cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15536902
title: ToxHabits-NER: A Gold-Standard annotated Dataset for Named Entity Recognition in Toxic Habits context.

description: ToxHabits-NER stands for Toxic Habits Named Entity Recognition. It is a gold-standard annotated dataset focused on the detection and classification of toxic habit mentions — such as tobacco use, alcohol consumption, and illicit drug use — within clinical texts written in Spanish.

This repository includes the corpus' train and test sets in multiple formats. The annotations cover mentions of toxic habits, associated behaviors, and contextual cues relevant for clinical and epidemiological studies. For more information, please check the attached README file.

ToxHabits-NER was developed by the Barcelona Supercomputing Center's NLP for Biomedical Information Analysis team. It is intended as a resource to advance research on toxic habit extraction and normalization tasks from medical documents.

This dataset is part of the ToxHabits Shared Task of BioCreative IX. 

For more information on the corpus, annotation scheme, and usage instructions, please visit: [link to your project page if you have one, or Zenodo landing page].

Please cite if you use this resource:



Salvador Lima-López, Wesam Alnabki, Gabriel Vayá-Abad, and Martin Krallinger.ToxHabits-NER: A Gold-Standard Annotated Dataset for Named Entity Recognition in Toxic Habits Context.Zenodo. 2025.DOI: 10.5281/zenodo.15304758.


@misc{toxhabitsner,    title={ToxHabits-NER: A Gold-Standard Annotated Dataset for Named Entity Recognition in Toxic Habits Context},    author={Lima-López, Salvador and Alnabki, Wesam and Vayá-Abad, Gabriel and Krallinger, Martin},    year={2025},    publisher={Zenodo},    doi={YOUR_DOI_HERE},    url={https://doi.org/10.5281/zenodo.15304758}

Related Links:





Annotation Guidelines (Spanish): -




Annotation Guidelines (English): -



License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Contact

If you have any questions or suggestions, please contact us at:

- Salvador Lima-López (<salvador [dot] limalopez [at] gmail [dot] com>)- Martin Krallinger (<krallinger [dot] martin [at] gmail [dot] com>)
DOI: 10.6084/m9.figshare.29115359
title: Additional file 1 of A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing variant in the GNPAT gene

description: Additional file 1: Table S1. Details of the whole genome sequences used as controls in this study. See the following URLs for more information on the biosample and bioproject IDs: https://www.ncbi.nlm.nih.gov/biosample/ and https://www.ncbi.nlm.nih.gov/bioproject/ . Nb_Ind_Breed: Number of individuals per breed.
DOI: 10.6084/m9.figshare.29115359.v1
title: Additional file 1 of A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing variant in the GNPAT gene

description: Additional file 1: Table S1. Details of the whole genome sequences used as controls in this study. See the following URLs for more information on the biosample and bioproject IDs: https://www.ncbi.nlm.nih.gov/biosample/ and https://www.ncbi.nlm.nih.gov/bioproject/ . Nb_Ind_Breed: Number of individuals per breed.
DOI: 10.6084/m9.figshare.29115365
title: Additional file 3 of A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing variant in the GNPAT gene

description: Additional file 3: Table S2. List of homozygous positional candidate variants found in the genomes of two RDCP-affected calves. Chr: Chromosome. "Present_in_39_Aubrac_controls" and "Present_in_1828_controls_from_other_breeds" indicate whether the variant was observed in at least one of the 39 Aubrac individuals not carrying the at-risk haplotype or in 1828 genomes of individuals from 70 other breeds used as controls (see Additional file 1: Table S1).
DOI: 10.6084/m9.figshare.29115365.v1
title: Additional file 3 of A bovine model of rhizomelic chondrodysplasia punctata caused by a deep intronic splicing variant in the GNPAT gene

description: Additional file 3: Table S2. List of homozygous positional candidate variants found in the genomes of two RDCP-affected calves. Chr: Chromosome. "Present_in_39_Aubrac_controls" and "Present_in_1828_controls_from_other_breeds" indicate whether the variant was observed in at least one of the 39 Aubrac individuals not carrying the at-risk haplotype or in 1828 genomes of individuals from 70 other breeds used as controls (see Additional file 1: Table S1).
DOI: 10.6084/m9.figshare.27925419
title: Space-Time Optical Diffraction from Synthetic Motion

description: Space-time diffraction efficiency as a function of pump-probe delay (Fig.2b)Probe pulse duration and spectral width as a function of 4f slit aperture width (Fig.S2b)
DOI: 10.15468/dl.5chpwz
title: Occurrence Download

description: A dataset containing 118 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Registro de anuros presentes en parcelas distribuidas en el páramo del Parque Nacional Natural Chingaza, Colombia"
 ]
}

 The dataset includes 118 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002721-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.afdzgr
title: Occurrence Download

description: A dataset containing 1493 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-1000.0",
 "Geometry POLYGON((23.51739 46.9198,47.56594 46.9198,47.56594 56.78643,23.51739 56.78643,23.51739 46.9198))",
 "OccurrenceStatus is Present",
 "TaxonKey is Corydalis cava (L.) Schweigg. & Körte",
 "Year 2000-2025"
 ]
}

 The dataset includes 1493 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002715-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/5fp-5b7-vmk
title: Orthiopteris Copel.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/sqr-9mq-0r1
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/8ez-0qp-b36
title: †Carbonicola McCoy, 1855

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vcx-pk3-8gh
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vlb-0ep-qje
title: †Orbitoina trinitatis (Douvillé, 1924)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/a2b-bha-b2p
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qg7-2s3-4mx
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7h2-rmk-6e6
title: Voacanga Thouars

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gwr-t93-evy
title: Orthiopteris Copel.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/awt-75t-pq5
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ebt-824-97j
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3a7-0y0-8k9
title: Taxodium Rich.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qc4-mep-5tv
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f3e-wkb-hd2
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/d31-gpq-b1g
title: Cycloclypeus W.B. Carpenter, 1856

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xqj-cz7-c31
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kz7-2q0-y0s
title: Abies Mill.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/cbz-1mg-6m7
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/chh-3q3-jlk
title: Orthiopteris Copel.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/730-q6s-y2r
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/xdx-nyf-318
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g28-g5g-lms
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yv7-syy-51h
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/2sl-msf-emk
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/35e-dc4-x3v
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7lk-53h-1wq
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/0vq-t9k-523
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/h85-ptn-2xh
title: †Anthracosia concinna (W. B. Wright, 1929)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/91c-r9v-6f2
title: Ulmus glabra Huds.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ma1-79g-5kz
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j9x-3kg-21r
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jr3-yzz-n79
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dnj-w0e-4m4
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/rz6-7za-p5z
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/g36-w6w-gat
title: Salix L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/nsy-508-7ck
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pkd-rkw-arb
title: Gluta L.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3t8-zlk-9az
title: Ilex cornuta Lindl. & Paxton

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6te-s0z-cpx
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lf0-ega-c9a
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zrf-qgr-g00
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.qt2ppz
title: Occurrence Download

description: A dataset containing 5452 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Oligosoma Girard, 1857",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5452 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006280-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xrsqj9
title: Occurrence Download

description: A dataset containing 195 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "Year 2023-2025",
 "Geometry POLYGON((8.96136 47.7155,9.02477 47.7155,9.02477 47.74642,8.96136 47.74642,8.96136 47.7155))",
 "TaxonKey is Aves",
 "CoordinateUncertaintyInMeters is less than or equal to 100"
 ]
}

 The dataset includes 195 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006812-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.35uuqn
title: Occurrence Download

description: A dataset listing the 38 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-92.66692 -4.23786,-79.24957 -4.23786,-79.24957 2.58556,-92.66692 2.58556,-92.66692 -4.23786))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Myliobatiformes",
 "Year 1950-2025"
 ]
}

 The dataset's 38 records were derived from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006799-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f88yxm
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Stolephorus indicus (van Hasselt, 1823)",
 "Year 2000-2025"
 ]
}

 The dataset includes 14 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006813-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.paye8f
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-9.62868 36.73069,-6.0155 36.73069,-6.0155 42.33343,-9.62868 42.33343,-9.62868 36.73069))",
 "OccurrenceStatus is Present",
 "TaxonKey is Aconitum napellus subsp. lusitanicum Rouy",
 "Year 1975-2025"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006814-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/ap3p-zktk
title: Measurement of Pm10_mass at Melpitz

description: Measurement of Pm10_mass at Melpitz
DOI: 10.48597/kcn5-9t43
title: Measurement of Pm25_mass at Melpitz

description: Measurement of Pm25_mass at Melpitz
DOI: 10.48597/7ur6-865d
title: Measurement of Pm25_mass at Melpitz

description: Measurement of Pm25_mass at Melpitz
DOI: 10.48597/gx8n-a9vz
title: Measurement of Pm25_mass at Melpitz

description: Measurement of Pm25_mass at Melpitz
DOI: 10.48597/jrjv-776g
title: Pm25_mass at Melpitz

description: Measurement of Pm25_mass at Melpitz
DOI: 10.48597/mkk3-yx9s
title: Measurement of Pm25_mass at Melpitz

description: Measurement of Pm25_mass at Melpitz
DOI: 10.48597/rqqu-gs2j
title: Measurement of Pm25_mass at Melpitz

description: Measurement of Pm25_mass at Melpitz
DOI: 10.48597/5rs3-ke92
title: Methane at Erie Community Center

description: Measurement of Methane at Erie Community Center
DOI: 10.48597/7nsv-w57m
title: Pm10_mass at Melpitz

description: Measurement of Pm10_mass at Melpitz
DOI: 10.48597/877a-j58n
title: Measurement of Pm10_mass at Melpitz

description: Measurement of Pm10_mass at Melpitz
DOI: 10.48597/aby8-w9mt
title: Measurement of Pm10_mass at Melpitz

description: Measurement of Pm10_mass at Melpitz
DOI: 10.48597/by3p-9rt8
title: Measurement of Pm10_mass at Melpitz

description: Measurement of Pm10_mass at Melpitz
DOI: 10.48597/gyv2-qnzm
title: Measurement of Pm10_mass at Melpitz

description: Measurement of Pm10_mass at Melpitz
DOI: 10.48597/wwzh-gvfb
title: Measurement of Methane at Erie Community Center

description: Measurement of Methane at Erie Community Center
DOI: 10.48597/bn4d-p285
title: Measurement of Pm10_mass at Melpitz

description: Measurement of Pm10_mass at Melpitz
DOI: 10.48597/bxyj-gx3q
title: Measurement of Methane at Erie Community Center

description: Measurement of Methane at Erie Community Center
DOI: 10.48597/xu57-gznw
title: Measurement of Pm10_mass at Melpitz

description: Measurement of Pm10_mass at Melpitz
DOI: 10.48597/k6qc-g7we
title: Measurement of Pm25_mass at Melpitz

description: Measurement of Pm25_mass at Melpitz
DOI: 10.15468/dl.gtxzrd
title: Occurrence Download

description: A dataset listing the 24 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-85.9353 -4.06193,-79.61675 -4.06193,-79.61675 0.6808,-85.9353 0.6808,-85.9353 -4.06193))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Myliobatiformes",
 "Year 1950-2025"
 ]
}

 The dataset's 24 records were derived from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006809-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2yafrg
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-9.63736 36.6311,-6.68417 36.6311,-6.68417 42.17733,-9.63736 42.17733,-9.63736 36.6311))",
 "OccurrenceStatus is Present",
 "TaxonKey is Aizoon hispanicum L."
 ]
}

 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006815-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bqn3j9
title: Occurrence Download

description: A dataset listing the 38 species recorded in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Geometry POLYGON((-92.66692 -4.23786,-88.94923 -4.23786,-79.61675 -4.23786,-79.24957 -4.23786,-79.24957 2.58556,-92.66692 2.58556,-92.66692 -4.23786))",
 "Geometry POLYGON((-85.9353 -4.06193,-79.61675 -4.06193,-79.61675 0.6808,-85.9353 0.6808,-85.9353 -4.06193))"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Myliobatiformes",
 "Year 1950-2025"
 ]
}

 The dataset's 38 records were derived from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006806-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rfunry
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-5.70341 36.06573,-5.70207 36.06598,-5.70072 36.06619,-5.70017 36.06645,-5.69966 36.06597,-5.69762 36.06621,-5.69707 36.06652,-5.69573 36.06705,-5.69477 36.06788,-5.69605 36.0686,-5.69866 36.06866,-5.69955 36.06804,-5.7006 36.0675,-5.70128 36.06706,-5.70235 36.06649,-5.70341 36.06573))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 67 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006816-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c7m58b
title: Occurrence Download

description: A dataset containing 20012290 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-10.5488 36.50328,-6.18206 36.50328,-6.18206 42.35211,-10.5488 42.35211,-10.5488 36.50328))",
 "OccurrenceStatus is Present",
 "Year 1975-2025"
 ]
}

 The dataset includes 20012290 records from 1040 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006783-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nesjrv
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-10.15897 36.72858,-6.19443 36.72858,-6.19443 42.27206,-10.15897 42.27206,-10.15897 36.72858))",
 "OccurrenceStatus is Present",
 "TaxonKey is Alchemilla transiens (Buser) Buser",
 "Year 1975-2025"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006818-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.whgmkx
title: Occurrence Download

description: A dataset containing 159606 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Mimosa L."
 ]
}

 The dataset includes 159606 records from 1026 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006810-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18258824
title: 15-the-hollow-sea-arabic
DOI: 10.5281/zenodo.18258825
title: 15-the-hollow-sea-arabic