br>it is not an antibody. Additional details on sample preparation (https://dx.doi.org/10.17504/protocols.io.bfskjncw)<br>and custom conjugation of antibodies (https://dx.doi.org/10.17504/protocols.io.667hhhn) are included in these links.<br>Representative datasets including two tubular segment and one glomerular segmentation 2D CyCIF images, and one<br>glomerular segmentation 3D image have been uploaded here:https://dx.doi.org/10.5281/zenodo.10407946;<br>https://dx.doi.org/10.5281/zenodo.10440320;<br>https://dx.doi.org/10.5281/zenodo.10445538; https://dx.doi.org/10.5281/zenodo.10445538;<br>https://dx.doi.org/10.5281/zenodo.10447488 ; https://dx.doi.org/10.5281/zenodo.10445551.
DOI: 10.15468/dl.tgskm6
title: Occurrence Download

description: A dataset containing 20980 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Populus balsamifera"
 ]
}

 The dataset includes 20980 records from 470 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053641-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm568.vjbk.732
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Brain, v1.4

description: This is a major update of the CT+B component of the table that extends it from well-curated high-resolution cell types<br>in a single small brain region (DOI: 10.1038/s41586-021-03465-8), to also include a first draft of cell types across<br>the entire human brain (DOI: 10.1101/2022.10.12.511898). There are no changes to the AS part of the table, EXCEPT<br>adding the appropriate reference (DOI: 10.1002/cne.24080) in each row of the table corresponding to anatomic<br>structures. Similarly, there are no changes to rows relating to cell types from v1.3 of this table, EXCEPT adding<br>“Human - Motor Cortex” in the “CT/1/NOTES” slot to distinguish these cell types from the newly added whole brain atlas<br>types described in detail below. In addition, Kimberly Siletti has replaced Raymond Sanchez as an author of this<br>table, as the updated CT components represent work that she led and participated in converting to this format.
DOI: 10.15468/dl.7yhxcp
title: Occurrence Download

description: A dataset listing the 488 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-0.08251 41.09044,0.19083 41.09044,0.19083 41.23449,-0.08251 41.23449,-0.08251 41.09044))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset's 488 records were derived from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053617-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm877.ztnj.972
title: cell type annotations for CellTypist, v1.1

description: This crosswalk maps the cell type annotations from CellTypist (Xu et al. 2023; Domínguez Conde et al. 2022) to the<br>Cell Ontology Version IRI: http://purl.obolibrary.org/obo/cl/releases/2025-04-10/cl.owl. More information on<br>CellTypist is available at https://www.celltypist.org/.<br><br>The Human Reference Atlas regularly adds new cell types to Cell Ontology; an overview and current numbers are<br>available under "Ontologies Extended" at https://apps.humanatlas.io/dashboard/data. <br><br>**Bibliography:**<br><br>* Domínguez Conde, C., C. Xu, L. B. Jarvis, D. B. Rainbow, S. B. Wells, T. Gomes, S. K. Howlett, et al. 2022. “Cross-Tissue Immune Cell Analysis Reveals Tissue-Specific Features in Humans.” *Science* 376 (6594): eabl5197. https://doi.org/10.1126/science.abl5197.<br>* Xu, Chuan, Martin Prete, Simone Webb, Laura Jardine, Benjamin J. Stewart, Regina Hoo, Peng He, Kerstin B. Meyer, and Sarah A. Teichmann. 2023. “Automatic Cell-Type Harmonization and Integration across Human Cell Atlas Datasets.” *Cell* 186 (26): 5876-5891.e20. https://doi.org/10.1016/j.cell.2023.11.026.
DOI: 10.48539/hbm433.mcbl.623
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Knee, 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.