cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.hqd6w3
title: Occurrence Download

description: A dataset containing 16176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-19.64856 17.17340,141.68598 17.17340,141.68598 81.65015,-19.64856 81.65015,-19.64856 17.17340))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anguis colchica"
 ]
}

 The dataset includes 16176 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002868-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xza22h
title: Occurrence Download

description: A dataset containing 36 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Loxoconcha pumicosa Brady, 1880"
 ]
}

 The dataset includes 36 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123580-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eh5654
title: Occurrence Download

description: A dataset containing 69254 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is Italy",
 "OccurrenceStatus is Present",
 "TaxonKey is Mollusca"
 ]
}

 The dataset includes 69254 records from 113 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0137748-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11505046
title: PretermBirth_Hypoxia_NocturnalSpO2_AMS

description: Dataset used to explore nocturnal oxygen saturation dynamics during a simulated high-altitude exposure of 4200 m in a group of prematurely-born healthy adults and a term-born group of control participants. The predictive value of nocturnal oxygen saturation for acute mountain sickness incidence was also explored.
DOI: 10.15468/dl.b9pc6s
title: Occurrence Download

description: A dataset containing 29639 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Martes martes (Linnaeus, 1758)",
 "Year 1980-2010"
 ]
}

 The dataset includes 29639 records from 210 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0130517-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d8km67
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidopa deamae J.E.Benedict, 1903"
 ]
}

 The dataset includes 17 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122564-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zrxpqm
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Loricoecia loricata (Claus, 1894)"
 ]
}

 The dataset includes 33 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123569-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x2yvqr
title: Occurrence Download

description: A dataset containing 32898 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mongolia",
 "GadmGid is MNG.21_1"
 ]
}

 The dataset includes 32898 records from 89 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0158752-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9db9u8
title: Occurrence Download

description: A dataset containing 804 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithobates megapoda (Taylor, 1942)"
 ]
}

 The dataset includes 804 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123582-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8gr4kz
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidopa mexicana Efford, 1971"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122568-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8j7eu6
title: Occurrence Download

description: A dataset containing 46007 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Martes martes (Linnaeus, 1758)",
 "Year is greater than or equal to 2010"
 ]
}

 The dataset includes 46007 records from 417 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0130518-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9bnxtt
title: Occurrence Download

description: A dataset containing 2287 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithobates pustulosus (Boulenger, 1883)"
 ]
}

 The dataset includes 2287 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123585-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9xavpu
title: Occurrence Download

description: A dataset containing 937116 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.10_1",
 "TaxonKey is Melanerpes carolinus (Linnaeus, 1758)"
 ]
}

 The dataset includes 937116 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0138190-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yhky7m
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paralaophonte subterranea (Lang, 1965)"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123571-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yq92nh
title: Occurrence Download

description: A dataset containing 3321 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Ixerbaceae)"
 ]
}

 The dataset includes 3321 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0158759-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dz3us4
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidophthalmus sinuensis Lemaitre & de Almeida Rodrigues, 1991"
 ]
}

 The dataset includes 17 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122580-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9xtzzp
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arisaema concinnum Schott"
 ]
}

 The dataset includes 148 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047960-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n4suez
title: Occurrence Download

description: A dataset containing 641 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithobates tarahumarae (Boulenger, 1917)"
 ]
}

 The dataset includes 641 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123589-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7r5j7d
title: Occurrence Download

description: A dataset containing 30478 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Nigeria, Benin, Cameroon, Central African Republic, Congo, Democratic Republic of the, Congo, Equatorial Guinea, Gabon, Ghana, Senegal, Togo, Burkina Faso, Côte d’Ivoire, Guinea, Guinea-Bissau, Liberia, Gambia, Sierra Leone)",
 "TaxonKey is Amphibia",
 "Year 1978-2022"
 ]
}

 The dataset includes 30478 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122566-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cn8ah8
title: Occurrence Download

description: A dataset containing 1314 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Biscutella auriculata L.",
 "HasCoordinate is true",
 "Year is greater than or equal to 1900",
 "BasisOfRecord is one of (Human Observation, Specimen, Unknown evidence)"
 ]
}

 The dataset includes 1314 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047986-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vxcrkv
title: Occurrence Download

description: A dataset containing 104247 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Geometry POLYGON((18.78986 -34.2161,18.79919 -34.39335,19.32631 -34.63935,19.51757 -34.44338,19.42427 -34.15822,19.27967 -34.20838,19.09774 -34.07325,18.78986 -34.2161))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 104247 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0066118-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4n8hxd
title: Occurrence Download

description: A dataset containing 1190 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithobates neovolcanicus (Hillis & Frost, 1985)"
 ]
}

 The dataset includes 1190 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123583-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2qzwyj
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leptalpheus denticulatus Anker & Marin, 2009"
 ]
}

 The dataset includes 28 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122581-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8defny
title: Occurrence Download

description: A dataset containing 3521 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Incilius alvarius (Girard, 1859)"
 ]
}

 The dataset includes 3521 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0130519-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fhh2zg
title: Occurrence Download

description: A dataset containing 32503 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Diadophis punctatus (Linnaeus, 1766)"
 ]
}

 The dataset includes 32503 records from 128 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123573-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n9ud4t
title: Occurrence Download

description: A dataset containing 73 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidopa richmondi J.E.Benedict, 1903"
 ]
}

 The dataset includes 73 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0122573-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a69pms
title: Occurrence Download

description: A dataset containing 1170 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Joinvilleaceae)"
 ]
}

 The dataset includes 1170 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0158773-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdvyxa
title: Occurrence Download

description: A dataset containing 3733 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lithobates vaillanti (Brocchi, 1877)"
 ]
}

 The dataset includes 3733 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0123591-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.anmhw6
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/0014606-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cfmyod
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/0000391-160509122628363/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tpsfh6
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "Geometry POLYGON((64.97904 -0.13555,99.67585 -0.13555,99.67585 38.18812,64.97904 38.18812,64.97904 -0.13555))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Coffea arabica L.",
 "Year 2000-2023"
 ]
}

 The dataset's 1 records were derived from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0249828-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wr7b1y
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/0011495-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5jszfx
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/0022356-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cwtz4z
title: Occurrence Download

description: A dataset containing 280214333 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is United States of America",
 "Year 1960-2018",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 280214333 records from 351 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013917-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mfhcn5
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "InstitutionCode is one of (ummz, rom)",
 "TaxonKey is Mazarunia mazarunii Kullander, 1990"
 ]
}

 The dataset includes 17 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0229321-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rvf557
title: Occurrence Download

description: A dataset containing 185066140 species occurrences available in GBIF matching the query:
{
 "BasisOfRecord" : [
 "is Specimen"
 ]
}

 The dataset includes 185066140 records from 16988 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0231954-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pfnfe9
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Luidia magnifica",
 "Country is Mexico",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008249-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gprvy6
title: Occurrence Download

description: A dataset containing 21089 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Chamaerops humilis L.",
 "Continent is Europe",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 21089 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008248-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17488067
title: Spontaneous behavior is a succession of self-directed tasks

description: Data and code from the paper "Spontaneous behavior is a succession of self-directed tasks."

Behavioral data

Files named *-behavior.parquet contain dataframes with processed behavioral data (MoSeq syllabes, shMoSeq states, pose information and other metadata). Supplemental Table 2 from the paper specifies which figure panels each dataset contributed to. Files can be loaded into python using the command pandas.read_parquet. Note that shMoSeq states were filtered and renumbered post-hoc to remove state with extremely low frequency; timepoints assigned to these low-frequency states are treated as missing data. All centroid locations, distances, heights, and 3D keypoint coordinates are in mm. 2D keypoint coordinates and object bounding boxes are in pixel units. "Egocentric angle to wall" is defined as the angle between the mouse's heading and a vector pointing toward the nearest wall location. "Wall direction" is the cosine of this angle.

Neural data

Files named *-neural.parquet contain neural activity for each recording. Each array has shape (n_timepoints, n_neurons). The data have been resampled so that the n'th row of the neural activity array corresponds to the n'th row of the behavior dataframe (after filtering the dataframe by session). For calcium recordings, activity levels correspond to Z-scored dF/F. For ephys data, activity levels correspond to spike counts within 1/120-second intervals (since behavior was recorded at 120 frames/second). In some datasets, neural data is missing from the first and last few seconds of each recording. Arrays have been padded with constant values to cover these missing timepoints.

Model parameters

File named *-model_params.h5 contain parameters for the final shMoSeq models derived from each dataset. The parameters can loaded to a dictionary using state_moseq.load_hdf5. In a subset of models, states were renumbered before downstream analysis. The file state_indexes.csv specifies the renumbering for each dataset. For example, the following row in state_indexes.csv would mean that state 3 in lesion-model_params.h5 corresponds to  state 1 in lesion-behavior.parquet.




dataset
original index
renumbered index


lesion
3
1




Code



top-bottom-moseq-shMoSeq-paper.zip contains code from the top-bottom-moseq github repo, which was used for preprocessing depth videos as part of the MoSeq pipeline.

multicam-calibration-0.0.0.zip contains code from the multicam-calibration github repo, which was used for 3D keypoint tracking.

state-moseq-0.0.0.zip contains code from the state-moseq github repo, which was used for estimating behavioral states.