cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25549/examiner-c44-112823
title: Mount San Antonio College freshman day, 1952

description: 6 images. Mount San Antonio College freshman day, 28 August 1952. Per Martini (from Denmark); Elna Pantalin (from Finland); Bob Carr -- 17 years (El Monte); Jolene Bufkin -- 17 years (Baldwin Park); Lee Farnsworth (Student Body President); Mrs. Marie T. Mills (Dean of Women). ; Caption slip reads: "Photographer: Mercurio. Date: 1952-08-28. Reporter: Osler. Assignment: Mt. San Antonio College Freshman Day (For Monday). 160: Of the nearly 600 freshman students enrolled for the fall semester at Mt. San Antonio College this year are foreign students Per Martini from Denmark, an exchange student; and Elna Pantalin, an immigrant here from Finland. 161. Part of the orientation to campus life was a cool afternoon dip in the school's plunge. Seen in pix [sic] are Shari Gillmann, San Gabriel; and Carole Kriger of Covina. Both Frosh. 158: Gen. view of portion of new frosh [sic] class as they toured campus. They are seen entering the grounds of the gymnasium. Guide in picture is Richard Kriger, former Mt. SAC student. 11: Engrossed in mediation during entrance exams at Mt. San Antonio College are Freshmen Bob Carr, 17, of El Monte; and Jolene Bufkin, 17, of Baldwin Park. Examination lasted three hours. 12: Student Body President Lee Farnsworth leads new Frosh class in Alma Mater Song, one of the activities of the school function. 159: Registration pix. [sic] with Dean of Women Mrs. Marie T. Mills offering advice to freshman students L-R: Sharon Deards, of Pomona; Sharon Davis, Covina; Ron McIntyre, Covina; and Don Nichols, Covina."
DOI: 10.25582/data.2020-06.2002633/2358349
title: Data for EMSL Project 48666 from June 2020
DOI: 10.15468/dl.2j7yzu
title: Occurrence Download

description: A dataset containing 70276 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-130 40,-110 40,-110 50,-130 50,-130 40))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Rubus L."
 ]
}

 The dataset includes 70276 records from 121 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024516-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbhf9j
title: Occurrence Download

description: A dataset containing 480 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Buddleja nivea Duthie"
 ]
}

 The dataset includes 480 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065468-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xjtw8g
title: Occurrence Download

description: A dataset containing 254784 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Glyceria maxima (Hartm.) Holmb."
 ]
}

 The dataset includes 254784 records from 801 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013480-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm624.pjsr.685
title: Organ Mapping Antibody Panel (OMAP)  for Multiplexed Antibody-Based Imaging of Human Lymph Node with IBEX, v1.1

description: The OMAP Lymph Node panel was designed for IBEX (Iterative Bleaching Extends multi-pleXity) imaging of fixed frozen<br>human lymph nodes. The panel contains 39 antibodies and the nuclear marker Hoechst 33342 for image alignment and<br>nuclear segmentation. This OMAP provides a spatial context for all anatomical structures and most cell types present<br>in the [ASCT+B lymph node table, v1.1](https://doi.org/10.48539/HBM573.SHCQ.259). Additionally, the inclusion of<br>protein biomarkers BCL2 and CD10 and CD138 and CD44 allow profiling of lymph node disease states, e.g. follicular<br>lymphoma malignancy and metastasis, respectively. The core and essential protein biomarkers detailed here overlap<br>(~50-85%) with panels developed for multiplexed imaging of lymphoid samples using other technologies and sample<br>preparations [Kennedy-Darling et al](https://doi.org/10.7554/eLife.31657.001), [Lin et<br>al](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 in situ.
DOI: 10.5281/zenodo.14867816
title: The Blind Men and the Elephant - Mapping Interdisciplinarity in Research on Decentralized Autonomous Organizations
title: Dataset

description: This files provide the python scripts and the datasets employed in the homonimous paper.
DOI: 10.5281/zenodo.17099852
title: The Blind Men and the Elephant - Mapping Interdisciplinarity in Research on Decentralized Autonomous Organizations
title: Dataset

description: This files provide the python scripts and the datasets employed in the homonimous paper.
DOI: 10.15468/dl.awt3bc
title: Occurrence Download

description: A dataset containing 3687 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "OccurrenceStatus is Present",
 "TaxonKey is Melastomataceae"
 ]
}

 The dataset includes 3687 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053603-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48539/hbm869.wzfk.485
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Spinal Cord, 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 Spinal Cord<br>v1.0 table focuses on lumbar spinal cord cell types from [Yadav et al., “A Cellular Taxonomy of the Adult Human<br>Spinal Cord.”): 328-344.e7.](https://doi.org/10.1016/j.neuron.2023.01.00) with a companion [Human Spinal Cord snRNAseq<br>Viewer](https://vmenon.shinyapps.io/humanspinalcord/) which presents a cellular taxonomy of the adult human spinal<br>cord using single-nucleus RNA sequencing with spatial transcriptomics and antibody validation.
DOI: 10.48539/hbm268.zqnv.826
title: OMAP-3 Organ Mapping Antibody Panel (OMAP)  for Multiplexed Antibody-Based Imaging of Kidney with CODEX, v1.3

description: OMAP-3 was designed for CODEX (CO Detection by IndEXing) of fresh frozen human kidney samples<br>(https://doi.org/10.1038/s41596-021-00556-8, https://doi.org/10.1002/eji.202048891). The panel contains 24 antibodies<br>and the nuclear marker DAPI for image alignment and nuclear segmentation. Additional details on tissue preparation,<br>panel design, image analysis, and representative images can be found in accompanying publications<br>(https://doi.org/10.1016/j.kint.2021.08.033, https://doi.org/10.1016/j.xpro.2021.100747). This OMAP provides a spatial<br>context for all anatomical structures and most cell types present in the [ASCT+B kidney table<br>v1.1](https://doi.org/10.48539/HBM673.ZZDK.622). Additionally, the inclusion of tryptase and MARCKS allow profiling of<br>different regions in the glomeruli that are often affected by disease. Several cell types are identified by their<br>morphology, location in the kidney, and expression of Cytokeratin 7. The panel was designed to provide a survey of the<br>cell types found in the kidney and does not allow for granular phenotyping of immune cell populations. However, mast<br>cells, NK cells, T cells, and B cells are broadly classified by several markers included in this OMAP. The core and<br>essential protein biomarkers detailed here overlap (>40%) with a panel developed for multiplexed imaging of kidney<br>samples using imaging mass cytometry (IMC) (10.1172/jci.insight.129477).
DOI: 10.48539/hbm326.vljc.467
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Blood/Pelvis, v1.4

description: The Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables (https://humanatlas.io/asctb-tables) aim to<br>capture the nested blood-pelvis structure of anatomical human body parts, the typology of cells, and biomarkers used<br>to identify cell types. The tables are authored and reviewed by an international team of experts. A description of<br>this Blood Pelvis ASCT+B table can be found in "Anatomical Structures, Cell Types, and Biomarkers Tables Plus 3D<br>Reference Organs in Support of a Human Reference Atlas" by Börner et al. 2021. The database and code used to generate<br>the more simplified view of the Blood Pelvis 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. <br>* Boppana, Avinash, Sujin Lee, Rajeev Malhotra, Marc Halushka, Katherine S. Gustilo, Ellen M. Quardokus, Bruce W. Herr II , Katy Börner, and Griffin M. Weber. 2023. “Anatomical Structures, Cell Types, and Biomarkers of the Healthy Human Blood Vasculature.” *Scientific Data* 10 (1): 452. https://doi.org/10.1038/s41597-023-02018-0.
DOI: 10.5281/zenodo.14578161
title: Brown-Algae.dataset

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

1. Reference Databases:

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

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

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

2. Input FASTA Files:

• brown-algae_dataset.fa:

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

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

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

3. Sample Input Files:

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

 

Purpose:

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

Note: If you wish to use the pipeline with custom datasets, replace the example files in this folder with your own, following the required format.
DOI: 10.5281/zenodo.14578162
title: Brown-Algae.dataset

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

1. Reference Databases:

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

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

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

2. Input FASTA Files:

• brown-algae_dataset.fa:

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

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

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

3. Sample Input Files:

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

 

Purpose:

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

Note: If you wish to use the pipeline with custom datasets, replace the example files in this folder with your own, following the required format.
DOI: 10.48539/hbm262.hrhh.693
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Eye, v1.3

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/hbm842.ttzn.256
title: Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Blood Vasculature, v1.5

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. A description of this blood vasculature ASCT+B table can be<br>found in "Anatomical structures, cell types, and biomarkers of the healthy human blood vasculature" by [Boppana et al.<br>2023](https://doi.org/10.1038/s41597-023-02018-0). The database and code used to generate the more simplified view of<br>the blood vasculature in these ASCT+B tables may be found [here](https://github.com/hubmapconsortium/hra-vccf).
DOI: 10.48539/hbm979.rcxh.454
title: OMAP-12: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Retina with IBEX, v1.0

description: OMAP-12 was designed for IBEX imaging of fixed frozen human retina samples<br>(https://doi.org/10.1038/s41596-021-00644-9; https://doi.org/10.1073/pnas.2018488117). The panel contains 14<br>antibodies, 3 lectins, and DAPI for image alignment and nuclear segmentation. The OMAP provides a spatial context for<br>the main anatomical structures and key cell types present in the healthy human retina including photoreceptors,<br>bipolar cells, ganglion cells, astrocytes, microglia, Muller glia, and retinal vascular endothelium. Broad neuronal<br>classes are imaged, but not separated into fine subpopulations partly due to the lack of antibody reagents (e.g., all<br>amacrine, ganglion cell, and bipolar cell subtypes). Fluorescent lectins PNA, Isolectin B4, and Phalloidin were used<br>to visualize oligosaccharides for typing cell types such as cone photoreceptors, vascular endothelium, and outer<br>limiting membrane, respectively. These reagents are visualized in the accompanying dataset but not included in the<br>OMAP because they are not antibodies. Additional details on sample preparation and imaging can be found here: (doi:<br>10.1038/s41596-021-00644-9) Custom conjugations were performed for several antibodies according to the standard<br>manufacturer protocols. A representative dataset acquired using this OMAP has been uploaded here:<br>https://doi.org/10.5281/zenodo.7777285.
DOI: 10.15468/dl.y56hwh
title: Occurrence Download

description: A dataset containing 491710 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lamium purpureum"
 ]
}

 The dataset includes 491710 records from 2736 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053545-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gnm6g9
title: Occurrence Download

description: A dataset containing 47485 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cerastium tomentosum L."
 ]
}

 The dataset includes 47485 records from 457 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087169-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cxs5sn
title: Occurrence Download

description: A dataset containing 4313394 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Poecile atricapillus (Linnaeus, 1766)"
 ]
}

 The dataset includes 4313394 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032018-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rz3hgv
title: Occurrence Download

description: A dataset containing 245 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Clinopodium mexicanum (Benth.) Govaerts"
 ]
}

 The dataset includes 245 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0179423-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cyah3z
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Leptobrachium leucops Stuart, Rowley, Tran, Le & Hoang, 2011"
 ]
}

 The dataset includes 13 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025126-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.1mjnzs
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriosyce sociabilis (F.Ritter) Katt."
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032019-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bs55kn
title: Occurrence Download

description: A dataset listing the 140 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 {
 "or" : [
 "Country is Brazil",
 "Country is Colombia",
 "Country is Chile",
 "Country is Argentina",
 "Country is Bonaire, Sint Eustatius and Saba"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Stylommatophora",
 "Year 1960-2020"
 ]
}

 The dataset's 140 records were derived from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0169332-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uhm93k
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Campyloneurum poloense (Rosenst.) B.León"
 ]
}

 The dataset includes 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0146047-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f3jkt6
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Hylodes pipilans Canedo & Pombal, 2007"
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025131-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hfdra4
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Horsfieldia kingii (Hook.fil.) Warb.",
 "Year 1950-2021"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0184464-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vmszia
title: Occurrence Download

description: A dataset containing 1812710 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bombycilla cedrorum Vieillot, 1808"
 ]
}

 The dataset includes 1812710 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032020-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.13dhq1
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriosyce subgibbosa subsp. subgibbosa"
 ]
}

 The dataset includes 84 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032020-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hymkeu
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Sclerophrys asmarae (Tandy, Bogart, Largen & Feener, 1982)"
 ]
}

 The dataset includes 58 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025151-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8kkuhp
title: Occurrence Download

description: A dataset containing 14141 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ursus americanus Pallas, 1780"
 ]
}

 The dataset includes 14141 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0184454-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4q5g3z
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Balaustion quinquelobum Rye"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0146048-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2pce2r
title: Occurrence Download

description: A dataset containing 88 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Colección de Poales del Museo Botánico CORD - IMBIV",
 "TaxonKey is Erioneuron pilosum (Buckley) Nash"
 ]
}

 The dataset includes 88 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032020-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.