cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.m463yc
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyclotella ocellata Pantocsek, 1901",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.7576 -24.3688,20.529 -24.0715,20.509 -24.0715,20.509 -28.5786,25.5395 -28.5786,25.5395 -24.0715,25.1306 -24.0715,24.9333 -24.4571,23.8962 -24.2467,22.8065 -24.295,22.3719 -24.7207,22.2323 -25.547,22.0387 -25.7188,21.7833 -25.7784,21.5388 -25.7113,21.3553 -25.5415,20.7576 -24.3688))"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043677-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q4q48r
title: Occurrence Download

description: A dataset containing 127 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-71.97592 12.25446,-72.02363 12.1901,-72.00073 12.14579,-71.96208 12.13366,-71.91818 12.13226,-71.87667 12.16865,-71.84899 12.20503,-71.86092 12.24327,-71.87142 12.27404,-71.92152 12.29129,-71.94347 12.29129,-71.97592 12.25446))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Squamata"
 ]
}

 The dataset includes 127 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043678-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5b9dx2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyclotella ocellata Pantocsek, 1901",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.529 -24.0715,20.509 -24.0455,20.509 -24.0715,20.529 -24.0715))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043682-250525065834625/datasets/export for details.
DOI: 10.15468/dl.egtpdc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Abronia latifolia",
 "HasCoordinate is true",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043680-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15658705
title: Data products for Ha et al. 'Microbiome dynamics associated with the infection of grey field slugs by the biocontrol nematode Phasmarhabditis hermaphrodita'.

description: - Processed data products:



ASV_sequences.fasta: fasta sequences of all ASVs found in samples

ASV_table_Decontam_TrueSamples.rds: phyloseq object containing ASVs and their abundances in decontaminated, real (i.e. non-control) samples

asv_table.txt: raw data containing the ASVs and their abundances (before decontamination and subsetting) in samples

rooted_tree.nwk: phylogenetic tree of present taxa

sample_data.txt: mapping metadata to all samples (controls and non-controls)

taxonomy_tab.tsv: matching ASVs to their assigned taxonomy


- Supplementary materials
DOI: 10.5281/zenodo.15658706
title: Data products for Ha et al. 'Microbiome dynamics associated with the infection of grey field slugs by the biocontrol nematode Phasmarhabditis hermaphrodita'.

description: - Processed data products:



ASV_sequences.fasta: fasta sequences of all ASVs found in samples

ASV_table_Decontam_TrueSamples.rds: phyloseq object containing ASVs and their abundances in decontaminated, real (i.e. non-control) samples

asv_table.txt: raw data containing the ASVs and their abundances (before decontamination and subsetting) in samples

rooted_tree.nwk: phylogenetic tree of present taxa

sample_data.txt: mapping metadata to all samples (controls and non-controls)

taxonomy_tab.tsv: matching ASVs to their assigned taxonomy


- Supplementary materials
DOI: 10.15468/dl.w4xkrr
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schoenoplectiella praelongata (Poir.) Lye",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((15.4784 -23.4046,15.4933 -24.0715,20.509 -24.0715,20.509 -24.0455,20.0952 -23.5072,19.9968 -23.017,19.7843 -22.5405,19.1988 -21.8785,18.5972 -21.5447,17.8859 -21.3993,17.1626 -21.4805,16.5332 -21.7596,16.1257 -22.0882,15.8234 -22.4662,15.606 -22.8993,15.4784 -23.4046))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043681-250525065834625/datasets/export for details.
DOI: 10.15468/dl.uhwq7a
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyclotella ocellata Pantocsek, 1901",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.5395 -23.2724,25.1306 -24.0715,25.5395 -24.0715,25.5395 -23.2724))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043683-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15644415
title: Delete (Incorrect Upload)

description: Processed data products for Ha et al., "Microbiome dynamics associated with the infection of grey field slugs by the biocontrol nematode Phasmarhabditis hermaphrodita".
DOI: 10.5281/zenodo.15644416
title: Delete (Incorrect Upload)

description: Processed data products for Ha et al., "Microbiome dynamics associated with the infection of grey field slugs by the biocontrol nematode Phasmarhabditis hermaphrodita".
DOI: 10.15468/dl.2bu5zw
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schoenoplectiella praelongata (Poir.) Lye",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((25.5395 -28.5786,20.509 -28.5786,20.509 -32.9007,25.5395 -32.9007,25.5395 -28.5786))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043684-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15658622
title: ibIDS - A dataset of real-world network communication and user physical contextual data

description: This is a novel dataset that integrates both synthetic attack traces and real-world benign behaviour. Specifically, the malicious data is sourced from the widely referenced CIC-AndMal2017 dataset, while the benign data is collected through our in-situ data acquisition process using a real Android device.
DOI: 10.5281/zenodo.15658699
title: ibIDS - A dataset of real-world network communication and user physical contextual data

description: This is a novel dataset that integrates both synthetic attack traces and real-world benign behaviour. Specifically, the malicious data is sourced from the widely referenced CIC-AndMal2017 dataset, while the benign data is collected through our in-situ data acquisition process using a real Android device.
DOI: 10.34740/kaggle/dsv/12157325
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.9d8r9g
title: Occurrence Download

description: A dataset containing 288 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "GadmGid is CAN.2_1",
 "TaxonKey is Rhinichthys cataractae (Valenciennes, 1842)"
 ]
}

 The dataset includes 288 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043685-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bpb6jb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyclotella ocellata Pantocsek, 1901",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.2855 -34.7533,20.509 -34.5676,20.509 -32.9007,17.7723 -32.9007,17.8156 -33.0786,18.3471 -33.7176,18.3748 -33.8287,18.2181 -34.0492,18.3197 -34.3408,18.4452 -34.429,18.5435 -34.4213,18.5872 -34.3667,18.5363 -34.167,18.7345 -34.1508,18.7216 -34.3637,18.7808 -34.4521,19.0289 -34.4206,19.0831 -34.4835,19.2655 -34.5017,19.2032 -34.6157,19.2394 -34.6926,19.375 -34.6963,19.6091 -34.8524,19.8251 -34.8396,19.9798 -34.9064,20.1081 -34.8731,20.1517 -34.7847,20.2855 -34.7533))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043686-250525065834625/datasets/export for details.
DOI: 10.15468/dl.typqsv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schoenoplectiella praelongata (Poir.) Lye",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.7576 -24.3688,20.529 -24.0715,20.509 -24.0715,20.509 -28.5786,25.5395 -28.5786,25.5395 -24.0715,25.1306 -24.0715,24.9333 -24.4571,23.8962 -24.2467,22.8065 -24.295,22.3719 -24.7207,22.2323 -25.547,22.0387 -25.7188,21.7833 -25.7784,21.5388 -25.7113,21.3553 -25.5415,20.7576 -24.3688))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043687-250525065834625/datasets/export for details.
DOI: 10.15468/dl.8c34e7
title: Occurrence Download

description: A dataset containing 277 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ireland",
 "OccurrenceStatus is Present",
 "RecordedBy is one of (William Wilson, W. WILSON, W. Wilson, Thomas Taylor, T. Taylor, TAYLOR, T., J. T. Mackay, MacKay, James Townsend LLD ALS - BSL, Mackay, J., T. Drummond, Drummond, T., James E. Smith, J. E. Smith, SMITH, J. E., Smith, James Edward, W.J. Hooker, W. J. Hooker, William Jackson Hooker, Hooker, W.J., Hooker, William Jackson, Hooker, W. J. (Sir), Ellen Hutchins, E. Hutchins, Hutchins, E., Miss Hutchins)",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 277 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043688-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25345/c5hx16372
title: MassIVE MSV000098189 - Effect of dipeptides on PKM2 in HEK293T cells
title: Experiment main 1: Metabolomics on dipeptide- and amino acid-treated HEK293T cells using G2-XS QTof Experiment main 2: Repeat of experiment 1 to have more biological replicates, using G2-XS QTof Experiment main 2.2: Amino acids quantification of samples from experiment main 2 using TQSm
DOI: 10.15468/dl.3jrkxz
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Abronia latifolia",
 "HasCoordinate is true",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043690-250525065834625/datasets/export for details.
DOI: 10.5281/zenodo.15622739
title: Initial and boundary conditions and namelists for the MITgcm northern Adriatic Sea 2017-2021 hindcasts

description: This upload contains the initial and boundary conditions, together with namelists and bathymetry file, needed to launch the MITgcm northern Adriatic Sea hindcasts spanning from 2017 to 2021.The original setup was defined starting from the one developed for the CADEAU reanalysis (https://doi.org/10.1016/j.jenvman.2021.112878) and MedEAF operational forecast system (https://medeaf.ogs.it/adriatic).4 configurations are described, obtained by combinations of 2 different vertical grid resolutions (named "old" and "new") and 2 different mixing schemes (KPP and GGL).
DOI: 10.5281/zenodo.15622740
title: Initial and boundary conditions and namelists for the MITgcm northern Adriatic Sea 2017-2021 hindcasts

description: This upload contains the initial and boundary conditions, together with namelists and bathymetry file, needed to launch the MITgcm northern Adriatic Sea hindcasts spanning from 2017 to 2021.The original setup was defined starting from the one developed for the CADEAU reanalysis (https://doi.org/10.1016/j.jenvman.2021.112878) and MedEAF operational forecast system (https://medeaf.ogs.it/adriatic).4 configurations are described, obtained by combinations of 2 different vertical grid resolutions (named "old" and "new") and 2 different mixing schemes (KPP and GGL).
DOI: 10.15468/dl.hqb9db
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "and" : [
 "StateProvince is MInnesota",
 "TaxonKey is Lonicera maackii (Rupr.) Maxim.",
 "Year 1000-2024"
 ]
}

 The dataset includes 68 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043691-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nnc4rb
title: Occurrence Download

description: A dataset containing 747 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Eremanthus incanus (Less.) Less."
 ]
}

 The dataset includes 747 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043689-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pk9qp7
title: Occurrence Download

description: A dataset containing 964 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Haploblepharus edwardsii (Schinz, 1822)"
 ]
}

 The dataset includes 964 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043693-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15658727
title: CARDIOVASCULAR DISEASE BURDEN IN HOSPITALIZED PATIENTS WITH NON- ALCOHOLIC FATTY LIVER DISEASE: AN OBSERVATIONAL STUDY
DOI: 10.5281/zenodo.15658726
title: CARDIOVASCULAR DISEASE BURDEN IN HOSPITALIZED PATIENTS WITH NON- ALCOHOLIC FATTY LIVER DISEASE: AN OBSERVATIONAL STUDY
DOI: 10.15468/dl.gt4gs2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cyclotella ocellata Pantocsek, 1901",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.628 -23.023,35.6007 -22.9702,35.6007 -23.165,35.628 -23.023))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043692-250525065834625/datasets/export for details.
DOI: 10.15468/dl.qq2dk4
title: Occurrence Download

description: A dataset containing 2455 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Astragalus monspessulanus subsp. gypsophilus Rouy",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2455 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043695-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c8fzgd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schoenoplectiella praelongata (Poir.) Lye",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((20.529 -24.0715,20.509 -24.0455,20.509 -24.0715,20.529 -24.0715))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043694-250525065834625/datasets/export for details.
DOI: 10.15468/dl.7vwb4s
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "StateProvince is MInnesota",
 "TaxonKey is Lonicera xylosteum L.",
 "Year 1000-2024"
 ]
}

 The dataset includes 19 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043696-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.7786763
title: Delete (Incorrect Upload)

description: Phylogenetic tree of the giant viruses detected in bioGEOTRACES samples and 1,188 Nucleocytoviricota reference genomes.
DOI: 10.5281/zenodo.7786764
title: Delete (Incorrect Upload)

description: Phylogenetic tree of the giant viruses detected in bioGEOTRACES samples and 1,188 Nucleocytoviricota reference genomes.
DOI: 10.5281/zenodo.15631485
title: PEQQS: a Dataset for Probing Extractive Quantity-focused Question Answering from Scientific Literature

description: Question Answering (QA) and Information Retrieval (IR) play a crucial role in information-seeking pipelines implemented in many emerging AI research assistant applications. Large Language Models (LLMs) have demonstrated exceptional effectiveness on QA tasks, with Retrieval Augmented Generation (RAG) techniques often boosting the results. However, in many of those emerging applications, the onus of conducting the actual literature search falls on the user, i.e. the user searches for the relevant literature and the LLM-based assistant extracts the solicited answers from each of the user-supplied documents. The interplay between the quality of the user-conducted search and the quality of the final results remains understudied.

In this work, we focus on a specific version of such pipeline, where users aim to obtain a specific quantity as an extractive answer (e.g., a value of a particular measurable parameter). To this end, we provide a dataset of 1031 agricultural sciences abstracts annotated with correct extractive answers. Additionally, this dataset builds on our previous work, which focused on quantity-centric search from a corpus of over 3.3M documents, which means the dataset also consists of 1130 query-document relevance judgments for 39 queries. The availability of both document-level annotations and corpus-level relevance judgments means that our dataset allows for an end-to-end evaluation of an information-seeking pipeline consisting of both literature search and the QA module. We present how our dataset can be used both for the evaluation of extractive quantity-focused QA from science literature and for exploring the impact of search on the downstream results, specifically focusing on hallucinations resulting from processing irrelevant documents with LLMs.
DOI: 10.5281/zenodo.15631486
title: PEQQS: a Dataset for Probing Extractive Quantity-focused Question Answering from Scientific Literature

description: Question Answering (QA) and Information Retrieval (IR) play a crucial role in information-seeking pipelines implemented in many emerging AI research assistant applications. Large Language Models (LLMs) have demonstrated exceptional effectiveness on QA tasks, with Retrieval Augmented Generation (RAG) techniques often boosting the results. However, in many of those emerging applications, the onus of conducting the actual literature search falls on the user, i.e. the user searches for the relevant literature and the LLM-based assistant extracts the solicited answers from each of the user-supplied documents. The interplay between the quality of the user-conducted search and the quality of the final results remains understudied.

In this work, we focus on a specific version of such pipeline, where users aim to obtain a specific quantity as an extractive answer (e.g., a value of a particular measurable parameter). To this end, we provide a dataset of 1031 agricultural sciences abstracts annotated with correct extractive answers. Additionally, this dataset builds on our previous work, which focused on quantity-centric search from a corpus of over 3.3M documents, which means the dataset also consists of 1130 query-document relevance judgments for 39 queries. The availability of both document-level annotations and corpus-level relevance judgments means that our dataset allows for an end-to-end evaluation of an information-seeking pipeline consisting of both literature search and the QA module. We present how our dataset can be used both for the evaluation of extractive quantity-focused QA from science literature and for exploring the impact of search on the downstream results, specifically focusing on hallucinations resulting from processing irrelevant documents with LLMs.
DOI: 10.15468/dl.t6cap5
title: Occurrence Download

description: A dataset containing 568493 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Poa trivialis L.",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "Year is greater than or equal to 1900",
 "Year is less than or equal to 2010"
 ]
}

 The dataset includes 568493 records from 1036 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043679-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u4bw58
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Sinocyclocheilus brevibarbatus Zhao, Lan & Zhang, 2009"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0172253-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.