cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28661591.v1
title: Repeat Modeler analysis for B. pensylvanicus

description: Repeatmasker/RepeatModeler Analysis was performed using Singularity dfam-tetools-latest.sif (from https://github.com/Dfam-consortium/TETools).<b>The repeat database was built with Repeatmasker:</b>BuildDatabase -name pens Bombus_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fastaRepeatModeler -database pens -threads 20 -LTRStruct<b>The Hymenoptera dfam database was fetched with</b>wget "https://www.dfam.org/releases/current/families/FamDB/dfam38-1_full.0.h5.gz"wget "https://www.dfam.org/releases/current/families/FamDB/dfam38-1_full.7.h5.gz"wget "https://www.dfam.org/releases/current/families/FamDB/README.txt"famdb.py -i Libraries families --format fasta_name --include-class-in-name --ancestors --descendants 7458 &gt; Apidae-rm.fa<b>The Apidae repeat library was merged with the B pensylvanicus library output (pens_curated-families.fa) to create the </b><b>Apidae_pens-families-rm.fa</b><b> repeatmasker library.</b><b>RepeatMasker was run:</b>RepeatMasker -lib Apidae_pens-families-rm.fa -pa 16 -gff Bombus_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fasta<b>Subdirectory pens_repeatmodeler_figshare</b> contains repeatmodeler libraries, outputs from repeatmasker (masked genome fasta, gff, summary count tables, etc) and logs.<b>Subdirectory OtherSp </b>contains output summaries (.tbl) files for repeats in other Bombus species and their relevant species-specific RepeatModeler + Apidae dfam custom repeat libraries (.fa). <b>Subdirectory RepeatModelerLibsOnly </b>contains output summaries (.tbl) files for repeats for B. pensylvanicus and other Bombus species using ONLY their relevant species-specific RepeatModeler output as the custom repeat library (.fa) (without the Apidae dfam)<br>
DOI: 10.21233/n39g8p
title: Exchequer Meadow pollen dataset

description: Raw data for the Exchequer Meadow pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.6084/m9.figshare.29831288
title: VHL Apps Survey (Responses).xlsx

description: This dataset includes anonymous survey responses from learners (n = 85) across four user groups who evaluated the usability and educational value of VHL cardiac physiology and anatomy apps.
DOI: 10.6084/m9.figshare.29831288.v1
title: VHL Apps Survey (Responses).xlsx

description: This dataset includes anonymous survey responses from learners (n = 85) across four user groups who evaluated the usability and educational value of VHL cardiac physiology and anatomy apps.
DOI: 10.21233/n35s5d
title: Faith Pond pollen dataset

description: Raw data for the Faith Pond pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.6084/m9.figshare.28661564
title: BUSCO analysis of the B. pensylvanicus genome and protein set (longest isoform)

description: BUSCO v5.8.2 analysis script (busco_figshare.sh) and outputs for protein and genome modes.
DOI: 10.6084/m9.figshare.28661564.v1
title: BUSCO analysis of the B. pensylvanicus genome and protein set (longest isoform)

description: BUSCO v5.8.2 analysis script (busco_figshare.sh) and outputs for protein and genome modes.
DOI: 10.15468/dl.vsx8j3
title: Occurrence Download

description: A dataset containing 5968 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Occurrences of protected species of insects in Italy"
 ]
}

 The dataset includes 5968 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016152-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/n3203s
title: Fallback Lake pollen dataset

description: Raw data for the Fallback Lake pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/n3hb04
title: Lac Faribault loss-on-ignition dataset

description: Raw data for the Lac Faribault loss-on-ignition dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.6084/m9.figshare.28661291
title: B. pensylvanicus genome assembly and annotation

description: <b>Bombus_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fasta</b> Bombus pensylvanicus reference genome assembly (scaffold0001-0019 represent main assembled chromosomes using PacBio long reads and HiC scaffolding). Assembly is also available on NCBI genbank. Scripts used for assembly are taken from https://doi.org/10.15482/USDA.ADC/25762431.v1; SIM, SHEINA (2024). Bombus huntii genome assembly scripts. Ag Data Commons. Workflow. https://doi.org/10.15482/USDA.ADC/25762431.v1)<b>Bomb</b><b>us_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fasta</b><b>.fai</b>: genome index<b>mtDNA_scaffold0168 subdirectory: </b>Contains the fasta sequence and gff annotation for scaffold0168 which was identified from the MitoHiFi v2 workflow (https://github.com/marcelauliano/MitoHiFi) as the probable mitochondrial genome and removed from the main assembly above and the NCBI genome submission.<b>non_arth_scaffolds subdirectory: </b>Contains the FASTA sequence and a CSV of taxonomic identifiers to the family level of scaffolds removed from the final assembly during the BlobTools QC step.<b>iyBomPens_scaff_egapx_RNA_out</b>: directory containing EGAPx annotation information. Runs performed by Sheina Sim @ U.S. Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI using the external version of NCBI Eukaryotic Genome Annotation Pipeline (EGAPx 0.3.1-alpha).annotation_data.cmt: summary of annotation runrun_params.yaml: specific egap x run parametersresume.sh: scriptcomplete.genomic.gff: genomic features file 3 of complete annotation from EGAPxcomplete.genomic.gtf: EGAPx annotations in gtf 2.2 formatcomplete.proteins.faa: amino acid fasta of proteinscomplete.transcripts.fna: nucleic acid fasta of transcriptsstats subdirectory: contains feature count summaries of EGAPx annotationsannot_builder_output subdirectory: contains data from annotation builder<br>
DOI: 10.6084/m9.figshare.28661291.v1
title: B. pensylvanicus genome assembly and annotation

description: <b>Bombus_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fasta</b> Bombus pensylvanicus reference genome assembly (scaffold0001-0019 represent main assembled chromosomes using PacBio long reads and HiC scaffolding). Assembly is also available on NCBI genbank. Scripts used for assembly are taken from https://doi.org/10.15482/USDA.ADC/25762431.v1; SIM, SHEINA (2024). Bombus huntii genome assembly scripts. Ag Data Commons. Workflow. https://doi.org/10.15482/USDA.ADC/25762431.v1)<b>Bomb</b><b>us_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fasta</b><b>.fai</b>: genome index<b>mtDNA_scaffold0168 subdirectory: </b>Contains the fasta sequence and gff annotation for scaffold0168 which was identified from the MitoHiFi v2 workflow (https://github.com/marcelauliano/MitoHiFi) as the probable mitochondrial genome and removed from the main assembly above and the NCBI genome submission.<b>non_arth_scaffolds subdirectory: </b>Contains the FASTA sequence and a CSV of taxonomic identifiers to the family level of scaffolds removed from the final assembly during the BlobTools QC step.<b>iyBomPens_scaff_egapx_RNA_out</b>: directory containing EGAPx annotation information. Runs performed by Sheina Sim @ U.S. Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI using the external version of NCBI Eukaryotic Genome Annotation Pipeline (EGAPx 0.3.1-alpha).annotation_data.cmt: summary of annotation runrun_params.yaml: specific egap x run parametersresume.sh: scriptcomplete.genomic.gff: genomic features file 3 of complete annotation from EGAPxcomplete.genomic.gtf: EGAPx annotations in gtf 2.2 formatcomplete.proteins.faa: amino acid fasta of proteinscomplete.transcripts.fna: nucleic acid fasta of transcriptsstats subdirectory: contains feature count summaries of EGAPx annotationsannot_builder_output subdirectory: contains data from annotation builder<br>
DOI: 10.15468/dl.qyc5wd
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Neotis heuglinii)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 177 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016154-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fxxsgw
title: Occurrence Download

description: A dataset containing 9657 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Larix sibirica"
 ]
}

 The dataset includes 9657 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016153-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/n3cm5j
title: Lac Faribault pollen dataset

description: Raw data for the Lac Faribault pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/n37t40
title: Tourbière de Farnham pollen dataset

description: Raw data for the Tourbière de Farnham pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.cgcudz
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acentrogobius dayi)",
 "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 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016155-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/n3440n
title: Farquar Lake pollen dataset

description: Raw data for the Farquar Lake pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/n3099j
title: Fawn Lake (CA:Ontario) pollen dataset

description: Raw data for the Fawn Lake (CA:Ontario) pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.7x3b49
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eichhornia crassipes",
 "Country is Haiti",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016156-250802193616735/datasets/export for details.
DOI: 10.21233/n38g8c
title: Fawn Lake pollen dataset

description: Raw data for the Fawn Lake pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.ytamj8
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eichhornia crassipes",
 "Country is Honduras",
 "HasCoordinate is true"
 ]
}

 The dataset includes 14 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016157-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/n34s6g
title: Fernbank Interglacial pollen dataset

description: Raw data for the Fernbank Interglacial pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.buypdg
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Neotis nuba)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 37 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016159-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/n3104v
title: Ferndale Bog loss-on-ignition dataset

description: Raw data for the Ferndale Bog loss-on-ignition dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.cz2euk
title: Occurrence Download

description: A dataset containing 6776 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Betula lenta)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6776 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016158-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/n3g99w
title: Ferndale Bog pollen dataset

description: Raw data for the Ferndale Bog pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/n3bm6m
title: Fiddler's Pond pollen dataset

description: Raw data for the Fiddler's Pond pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/n36t4p
title: Figurnoye Lake pollen dataset

description: Raw data for the Figurnoye Lake pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.trqjyv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Strix occidentalis)",
 "Country is one of (American Samoa, Australia, Christmas Island, Cocos (Keeling) Islands, Cook Islands, Fiji, French Polynesia, Guam, Heard Island and McDonald Islands, Kiribati, Marshall Islands, Micronesia (Federated States of), Nauru, New Caledonia, New Zealand, Niue, Norfolk Island, Northern Mariana Islands, Palau, Papua New Guinea, Pitcairn, Samoa, Solomon Islands, Tokelau, Tonga, Tuvalu, United States Minor Outlying Islands, Vanuatu, Wallis and Futuna)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016160-250802193616735/datasets/export for details.
DOI: 10.21233/n33423
title: First pollen dataset

description: Raw data for the First pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.vnxmtw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Strix occidentalis)",
 "Country is one of (Åland Islands, Albania, Andorra, Austria, Belarus, Belgium, Bosnia and Herzegovina, Bulgaria, Croatia, Czechia, Denmark, Estonia, Faroe Islands, Finland, France, Germany, Gibraltar, Greece, Guernsey, Holy See, Hungary, Iceland, Ireland, Isle of Man, Italy, Jersey, Latvia, Liechtenstein, Lithuania, Luxembourg, Malta, Moldova, Republic of, Monaco, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Russian Federation, San Marino, Serbia, Slovakia, Slovenia, Spain, Svalbard and Jan Mayen, Sweden, Switzerland, Ukraine, United Kingdom of Great Britain and Northern Ireland)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016161-250802193616735/datasets/export for details.
DOI: 10.21233/n3c90j
title: Fish Lake pollen dataset

description: Raw data for the Fish Lake pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.zzv5qw
title: Occurrence Download

description: A dataset containing 301527 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Castor fiber"
 ]
}

 The dataset includes 301527 records from 614 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016140-250802193616735/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6xrrd8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Strix occidentalis)",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016162-250802193616735/datasets/export for details.
DOI: 10.21233/n37k7q
title: Beaverhouse Lake pollen dataset

description: Raw data for the Beaverhouse Lake pollen dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.5281/zenodo.16124448
title: Dominant negative variants in ATP5F1A uncouple oxidative phosphorylation and are associated with developmental delay, intellectual disability, and movement abnormalities.
title: Proteomics of fibroblasts from patients with Complex V disorders

description: Whole cell unlabeled proteomics data were collected from fibroblasts of patients with defects in Complex V of the respiratory chain. These are patients 1 and 4 in the publication. 

Further, whole cell unlabeled proteomics data were collected from peripheral blood mononuclear cells of a patient with a defect in complex V of the respiratory chain and the parents.  This is patient 2 in the publication.
DOI: 10.5281/zenodo.16124447
title: Dominant negative variants in ATP5F1A uncouple oxidative phosphorylation and are associated with developmental delay, intellectual disability, and movement abnormalities.
title: Proteomics of fibroblasts from patients with Complex V disorders

description: Whole cell unlabeled proteomics data were collected from fibroblasts of patients with defects in Complex V of the respiratory chain. These are patients 1 and 4 in the publication. 

Further, whole cell unlabeled proteomics data were collected from peripheral blood mononuclear cells of a patient with a defect in complex V of the respiratory chain and the parents.  This is patient 2 in the publication.