cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5665356
title: S85 | MICROCYSTINS | Microcystins from CyanoMetDB

description: A list of over 300 microcystins extracted from CyanoMetDB (latest version), mostly of natural origin. Provided by L. Janssen, Eawag. Dataset DOI: 10.5281/zenodo.5665355.

Over 300 microcystins extracted from CyanoMetDB (latest version), most of natural origin. This completes the draft version of S83 EPA CCL5 wherein Cyanotoxin "Microcystin".Another list with 7 entries under same name (singular) exists (https://comptox.epa.gov/dashboard/chemical_lists/MICROCYSTIN)

All fields provided by Lilli from CyanoMetDB retained* except for following changes



   DTXSIDs updated via comptox search using InChIKeys.

   Missing PubChem IDs updated using PubChem identifier exchange 

   "PREFERRED NAMES" obtained added as additional synonyms column
DOI: 10.15468/dl.9mb6bq
title: Occurrence Download

description: A dataset containing 17396 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Continent is one of (North America, Asia)",
 "Country is one of (United States of America, China, Japan, Canada, Chinese Taipei, Hong Kong, Korea, Republic of, Macao)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is one of (Coordinate rounded, Geodetic datum assumed WGS84, Country derived from coordinates, Continent derived from coordinates)",
 "TaxonKey is Saururus"
 ]
}

 The dataset includes 17396 records from 167 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028115-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/cen0nz
title: PAN-00107170 - coin/coin-related, stad, duit

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00107170&lt;/p&gt;
description: Modified: 2025-07-29T09:53:59+02:00
DOI: 10.5281/zenodo.17814856
title: Training Code and Dataset for AgriBioNER  (ncRNA and Disease NER)

description:  

This repository contains the dataset, training code, and associated resources developed for ncRNA and Disease Named Entity Recognition (NER) in agricultural scientific literature as part of the AgriBioNER project. These materials support reproducible research and enable further development in agricultural biomedical text mining.

1. Annotated Dataset for Agricultural NER

The dataset includes manually annotated agricultural research abstracts containing two specialized entity types: NON-CODING_RNA and DISEASE. All annotations follow a structured span-based format compatible with the spaCy NER framework. This dataset provides the foundation for training and comparing transformer-based and classical NER models within the agricultural domain.

2. Transformer Model Training Code (PubMedBERT + Other Transformers)

The repository provides complete training scripts for PubMedBERT and all other transformer-based models evaluated in our study. Each model was trained using spaCy’s en_core_web_trf pipeline, ensuring a consistent architecture and reproducible training environment. The scripts cover data preprocessing, model configuration, training, validation, and export for deployment.

3. spaCy Baseline Model Training Code (en_core_web_lg)

spaCy(en_core_web_lg) uses simple spacy pipeline without en_core_web_trf

4. AgriBioNER Web Application

To demonstrate real-world usability, we provide a publicly accessible web-based application, AgriBioNER, which allows users to upload text or input agricultural abstracts for automatic ncRNA and disease NER. The application highlights extracted entities and provides interactive outputs such as tables, word clouds, and co-occurrence networks.Web App Link: https://huggingface.co/spaces/BhaveshKChoubisa/AgriBioNER
DOI: 10.5281/zenodo.17814855
title: Training Code and Dataset for AgriBioNER  (ncRNA and Disease NER)

description:  

This repository contains the dataset, training code, and associated resources developed for ncRNA and Disease Named Entity Recognition (NER) in agricultural scientific literature as part of the AgriBioNER project. These materials support reproducible research and enable further development in agricultural biomedical text mining.

1. Annotated Dataset for Agricultural NER

The dataset includes manually annotated agricultural research abstracts containing two specialized entity types: NON-CODING_RNA and DISEASE. All annotations follow a structured span-based format compatible with the spaCy NER framework. This dataset provides the foundation for training and comparing transformer-based and classical NER models within the agricultural domain.

2. Transformer Model Training Code (PubMedBERT + Other Transformers)

The repository provides complete training scripts for PubMedBERT and all other transformer-based models evaluated in our study. Each model was trained using spaCy’s en_core_web_trf pipeline, ensuring a consistent architecture and reproducible training environment. The scripts cover data preprocessing, model configuration, training, validation, and export for deployment.

3. spaCy Baseline Model Training Code (en_core_web_lg)

spaCy(en_core_web_lg) uses simple spacy pipeline without en_core_web_trf

4. AgriBioNER Web Application

To demonstrate real-world usability, we provide a publicly accessible web-based application, AgriBioNER, which allows users to upload text or input agricultural abstracts for automatic ncRNA and disease NER. The application highlights extracted entities and provides interactive outputs such as tables, word clouds, and co-occurrence networks.Web App Link: https://huggingface.co/spaces/BhaveshKChoubisa/AgriBioNER
DOI: 10.26165/juelich-data/jafqma
title: delta-carene + OH - Gas-phase oxidation - product study - 2019-06-13

description: delta-carene + OH - Gas-phase oxidation - product study - 2019-06-13Chamber information:actris_nf: Yinstitute: FZJirradiation: Natural sunlightlink: https://www.eurochamp.org/simulation-chambers/SAPHIRname: SAPHIRvolume: 270 m3wallMaterial: FEP filmExperimental conditions:date: '2019-06-13'lightSource: Natural sunlightprojectName: Delta-Carene OxidationreactiveSpecies: OHtype: Gas-phase oxidation - product studyMolecules:- name: delta-carene
DOI: 10.15468/dl.4sqvec
title: Occurrence Download

description: A dataset containing 29385 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Occurrence evidence",
 "Geometry POLYGON((118.49975 19.80449,118.19923 18.4615,116.1642 9.12453,121.49179 4.4786,129.59814 6.22482,124.5451 18.79373,118.49975 19.80449))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 29385 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028122-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17727272
title: Dataset for "Observation and Control of Potential-Dependent Surface State Formation at a Semiconductor-Electrolyte Interface via Optical Anisotropy"

description: Experimental raw data for the article "Observation and Control of Potential-Dependent Surface State Formation at a Semiconductor-Electrolyte Interface via Optical Anisotropy", published in Physical Review Letters (2025). DOI:10.1103/7vfj-hl9f.

The dataset is organized according to the publication's figures. The instruments used for generating the raw data were a LayTec EpiRas (file endings .ers and .ert) and a Princeton Applied Research VersaSTAT 3F potentiostat (file endings .par and .txt). For the zero-line correction, the two spectra 'RAS_zeroline_HCl.ers' and 'RAS_rotated_90deg_for_zeroline_HCl.ers'', where the sample was rotated by 90 deg, were added to obtain the effective zeroline.
DOI: 10.15129/64cb56ea-6979-48d4-a45d-b1c59117921c
title: Data for: "Atmospheric Pressure Plasma Synthesis of Monophase Bismuth Nanocrystals"

description: The dataset that corresponds to the results reported in the paper are included within this record as zip files, each corresponding to a set of measurements in each figure of the manuscript.

Additional results and raw data underlying this work (including additional microscopy images and results from other measurements) are also available in the Supporting Information document of the published paper where each figure/set of data is described.

Any other relevant data that may have not been included can be obtained by contacting the corresponding author.
DOI: 10.5284/1138781
title: Land off Hall Barn Road, Isleham

description: null
DOI: 10.15468/dl.8ycw4n
title: Occurrence Download

description: A dataset containing 792 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Harvard University Herbaria: All Records",
 "Country is Croatia"
 ]
}

 The dataset includes 792 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028126-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kq79fe
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is R-Bryophyta - Herbário do Museu Nacional - Bryophyta",
 "Country is Croatia"
 ]
}

 The dataset includes 13 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028125-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5xknha
title: Occurrence Download

description: A dataset containing 29385 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Occurrence evidence",
 "Geometry POLYGON((118.49975 19.80449,118.19923 18.4615,116.1642 9.12453,121.49179 4.4786,129.59814 6.22482,124.5451 18.79373,118.49975 19.80449))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 29385 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028123-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ceycvf
title: Occurrence Download

description: A dataset containing 369 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Austria",
 "DatasetKey is Collection Malakologie - SNSD",
 "HasCoordinate is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 369 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028127-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26165/juelich-data/ek7uq4
title: isoprene + OH - Gas-phase oxidation - product study - 2016-07-20

description: isoprene + OH - Gas-phase oxidation - product study - 2016-07-20Chamber information:actris_nf: Yinstitute: FZJlink: https://www.eurochamp.org/simulation-chambers/SAPHIRname: SAPHIRvolume: 270 m3wallMaterial: FEP filmExperimental conditions:date: '2016-07-20'lightSource: Natural sunlightprojectName: Isoprene Isomerization NO dependencereactiveSpecies: OHtype: Gas-phase oxidation - product studyMolecules:- name: isoprene
DOI: 10.15468/dl.3ymwq3
title: Occurrence Download

description: A dataset containing 64 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eulemur sanfordi",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 64 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028128-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17026/ar/3bgd6z
title: PAN-00164490 - stone adze

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00164490&lt;/p&gt;
description: Modified: 2025-07-04T16:58:45+02:00
DOI: 10.26165/juelich-data/axkmyw
title: isoprene + OH - Gas-phase oxidation - product study - 2016-07-19

description: isoprene + OH - Gas-phase oxidation - product study - 2016-07-19Chamber information:actris_nf: Yinstitute: FZJlink: https://www.eurochamp.org/simulation-chambers/SAPHIRname: SAPHIRvolume: 270 m3wallMaterial: FEP filmExperimental conditions:date: '2016-07-19'lightSource: Natural sunlightprojectName: Isoprene Isomerization NO dependencereactiveSpecies: OHtype: Gas-phase oxidation - product studyMolecules:- name: isoprene
DOI: 10.15468/dl.62sqjn
title: Occurrence Download

description: A dataset containing 2652825 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Antarctica",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2652825 records from 1269 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0028087-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b7nkak
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Yushania longiaurita Q.F.Zheng & K.F.Huang"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140734-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zxb3tg
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Ateles chamek (Humboldt, 1812)"
 ]
}

 The dataset includes 151 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0161040-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8fexou
title: Occurrence Download

description: A dataset containing 710 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Scilla mischtschenkoana Grossh.",
 "TaxonKey is Scilla peruviana L."
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 710 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019746-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zbkq36
title: Occurrence Download

description: A dataset containing 442 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gymnosporia arbutifolia (Hochst. ex A.Rich.) Loes."
 ]
}

 The dataset includes 442 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018360-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pk96vr
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sphagnum subsecundum Nees",
 "HasCoordinate is true",
 "Country is Iceland",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000",
 "CoordinateUncertaintyInMeters is less than 10000"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140735-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jgkfk5
title: Occurrence Download

description: A dataset containing 146 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Living Specimen"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Galictis cuja (Molina, 1782)",
 "Year 1967-2021"
 ]
}

 The dataset includes 146 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0161081-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ww1euu
title: Occurrence Download

description: A dataset containing 3125 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Scilla luciliae (Boiss.) Speta"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3125 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019747-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.75dcvd
title: Occurrence Download

description: A dataset containing 115 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Zaolutus actius Hand, 1955",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is MANAGED"
 ]
 }
 },
 {
 "not" : {
 "EstablishmentMeans" : [
 "is not null"
 ]
 }
 }
 ]
 },
 {
 "or" : [
 "OccurrenceStatus is Present",
 {
 "not" : {
 "OccurrenceStatus" : [
 "is not null"
 ]
 }
 }
 ]
 }
 ]
}

 The dataset includes 115 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083732-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eucwle
title: Occurrence Download

description: A dataset containing 9100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((95.72088 21.38027,109.00435 21.38027,109.00435 33.18558,95.72088 33.18558,95.72088 21.38027))",
 "TaxonKey is Gentianaceae"
 ]
}

 The dataset includes 9100 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019747-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.a4epde
title: Occurrence Download

description: A dataset containing 278 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Eragrostis hispida K.Schum."
 ]
}

 The dataset includes 278 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0161059-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3ms969
title: Occurrence Download

description: A dataset containing 438 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cardamine uliginosa M.Bieb."
 ]
}

 The dataset includes 438 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083737-240229165702484/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8cpjci
title: Occurrence Download

description: A dataset containing 334 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Human Observation"
 ]
 },
 {
 "or" : [
 "Country is China",
 "Country is Korea, Republic of",
 "Country is Korea (Democratic People’s Republic of)",
 "Country is Russian Federation",
 "Country is Japan"
 ]
 },
 "Geometry POLYGON((107.45508 47.50488,116.87695 27.53613,134.45508 25.14551,152.66602 35.90332,165.11133 47.92676,140.71289 58.19238,121.30664 60.37207,107.45508 47.50488))",
 "HasCoordinate is true",
 "TaxonKey is Berberis amurensis Rupr.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 334 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019747-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aa2kvv
title: Occurrence Download

description: A dataset containing 2355 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Literature Occurrence",
 "BasisOfRecord is Specimen",
 "BasisOfRecord is Material sample",
 "BasisOfRecord is Living Specimen"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Leopardus pardalis (Linnaeus, 1758)",
 "Year 1967-2021"
 ]
}

 The dataset includes 2355 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0161060-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tfbsht
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossia virotii (Guillaumin) N.Snow"
 ]
}

 The dataset includes 35 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018348-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.i8842q
title: Occurrence Download

description: A dataset containing 1376 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Scilla sardensis (Whittall ex Barr & Sugden) Speta"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1376 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019748-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w28afm
title: Occurrence Download

description: A dataset containing 8338 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tsuga heterophylla (Raf.) Sarg."
 ]
}

 The dataset includes 8338 records from 204 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0161082-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f2cajc
title: Occurrence Download

description: A dataset containing 521 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Halopeplis amplexicaulis (Vahl) Ung.-Sternb. ex Ces., Pass. & Gibelli"
 ]
}

 The dataset includes 521 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018368-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.