cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.xq342s
title: Occurrence Download

description: A dataset containing 18156 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hypericum desetangsii, Hypericum dubium, Hypericum dubium, Hypericum maculatum, Hypericum maculatum, Hypericum maculatum, Hypericum maculatum, Hypericum maculatum, Hypericum maculatum, Hypericum maculatum)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 18156 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008265-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/k0aett
title: C.P. Gillette Museum of Arthropod Diversity

description: The collection houses approximately 5 million specimens representing about 60,000 species with fifty primary types and 1,000 secondary types. More than 10,000 specimens are added to the collection each year. As a large and comprehensive holding of arthropods, predominately insects, in the Southern Rocky Mountains, it is a major resource for regional and national biodiversity investigations. Much of the material has been identified by specialists to the specific level. Examples of the unique quality of material include the aphids, other Homoptera, Coleoptera, Diptera, Hymenoptera, Lepidoptera, and all aquatic orders. It serves as the repository for arthropod inventories of several National Parks including Canyonlands, Great Sand Dunes, Mesa Verde, Rocky Mountain, Dinosaur, and Yucca House and Colorado National Monuments.
DOI: 10.15468/dl.33hr8u
title: Occurrence Download

description: A dataset containing 4175 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hypericum montanum, Hypericum montanum, Hypericum montanum)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 4175 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008268-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ab9zf4
title: Occurrence Download

description: A dataset containing 1542 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhexia virginica",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1542 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008270-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18462858
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Harold St. John, http://www.wikidata.org/entity/Q2840308. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q2840308
DOI: 10.5281/zenodo.18462880
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Paul Henri Auquier, http://www.wikidata.org/entity/Q6067191. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q6067191
DOI: 10.5281/zenodo.11977943
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Paul Henri Auquier, http://www.wikidata.org/entity/Q6067191. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q6067191
DOI: 10.5281/zenodo.15364992
title: Supplementary Data for: MicroFinder: Conserved gene-set mapping and assembly ordering for manual curation of bird microchromosomes

description: Orthogroups, species tree and the MicroFinder protein set

Files listed below are found in the "./OrthoFinder_results_and_MicroFinder_protein_set/" subdirectory. Sample IDs used throughout correspond to those given in Supplementarty Table 1 of the main manuscript. 

SubdIrectory containing proteomes for each species included in the OrthoFinder analysis: ./input_proteomes/

SubdIrectory containing annotation GFF files for each species included in the OrthoFinder analysis: ./annotations/

OrthoFinder orthogroups: Orthogroups.txt

Per species gene counts per orthogroup annotated with whether each familiy was identied by KinFin as a broadly conserved "fuzzy" orothogroup and whether the orthogroup was included in the MicroFinder protein set: Orthogroups.GeneCount.KinFin_MicroFinder_annotated.tsv

SubdIrectory containing multiple sequence alignments for all orthogroups: ./MultipleSequenceAlignments_all_orthogroups/

SubdIrectory containing multiple sequence alignments for conserved single copy orthogroups used for IQTree species tree inference (FASTA headers have been simplified to just contain the species ID): ./species_tree_alignments/

IQtree species tree inference run details: species_tree.concat.iqtree

IQtree species tree: species_tree.concat.nwk

IQTree best fitting models and parititioning scheme: IQTree.concat.best_model.nex

The MicroFinder protein set used in the MicroFinder pipeline: MicroFinder_prot_set.fa

Re-curated bird genomes

The "./Recuration/" subdirectory contains files used for the MicroFinder-enabled genome assembly curation of 12 previously released bird genomes listed in Supplementary Table 4 of the main manuscript.

Subfolders in this directory are named by the TOL ID of each species and contain:

PretextView HI-C contact map of the original genome assembly.

PretextView savestate showing changes made during re-curation. 

AGP file summarising changes made to the orginal assembly.

Updated genome assembly FASTA file.

PretextView HI-C contact map of the updated genome assembly.

Minimap2 alignment file of the orginal assembly vs the GGswu chicken genome in paf format.

Minimap2 alignment file of the updated assembly vs the GGswu chicken genome in paf format.
DOI: 10.5281/zenodo.18459675
title: Supplementary Data for: MicroFinder: Conserved gene-set mapping and assembly ordering for manual curation of bird microchromosomes

description: Orthogroups, species tree and the MicroFinder protein set

Files listed below are found in the "./OrthoFinder_results_and_MicroFinder_protein_set/" subdirectory. Sample IDs used throughout correspond to those given in Supplementarty Table 1 of the main manuscript. 

SubdIrectory containing proteomes for each species included in the OrthoFinder analysis: ./input_proteomes/

SubdIrectory containing annotation GFF files for each species included in the OrthoFinder analysis: ./annotations/

OrthoFinder orthogroups: Orthogroups.txt

Per species gene counts per orthogroup annotated with whether each familiy was identied by KinFin as a broadly conserved "fuzzy" orothogroup and whether the orthogroup was included in the MicroFinder protein set: Orthogroups.GeneCount.KinFin_MicroFinder_annotated.tsv

SubdIrectory containing multiple sequence alignments for all orthogroups: ./MultipleSequenceAlignments_all_orthogroups/

SubdIrectory containing multiple sequence alignments for conserved single copy orthogroups used for IQTree species tree inference (FASTA headers have been simplified to just contain the species ID): ./species_tree_alignments/

IQtree species tree inference run details: species_tree.concat.iqtree

IQtree species tree: species_tree.concat.nwk

IQTree best fitting models and parititioning scheme: IQTree.concat.best_model.nex

The MicroFinder protein set used in the MicroFinder pipeline: MicroFinder_prot_set.fa

Re-curated bird genomes

The "./Recuration/" subdirectory contains files used for the MicroFinder-enabled genome assembly curation of 12 previously released bird genomes listed in Supplementary Table 4 of the main manuscript.

Subfolders in this directory are named by the TOL ID of each species and contain:

PretextView HI-C contact map of the original genome assembly.

PretextView savestate showing changes made during re-curation. 

AGP file summarising changes made to the orginal assembly.

Updated genome assembly FASTA file.

PretextView HI-C contact map of the updated genome assembly.

Minimap2 alignment file of the orginal assembly vs the GGswu chicken genome in paf format.

Minimap2 alignment file of the updated assembly vs the GGswu chicken genome in paf format.
DOI: 10.15468/dl.bcym87
title: Occurrence Download

description: A dataset containing 11201 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hypericum tetrapterum, Hypericum quadrangulum, Hypericum quadrangulum, Hypericum acutum, Hypericum acutum)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 11201 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008271-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sr27yb
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Japan",
 "TaxonKey is Epimedium sagittatum"
 ]
}

 The dataset includes 29 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008272-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9kpd3z
title: Occurrence Download

description: A dataset containing 1564 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhynchanthera grandiflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1564 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008273-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b8grau
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-72.29777358724385 -39.81046006666392,-72.21531918804675 -39.81046006666392,-72.21531918804675 -39.72800566746682,-72.29777358724385 -39.72800566746682,-72.29777358724385 -39.81046006666392))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 102 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008274-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25901/f1qb-7510
title: None
DOI: 10.15468/dl.vbaaxq
title: Occurrence Download

description: A dataset containing 142 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hypochaeris glabra, Hypochaeris glabra, Hypochaeris glabra)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 142 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008276-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48366/r1582129
title: Vision Language Action using affordance as action tokens

description: Vision Language Action using affordances as action tokens represents actions as object–action possibilities (e.g., graspable, pushable, pourable) rather than explicit motor commands. By predicting affordances grounded in visual and linguistic context, these models abstract action selection from low-level control, enabling better generalization, interpretability, and transfer across tasks and embodiments.
DOI: 10.15468/dl.vd2d54
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rousseauxia dionychoides",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 35 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008279-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s5hxyd
title: Occurrence Download

description: A dataset containing 377549 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Belgium",
 "TaxonKey is one of (Aponogeton distachyos, Arthurdendyus triangulatus, Cabomba caroliniana, Callosciurus finlaysonii, Cherax destructor, Corvus splendens, Crassula helmsii, Elodea densa, Eriocheir sinensis, Erythranthe guttata, Faxonius immunis, Faxonius juvenilis, Faxonius rusticus, Faxonius virilis, Gambusia affinis, Heracleum mantegazzianum, Heracleum persicum, Heracleum pubescens, Houttuynia cordata, , Impatiens glandulifera, Koenigia polystachya, Lagarosiphon major, Lepomis gibbosus, Limnoperna fortunei, Ludwigia grandiflora, Ludwigia peploides, Lysichiton americanus, Morone americana, Muntiacus reevesi, Myriophyllum aquaticum, Myriophyllum heterophyllum, Pacifastacus leniusculus, Petasites japonicus, Pontederia cordata, Procambarus acutus, Procambarus clarkii, Procambarus virginalis, Pseudorasbora parva, Pycnonotus cafer, Saururus cernuus, Sciurus carolinensis, Sciurus niger, Solenopsis invicta, Solenopsis richteri, Threskiornis aethiopicus, Vespa velutina, Zizania latifolia)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 377549 records from 90 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008232-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rygapm
title: Occurrence Download

description: A dataset containing 447 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lebiasina bimaculata"
 ]
}

 The dataset includes 447 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008278-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u52885
title: Occurrence Download

description: A dataset containing 73398 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Holcus lanatus)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 73398 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008251-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kn4rc5
title: Occurrence Download

description: A dataset containing 1545 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hypochaeris maculata)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 1545 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008280-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cdgux6
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rousseauxia madagascariensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008281-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w4p2hf
title: Occurrence Download

description: A dataset containing 2179670 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "OccurrenceStatus is Present",
 "TaxonKey is Nymphalidae",
 "Year 2024-2026"
 ]
}

 The dataset includes 2179670 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008255-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5683/sp3/lhpz73
title: GluN2B-specific NMDAR positive allosteric modulation reverses cognitive and behavioral abnormalities in Mecp2 and Disc1 transgenic mice

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;The GluN2B subunit of N-methyl-D-aspartate receptors (NMDAR) plays a central role in synaptic development and plasticity, and its hypofunction is linked to autism spectrum disorder, severe neurodevelopmental delay, and other neuropsychiatric diseases. Therefore, enhancing the function of this NMDAR subunit may provide an effective therapeutic strategy for correcting synaptic and behavioral deficits associated with GluN2B-hypofunction. Here, we developed a class of GluN2B-selective positive allosteric modulators and characterized the pharmacological properties and binding site of the lead compound, 175. Systemic application of 175 facilitates hippocampal long-term depression in rats. Importantly, 175 restores performances in open-field exploration and three-chamber test in Mecp2 overexpression mice. Treatment with 175 also reverses behavioral abnormalities in open-field, Y-maze spontaneous alternation, three-chamber test, and pre-pulse inhibition in Disc1 mutant mice. Our findings introduce a pharmacological tool for selectively potentiating GluN2B-NMDARs function and highlight its therapeutic potential for cognitive and behavioral symptoms associated with GluN2B hypofunction.&lt;/p&gt;
description: <b>Dryad version number:</b> 7
<b>Version status:</b> submitted
<b>Dryad curation status:</b> Published
<b>Sharing link:</b> http://datadryad.org/dataset/doi:10.5061/dryad.stqjq2cgj
<b>Storage size:</b> 63533
<b>Visibility:</b> public
DOI: 10.15468/dl.82tmbe
title: Occurrence Download

description: A dataset containing 23864 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hypochaeris radicata)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 23864 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008283-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/fvigdc
title: Clemson University Arthropod Collection

description: The Clemson University Arthropod Collection (CUAC) supports the teaching, research, and extension activities of the University. The Collection consists of approximately 1.3 million specimens from Classes Insecta, Arachnida, Branchipoda, Copepoda, Diplopoda, and Chilopoda. The wet, alcohol-preserved collection is exceptionally rich, with over 1,000,000 specimens, nearly half of which are Trichoptera, or caddisflies, resulting from 40 years of work by Director Emeritus Dr. John Morse. The pinned, dry collection comprises only about 200,000 specimens, but also has strong regional representation of all the major orders. The CUAC collection serves as a permanent repository for specimens used in University research. It serves as a reference collection for identifying economically and ecologically significant samples sent in from all over South Carolina. The specimens in the collection also provide a historical record of the changing biota of the southeastern region dating back nearly 100 years. The Museum's educational displays are used to enhance University courses and are viewed by visitors to the Collection and by participants in demonstrations at off-campus venues.
DOI: 10.15468/dl.9nwdsd
title: Occurrence Download

description: A dataset containing 687 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Hypochaeris uniflora, Hypochaeris uniflora, Hypochaeris uniflora)",
 "Year is greater than or equal to 1900",
 "Geometry POLYGON ((8.643 46.99, 14.1 46.92, 14.43 50.75, 8.534 50.83, 8.643 46.99))",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Observation, Human Observation, Machine Observation, Material sample)"
 ]
}

 The dataset includes 687 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008284-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6wjv8r
title: Occurrence Download

description: A dataset containing 143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salpinga maranonensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 143 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008285-260129131611470/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.