cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14271508
title: DataTD: A Dataset of Java Projects Including Test Doubles

description: This dataset contains 1,070 open-source Java projects including test doubles. The projects were mined from GitHub. The starting point for building the dataset included all projects whose main language is Java and that had at least five stars as of October 29, 2023. This set of projects is listed in java_repositories_with_five_stars.txt. The 1,070 projects comprising this dataset use Maven as their build system, containing JUnit tests, and use Mockito to create test doubles. The projects are available in the project.zip archive file. The dataset also contains metadata about the projects, which is available in the projects.json file. The metadata describes the characteristics of each project together with the test double definitions, stubbings, and verifications inside the project. Finally, we also make available the source code used to build DataTD for future research on using and extending the dataset.
DOI: 10.5281/zenodo.8030207
title: North Atlantic benthic d18O stack data

description: Files containing the data for our speleothem-tied North Atlantic benthic d18O stack, including: ages, d18O values, d18O err, age samples output by BIGMACS, and the composite depth scale used for this stack (based on IODP site U1308).
DOI: 10.5281/zenodo.14714574
title: Network-aware self-supervised learning enables high-content phenotypic screening for genetic modifiers of neuronal activity dynamics

description: This dataset contains the data archive for the paper titled "Network-aware self-supervised learning enables high-content phenotypic screening for genetic modifiers of neuronal activity dynamics".

The data archive is comprised of six folders:

The first folder is dataset_statistics, which contains JSON files that have the associated statistics for each plate, which is used in the inference for the self-supervised learning models.

The second folder is figure1_data, which contains the information necessary to recreate the panels in Figure 1 of the paper.

The third folder is metadata_files, which contains CSV files that provide a mapping for treatment to plate and well ID for all experiments. 

The fourth folder is called model_checkpoints. This folder contains all of the model checkpoints, which can be read for inference following the code found at the associated GitHub repository. Within the model checkpoint folder, the subfolders contain the checkpoints for models trained on each of the datasets, from either the neuroactive stimulation experiment, the simulated experiment, or the CRISPRi screen.

The fifth folder plexus_embeddings, contains h5ad files containing either the plexus model embeddings or manual features. The .obs DataFrame also contains all of the associated metadata for each of the experiments.

The sixth and final folder is processed_zarr_files, which contains all of the Zarr files (one per 384-well plate across the experiments). The Zarr files are hierarchical and have the form Plate / Well / Field-of-view. For each field of view, there are datasets containing the raw GCaMP6m traces, the baseline corrected traces, the cell segmentation masks, the inferred spike events, the nuclei masks in the case of the CRISPRi screening dataset, and the coefficients associated with the autoregressive model used to infer spike events.

This data archive is leveraged by the Plexus GitHub Repository to recreate the results presented in the paper.
DOI: 10.5281/zenodo.8135129
title: North Atlantic benthic d18O stack data

description: Files containing the data for our speleothem-tied North Atlantic benthic d18O stack, including: ages, d18O values, d18O err, age samples output by BIGMACS, and the composite depth scale used for this stack (based on IODP site U1308).
DOI: 10.5281/zenodo.14796413
title: North Atlantic benthic d18O stack data

description: Files containing the data for our speleothem-tied North Atlantic benthic d18O stack, including: ages, d18O values, d18O err, age samples output by BIGMACS, and the composite depth scale used for this stack (based on IODP site U1308).

Please read for information on what each file contains:'NA-stack_age-samples.txt' = 1000 sets of age model samples generated during stack construction, each column contains a unique age model.

'NA-stack_age-d18O.txt' = the median age model output by BIGMACS after stack construction with their corresponding d18O data points (this age model closely aligns with that of the LR04 stack since the LR04 stack was used as our initial alignment target).

'NA-stack_depth_composite.txt' = the composite depths used to reduce bias in our stack's age model.

'NA-stack_untuned_age_model.txt' = the stack ages after mapping them onto the composite depth scale of Site U1308. This is the data plotted in Fig. 3 of the paper. This file was added on February 3, 2025 to allow users to download this data directly without having to apply the extra step of interpolating the median age model onto the depth scale themselves.
DOI: 10.5281/zenodo.8030206
title: North Atlantic benthic d18O stack data

description: Files containing the data for our speleothem-tied North Atlantic benthic d18O stack, including: ages, d18O values, d18O err, age samples output by BIGMACS, and the composite depth scale used for this stack (based on IODP site U1308).

Please read for information on what each file contains:'NA-stack_age-samples.txt' = 1000 sets of age model samples generated during stack construction, each column contains a unique age model.

'NA-stack_age-d18O.txt' = the median age model output by BIGMACS after stack construction with their corresponding d18O data points (this age model closely aligns with that of the LR04 stack since the LR04 stack was used as our initial alignment target).

'NA-stack_depth_composite.txt' = the composite depths used to reduce bias in our stack's age model.

'NA-stack_untuned_age_model.txt' = the stack ages after mapping them onto the composite depth scale of Site U1308. This is the data plotted in Fig. 3 of the paper. This file was added on February 3, 2025 to allow users to download this data directly without having to apply the extra step of interpolating the median age model onto the depth scale themselves.
DOI: 10.5281/zenodo.14263195
title: DataTD: A Dataset of Java Projects Including Test Doubles

description: This dataset contains 1,070 open-source Java projects that include test doubles. The projects were mined from GitHub. The dataset was built by selecting all projects whose primary language is Java and that had at least five stars as of October 29, 2023. This list of projects is available in java_repositories_with_five_stars.txt. The 1,070 projects in this dataset use Maven as their build system, contain JUnit tests, and utilize Mockito to create test doubles. The projects are available in the project.zip archive file. Additionally, the dataset includes metadata about the projects, stored in the projects.json file. This metadata describes the characteristics of each project, along with test double definitions, stubbings, and verifications. Finally, we also provide the source code used to build DataTD, enabling future research on expanding and utilizing the dataset.
DOI: 10.5281/zenodo.14263196
title: DataTD: A Dataset of Java Projects Using Test Doubles
DOI: 10.5281/zenodo.14796282
title: DataTD: A Dataset of Java Projects Including Test Doubles

description: This dataset contains 1,070 open-source Java projects that include test doubles. The projects were mined from GitHub. The dataset was built by selecting all projects whose primary language is Java and that had at least five stars as of October 29, 2023. This list of projects is available in java_repositories_with_five_stars.txt. The 1,070 projects in this dataset use Maven as their build system, contain JUnit tests, and utilize Mockito to create test doubles. The projects are available in the project.zip archive file. Additionally, the dataset includes metadata about the projects, stored in the projects.json file. This metadata describes the characteristics of each project, along with test double definitions, stubbings, and verifications. Finally, we also provide the source code used to build DataTD, enabling future research on expanding and utilizing the dataset.
DOI: 10.15468/dl.rdfdwn
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bothrops hyoprora Amaral, 1937"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008015-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3dvp7h
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Neottia listeroides Lindl."
 ]
}

 The dataset includes 55 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035516-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ku2rgd
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adonis leiosepala Butkov"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016811-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5os3c2
title: Occurrence Download

description: A dataset containing 1228209 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Animalia",
 "HasGeospatialIssue is false",
 "Geometry POLYGON((-180 -82,-180 82,180 82,180 -82,-180 -82))",
 "PublishingCountry is Mexico"
 ]
}

 The dataset includes 1228209 records from 250 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008016-150615163101818/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.826wfa
title: Occurrence Download

description: A dataset containing 8731 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ursus maritimus Phipps, 1774"
 ]
}

 The dataset includes 8731 records from 144 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035566-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mgr2bc
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia joyae P.R.O.Bally & S.Carter"
 ]
}

 The dataset includes 37 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051443-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.21cmhx
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Microsorum membranaceum (D.Don) Ching",
 "Geometry POLYGON((119.882812 25.284437,119.882812 21.698265,122.080078 21.698265,122.080078 25.284437,119.882812 25.284437))"
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008016-160311141623029/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6aczwm
title: Occurrence Download

description: A dataset containing 219 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Iris vartanii Foster"
 ]
}

 The dataset includes 219 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035543-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.esdt2k
title: Occurrence Download

description: A dataset containing 586 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Penstemon floridus Brandegee"
 ]
}

 The dataset includes 586 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008016-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wkjk8f
title: Occurrence Download

description: A dataset containing 4647 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Pomatostomus halli Cowles, 1964"
 ]
}

 The dataset includes 4647 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051409-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8v9vcc
title: Occurrence Download

description: A dataset containing 732974 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anguilla anguilla (Linnaeus, 1758)"
 ]
}

 The dataset includes 732974 records from 622 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035525-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f35vr5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((-26.01029 74.47094, -24.10898 74.47094, -24.10898 74.59529, -26.01029 74.59529, -26.01029 74.47094))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042211-240229165702484/datasets/export for details.
DOI: 10.15468/dl.xmetqp
title: Occurrence Download

description: A dataset containing 53846 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Aves",
 "TaxonKey is Mamala Walker, 1865",
 "TaxonKey is Reptilia",
 "TaxonKey is Plantae"
 ]
 },
 "Geometry POLYGON((-81.5625 7.885147,-81.5625 -15.792253,-47.636718 -15.792253,-47.636718 7.885147,-81.5625 7.885147))",
 "HasCoordinate is true",
 "HasGeospatialIssue is true"
 ]
}

 The dataset includes 53846 records from 167 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008017-151016162008034/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d627j2
title: Occurrence Download

description: A dataset containing 197 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Knema cinerea (Poir.) Warb."
 ]
}

 The dataset includes 197 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035504-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tz42ht
title: Occurrence Download

description: A dataset containing 137 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Philander frenatus (Olfers, 1818)"
 ]
}

 The dataset includes 137 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043552-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7tgqdc
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Laelia speciosa (Kunth) Schltr.",
 "HasCoordinate is true"
 ]
}

 The dataset includes 63 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008017-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kspvxd
title: Occurrence Download

description: A dataset containing 75 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Knema communis J.Sinclair"
 ]
}

 The dataset includes 75 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035508-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3u5muq
title: Occurrence Download

description: A dataset containing 3768 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adonis microcarpa DC."
 ]
}

 The dataset includes 3768 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016812-240216155721649/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.docmo1
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Penstemon ovatus Douglas"
 ]
}

 The dataset includes 126 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008017-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qgquz5
title: Occurrence Download

description: A dataset containing 336 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Knema intermedia (Blume) Warb."
 ]
}

 The dataset includes 336 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035567-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9qymqm
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Hylodes fredi Canedo & Pombal, 2007"
 ]
}

 The dataset includes 19 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042215-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8xhb6j
title: Occurrence Download

description: A dataset containing 452 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Knema glomerata (Blanco) Merr."
 ]
}

 The dataset includes 452 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035557-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.lgskak
title: Occurrence Download

description: A dataset containing 352 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Spain",
 "Country is France"
 ]
 },
 "Year 2000-2017",
 {
 "or" : [
 "TaxonKey is Balaenoptera musculus (Linnaeus, 1758)",
 "TaxonKey is Balaenoptera physalus (Linnaeus, 1758)"
 ]
 }
 ]
}

 The dataset includes 352 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008017-171124123535762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s3r3z9
title: Occurrence Download

description: A dataset containing 43676 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cardellina rubrifrons (Giraud Jr, 1841)"
 ]
}

 The dataset includes 43676 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042276-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8juxjm
title: Occurrence Download

description: A dataset containing 4982448 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 4982448 records from 913 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005126-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s2jyu9
title: Occurrence Download

description: A dataset containing 416548 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aves)",
 "HasCoordinate is one of (true)",
 "Geometry POLYGON((-76.704181526849 3.46148617830778,-76.5946964229395 3.46148617830778,-76.5946964229395 3.6226162245619,-76.704181526849 3.6226162245619,-76.704181526849 3.46148617830778))"
 ]
}

 The dataset includes 416548 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005129-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mkyg55
title: Occurrence Download

description: A dataset containing 416548 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Aves)",
 "HasCoordinate is one of (true)",
 "Geometry POLYGON((-76.704181526849 3.46148617842167,-76.5946964229395 3.46148617842167,-76.5946964229395 3.62261622468105,-76.704181526849 3.62261622468105,-76.704181526849 3.46148617842167))"
 ]
}

 The dataset includes 416548 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005141-241107131044228/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wmdtgh
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Beet mild yellowing virus, Beet mild yellowing virus, Beet mild yellowing virus, Polerovirus Beet mild yellowing virus, Beet mild yellowing virus, Beet mild yellowing virus, Macrosiphum euphorbiae Thomas, 1878, Crambe hispanica subsp. abyssinica (Hochst. ex R.E.Fr.) Prina)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005158-241107131044228/datasets/export for details.