cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18686778
title: Linked collectors and determiners for: Canadian Museum of Nature Palynology Collection.

description: Natural history specimen data linked to collectors and determiners held within, "Canadian Museum of Nature Palynology Collection". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/21a0cb45-f0ec-4901-a868-cd45abe74601 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/21a0cb45-f0ec-4901-a868-cd45abe74601. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.13626168
title: Spatial Transcriptomics data (GeoMx) of midbrain tissue in control and PD subjects

description: he repository includes Spatial Transcriptomic datasets generated by Nanostring GeoMx (Hu WTA) analysis of midbrain unmasked (whole tissue) Regions of Interest from Controls (n=10), Incidental Lewy Body Disease (n=11), early Parkinsons Disease (ePD, n=5) and late Parkinsons Disease (lPD, n=6). A total 515 Regions of Interest were analysed. The raw and processed counts and metadata are provided as an R Seurat object (geomx_vila_unmask.rds). The scripts used for low level data processing are described in https://github.com/zchatt/ASAP-SpatialTranscriptomics/blob/main/geomx/lowlevel/README.md 

Tissue samples from pathologically confirmed asymptomatic stage I-II Lewy body disease, stage IV Lewy body PD (early-PD), stage VI Lewy body PD (late-PD)(Braak, Del Tredici et al. 2003) and controls without the neurological or neuropathological disease were obtained from the Sydney Brain Bank. The study was approved by the University of Sydney Human Research Ethics Committee (2021/845). All cases with PD were levodopa-responsive and fulfilled the UK Brain Bank Clinical Criteria for a diagnosis of clinical PD (Hughes, Ben-Shlomo et al. 1992) with no other neurodegenerative conditions. 

Cells were not extracted. Tissue sections were cut from FFPE blocks of post-mortem human midbrains at 6µm on a rotary microtome (HistoCore MULTICUT, Leica Biosystems) and mounted on Series 2 adhesive microscope slides (Trajan Scientific Medical, AU) for processing for spatial trranscriptomics. To remove the paraffin, slides were incubated in the oven at 60°C for 1hr and then submerged in HistoChoice Clearing Agent (Sigma-Aldrich, H2779) for 2x7mins, followed by rehydration in decreasing ethanol concentrations (100% ethanol for 2x3mins, 95% ethanol for 3mins, 70% ethanol for 3mins) and distilled H2O for 3mins. 

Tissue sections were immunohistochemically stained for tyrosine hydroxylase and Regions of Interest (ROIs) processed following Nanostring GeoMx® Digital Spatial Profiler using the manufacturer’s instructions. Libraries were sequenced on Illumina Novaseq 6000 platform using NovaSeq SP 100 cycle kit (XP workflow, 27-8-8-27).

This research was funded in whole or in part by Aligning Science Across Parkinson’s (ASAP-020505) through the Michael J. Fox Foundation for Parkinson’s Research (MJFF). For the purpose of open access, the author has applied a CC BY 4.0 public copyright license to all Author Accepted Manuscripts arising from this submission.
DOI: 10.5281/zenodo.13626167
title: Spatial Transcriptomics data (GeoMx) of midbrain tissue in control and PD subjects

description: he repository includes Spatial Transcriptomic datasets generated by Nanostring GeoMx (Hu WTA) analysis of midbrain unmasked (whole tissue) Regions of Interest from Controls (n=10), Incidental Lewy Body Disease (n=11), early Parkinsons Disease (ePD, n=5) and late Parkinsons Disease (lPD, n=6). A total 515 Regions of Interest were analysed. The raw and processed counts and metadata are provided as an R Seurat object (geomx_vila_unmask.rds). The scripts used for low level data processing are described in https://github.com/zchatt/ASAP-SpatialTranscriptomics/blob/main/geomx/lowlevel/README.md 

Tissue samples from pathologically confirmed asymptomatic stage I-II Lewy body disease, stage IV Lewy body PD (early-PD), stage VI Lewy body PD (late-PD)(Braak, Del Tredici et al. 2003) and controls without the neurological or neuropathological disease were obtained from the Sydney Brain Bank. The study was approved by the University of Sydney Human Research Ethics Committee (2021/845). All cases with PD were levodopa-responsive and fulfilled the UK Brain Bank Clinical Criteria for a diagnosis of clinical PD (Hughes, Ben-Shlomo et al. 1992) with no other neurodegenerative conditions. 

Cells were not extracted. Tissue sections were cut from FFPE blocks of post-mortem human midbrains at 6µm on a rotary microtome (HistoCore MULTICUT, Leica Biosystems) and mounted on Series 2 adhesive microscope slides (Trajan Scientific Medical, AU) for processing for spatial trranscriptomics. To remove the paraffin, slides were incubated in the oven at 60°C for 1hr and then submerged in HistoChoice Clearing Agent (Sigma-Aldrich, H2779) for 2x7mins, followed by rehydration in decreasing ethanol concentrations (100% ethanol for 2x3mins, 95% ethanol for 3mins, 70% ethanol for 3mins) and distilled H2O for 3mins. 

Tissue sections were immunohistochemically stained for tyrosine hydroxylase and Regions of Interest (ROIs) processed following Nanostring GeoMx® Digital Spatial Profiler using the manufacturer’s instructions. Libraries were sequenced on Illumina Novaseq 6000 platform using NovaSeq SP 100 cycle kit (XP workflow, 27-8-8-27).

This research was funded in whole or in part by Aligning Science Across Parkinson’s (ASAP-020505) through the Michael J. Fox Foundation for Parkinson’s Research (MJFF). For the purpose of open access, the author has applied a CC BY 4.0 public copyright license to all Author Accepted Manuscripts arising from this submission.
DOI: 10.5281/zenodo.18686780
title: Linked collectors and determiners for: A taxonomic review of the genus Azteca (Hymenoptera: Formicidae) in Costa Rica and a global revision of the aurita group..

description: Natural history specimen data linked to collectors and determiners held within, "A taxonomic review of the genus Azteca (Hymenoptera: Formicidae) in Costa Rica and a global revision of the aurita group.". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/21d21894-7003-4d6d-882b-5322ea07968d using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/21d21894-7003-4d6d-882b-5322ea07968d. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583284
title: Linked collectors and determiners for: A taxonomic review of the genus Azteca (Hymenoptera: Formicidae) in Costa Rica and a global revision of the aurita group..

description: Natural history specimen data linked to collectors and determiners held within, "A taxonomic review of the genus Azteca (Hymenoptera: Formicidae) in Costa Rica and a global revision of the aurita group.". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/21d21894-7003-4d6d-882b-5322ea07968d using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/21d21894-7003-4d6d-882b-5322ea07968d. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686779
title: Linked collectors and determiners for: Crustáceos de la Colección de Referencia de Biología Marina de la Universidad del Valle (CERBMcr-UV).

description: Natural history specimen data linked to collectors and determiners held within, "Crustáceos de la Colección de Referencia de Biología Marina de la Universidad del Valle (CERBMcr-UV)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/21b5400a-8810-40f1-b46a-7da00ab6ac70 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/21b5400a-8810-40f1-b46a-7da00ab6ac70. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.10583280
title: Linked collectors and determiners for: Crustáceos de la Colección de Referencia de Biología Marina de la Universidad del Valle (CERBMcr-UV).

description: Natural history specimen data linked to collectors and determiners held within, "Crustáceos de la Colección de Referencia de Biología Marina de la Universidad del Valle (CERBMcr-UV)". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/21b5400a-8810-40f1-b46a-7da00ab6ac70 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/21b5400a-8810-40f1-b46a-7da00ab6ac70. Formatted as a Frictionless Data package.
DOI: 10.15468/dl.vfd8bk
title: Occurrence Download

description: A dataset containing 39187 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Oriolus oriolus"
 ]
}

 The dataset includes 39187 records from 178 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028190-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10583288
title: Linked collectors and determiners for: Data generated from the digitization of CRSN herbarium with support from API project and JRS Biodiversity Foundation.

description: Natural history specimen data linked to collectors and determiners held within, "Data generated from the digitization of CRSN herbarium with support from API project and JRS Biodiversity Foundation". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/22252fe5-d06e-46d3-8f6d-dc1aa57de904 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/22252fe5-d06e-46d3-8f6d-dc1aa57de904. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686781
title: Linked collectors and determiners for: Data generated from the digitization of CRSN herbarium with support from API project and JRS Biodiversity Foundation.

description: Natural history specimen data linked to collectors and determiners held within, "Data generated from the digitization of CRSN herbarium with support from API project and JRS Biodiversity Foundation". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/22252fe5-d06e-46d3-8f6d-dc1aa57de904 using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/22252fe5-d06e-46d3-8f6d-dc1aa57de904. Formatted as a Frictionless Data package.
DOI: 10.5281/zenodo.18686783
title: Linked collectors and determiners for: HERBAM - Herbário da Amazônia Meridional.

description: Natural history specimen data linked to collectors and determiners held within, "HERBAM - Herbário da Amazônia Meridional". Claims or attributions were made on Bionomia by volunteer Scribes, https://bionomia.net/dataset/22331d58-4a7e-40da-b7db-652a4d4d85ed using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, https://gbif.org/dataset/22331d58-4a7e-40da-b7db-652a4d4d85ed. Formatted as a Frictionless Data package.
DOI: 10.15468/dl.g9wkxd
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023136-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.26k92a
title: Occurrence Download

description: A dataset containing 193 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hackelia cusickii (Piper) Brand"
 ]
}

 The dataset includes 193 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0236893-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.67mscl
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003439-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bnnsnv
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-71.11951 -53.85593,-71.07531 -53.83845,-71.07822 -53.83067,-71.10883 -53.81659,-71.1438 -53.83553,-71.11951 -53.85593))",
 "TaxonKey is Mollusca"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034783-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mc1rwe
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is (Table 1) Proportion of Toxoplasma gondii seropositive arctic foxes (Alopex lagopus) by age group and geographic area"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066758-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a7b72f
title: Occurrence Download

description: A dataset containing 17904923 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 17904923 records from 2087 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0093697-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17337531
title: Wintering Anatidae Occurrence Coordinates in South Korea (WGS84, 2022–2024)

description: This dataset combines occurrence coordinates from GBIF and author field observations collected during 2022–2024 in South Korea. Coordinates are provided in WGS84 and have been spatially thinned and privacy-masked (1-km rounding) to protect sensitive sites.
DOI: 10.5281/zenodo.17337530
title: Wintering Anatidae Occurrence Coordinates in South Korea (WGS84, 2022–2024)

description: This dataset combines occurrence coordinates from GBIF and author field observations collected during 2022–2024 in South Korea. Coordinates are provided in WGS84 and have been spatially thinned and privacy-masked (1-km rounding) to protect sensitive sites.
DOI: 10.15468/dl.rmy78f
title: Occurrence Download

description: A dataset containing 583088 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gastropoda)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((-150 30,-120 30,-120 60,-150 60,-150 30))"
 ]
}

 The dataset includes 583088 records from 119 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012492-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15156/bio/sh1375267.10fu
title: SH1375267.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1375271.10fu
title: SH1375271.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1375276.10fu
title: SH1375276.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1375282.10fu
title: SH1375282.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1375283.10fu
title: SH1375283.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1375285.10fu
title: SH1375285.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1375286.10fu
title: SH1375286.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.