cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13735622
title: YTU-CH Dataset

description: YTU-CH (Yildiz Technical University - Cultural Heritage) Dataset was specifically developed for edge detection in cultural heritage structures. The dataset comprises a variety of images captured from the Internet, cameras, and low-cost UAVs, all featuring three bands (RGB) and an 8-bit radiometric resolution. In the dataset, contours and cracks have been manually digitized in all images. To standardize the dataset, images were divided into 512×512 pixel patches due to their variable sizes. Patches with an edge detail ratio of less than 2% were excluded, resulting in a final set of 5,380 labeled image patches. The dataset is then split into 90% (4880 image patches) and 10% (500 image patches) for training and testing, respectively. 

The creation of this dataset was funded by the Scientific and Technological Research Council of Türkiye (TUBITAK) 1001 program under Project no. 122Y017.
DOI: 10.15468/dl.c2q67v
title: Occurrence Download

description: A dataset containing 3853 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Gazania rigens (L.) Gaertn."
 ]
}

 The dataset includes 3853 records from 142 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007434-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5zgfwd
title: Occurrence Download

description: A dataset containing 313 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Japan",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Sciadopitys verticillata (Thunb.) Siebold & Zucc."
 ]
}

 The dataset includes 313 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007433-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gbwncq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Paracontias kankana Köhler, Vieites, Glaw, Kaffenberger & Vences, 2009)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007435-240906103802322/datasets/export for details.
DOI: 10.15468/dl.t876wh
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Micrixalus kottigeharensis (Rao, 1937))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 60 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007437-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ytbbkt
title: Occurrence Download

description: A dataset containing 204 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chelonoidis guntheri (Baur, 1889))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 204 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007436-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8pgf2f
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Paracontias fasika Köhler, Vences, Erbacher & Glaw, 2010)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007438-240906103802322/datasets/export for details.
DOI: 10.15468/dl.meacdh
title: Occurrence Download

description: A dataset containing 2619112 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Banco de Datos de la Biodiversidad de la Comunitat Valenciana"
 ]
}

 The dataset includes 2619112 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007358-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tf5qqa
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Nyctibatrachus beddomii (Boulenger, 1882))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007439-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8yskqk
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Chelonoidis microphyes (Günther, 1875))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 30 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007440-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10559052
title: Genome-wide tool for sensitive de novo identification of interspersed and tandem repeats
title: Repeated elements de novo identification tool

description: Genomic repeats are functionally ubiquitous structural units found in all genomes. These repeating patterns have a manifold signature and structure, making identification challenging. To address this challenge, we developed software that can rapidly and accurately detect any type of repeated sequences de novo in genomic sequences in the form of interspersed or clustered repeats. Numerous forms of repeated sequences and “repeat within repeat” patterns can be identified even for very complex sequence variants and for implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any type of short- or long-tandem repeats belonging to a wide range of organized into higher-order repeat structures of telomers or large satellite sequences can be detected. By combining precision and versatility, our tool significantly contributes to elucidating the intricate landscape of genomic repeats.
description: The online tool to perform tandem repeat searching is accessible at:
https://primerdigital.com/tools/pcr.html

The source code is available at: 
https://github.com/rkalendar/Repeater
DOI: 10.5281/zenodo.10664228
title: Genome-wide tool for sensitive de novo identification of interspersed and tandem repeats
title: Repeated elements de novo identification tool

description: Genomic repeats are functionally ubiquitous structural units found in all genomes. These repeating patterns have a manifold signature and structure, making identification challenging. To address this challenge, we developed software that can rapidly and accurately detect any type of repeated sequences de novo in genomic sequences in the form of interspersed or clustered repeats. Numerous forms of repeated sequences and “repeat within repeat” patterns can be identified even for very complex sequence variants and for implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any type of short- or long-tandem repeats belonging to a wide range of organized into higher-order repeat structures of telomers or large satellite sequences can be detected. By combining precision and versatility, our tool significantly contributes to elucidating the intricate landscape of genomic repeats.
description: The online tool to perform tandem repeat searching is accessible at: https://primerdigital.com/tools/pcr.html The source code is available at: https://github.com/rkalendar/Repeater
DOI: 10.5281/zenodo.10395176
title: Genome-wide tool for sensitive de novo identification of interspersed and tandem repeats
title: Repeated elements de novo identification tool

description: Genomic repeats are functionally ubiquitous structural units found in all genomes. These repeating patterns have a manifold signature and structure, making identification challenging. To address this challenge, we developed software that can rapidly and accurately detect any type of repeated sequences de novo in genomic sequences in the form of interspersed or clustered repeats. Numerous forms of repeated sequences and “repeat within repeat” patterns can be identified even for very complex sequence variants and for implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any type of short- or long-tandem repeats belonging to a wide range of organized into higher-order repeat structures of telomers or large satellite sequences can be detected. By combining precision and versatility, our tool significantly contributes to elucidating the intricate landscape of genomic repeats.
description: The online tool to perform tandem repeat searching is accessible at:
https://primerdigital.com/tools/pcr.html

The source code is available at: 
https://github.com/rkalendar/Repeater
DOI: 10.5281/zenodo.10700770
title: Genome-wide tool for sensitive de novo identification of interspersed and tandem repeats
title: Repeated elements de novo identification tool

description: Genomic repeats are functionally ubiquitous structural units found in all genomes. These repeating patterns have a manifold signature and structure, making identification challenging. To address this challenge, we developed software that can rapidly and accurately detect any type of repeated sequences de novo in genomic sequences in the form of interspersed or clustered repeats. Numerous forms of repeated sequences and “repeat within repeat” patterns can be identified even for very complex sequence variants and for implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any type of short- or long-tandem repeats belonging to a wide range of organized into higher-order repeat structures of telomers or large satellite sequences can be detected. By combining precision and versatility, our tool significantly contributes to elucidating the intricate landscape of genomic repeats.
description: The online tool to perform tandem repeat searching is accessible at: https://primerdigital.com/tools/pcr.html The source code is available at: https://github.com/rkalendar/Repeater
DOI: 10.5281/zenodo.10720281
title: Genome-wide tool for sensitive de novo identification of interspersed and tandem repeats
title: Repeated elements de novo identification tool

description: Genomic repeats are functionally ubiquitous structural units found in all genomes. These repeating patterns have a manifold signature and structure, making identification challenging. To address this challenge, we developed software that can rapidly and accurately detect any type of repeated sequences de novo in genomic sequences in the form of interspersed or clustered repeats. Numerous forms of repeated sequences and “repeat within repeat” patterns can be identified even for very complex sequence variants and for implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any type of short- or long-tandem repeats belonging to a wide range of organized into higher-order repeat structures of telomers or large satellite sequences can be detected. By combining precision and versatility, our tool significantly contributes to elucidating the intricate landscape of genomic repeats.
description: The online tool to perform tandem repeat searching is accessible at: https://primerdigital.com/tools/pcr.html The source code is available at: https://github.com/rkalendar/Repeater
DOI: 10.5281/zenodo.13735264
title: Genome-wide tool for rapid de novo identification and visualisation of interspersed and tandem
title: Repeated elements de novo identification tool

description: Genomic repeats are functionally ubiquitous structural units found in all genomes. Studying these repeats of different origins is essential for the evolution and adaptation of a given organism. These repeating patterns have manifold signatures and structures with varying degrees of homology, making their identification challenging. To address this challenge, we developed a new algorithm and software that can rapidly and accurately detect any repeated sequences de novo with varying degrees of homology in genomic sequences in interspersed or clustered repeats. Numerous forms of repeated sequences and complex patterns can be identified, even for complex sequence variants and implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any short- or long-tandem repeat belonging to a wide range of higher-order repeat structures of telomers or large satellite sequences can be detected. By combining precision and versatility, our tool contributes significantly to elucidating the intricate landscape of genomic repeats.
description: The online tool to perform tandem repeat searching is accessible at:https://primerdigital.com/tools/repeat.html

The source code is available at: https://github.com/rkalendar/Repeater
DOI: 10.5281/zenodo.8266485
title: Genome-wide tool for rapid de novo identification and visualisation of interspersed and tandem
title: Repeated elements de novo identification tool

description: Genomic repeats are functionally ubiquitous structural units found in all genomes. Studying these repeats of different origins is essential for the evolution and adaptation of a given organism. These repeating patterns have manifold signatures and structures with varying degrees of homology, making their identification challenging. To address this challenge, we developed a new algorithm and software that can rapidly and accurately detect any repeated sequences de novo with varying degrees of homology in genomic sequences in interspersed or clustered repeats. Numerous forms of repeated sequences and complex patterns can be identified, even for complex sequence variants and implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any short- or long-tandem repeat belonging to a wide range of higher-order repeat structures of telomers or large satellite sequences can be detected. By combining precision and versatility, our tool contributes significantly to elucidating the intricate landscape of genomic repeats.
description: The online tool to perform tandem repeat searching is accessible at:https://primerdigital.com/tools/repeat.html

The source code is available at: https://github.com/rkalendar/Repeater
DOI: 10.15468/dl.6f2sdx
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Phelsuma roesleri Glaw, Gehring, Köhler, Franzen & Vences, 2010)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007441-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5efbyb
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is one of (Daphnimorpha kudoi (Makino) Nakai, Daphnimorpha capitellata (H.Hara) Nakai, Apodicarpum ikenoi Makino)"
 ]
}

 The dataset includes 83 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007442-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13151369
title: Datasets for "Exploring the potential of neural machine translation for cross-language clinical NLP resource generation through annotation projection"

description: This repository contains the data and additional resources used for the paper:

"Exploring the Potential of Neural Machine Translation for Cross-Language Clinical NLP Resource Generation through Annotation Projection. Rodriguez Miret et al. Information (2024)".

There are four different datasets included, namely:



The (1)  DisTEMIST, (2)  DrugTEMIST and (3) MEDDOPROF Spanish corpora and corresponding versions in 10 different languages, created through Machine Translation and annotation projection techniques. The Catalan annotations, used in the paper's experiments, were validated by bilingual expert annotators, who also provided alternative translations for the annotated terms in case they were wrongly translated. Thus, for Catalan we provide two different versions of the data: (i) the output of the annotation projection process as is, without any further validation, and (ii) the validated version of the data. For the rest of the languages (with the exception of the DrugTEMIST English and Italian data, used for the MultiCardioNER shared task), only an unvalidated version is provided.

The (4) Catalan Clinical Case Corpus (CataCCC), a collection of 200 clinical case reports in originally written in Catalan covering a variety of clinical specialties. This corpus includes manually validated annotations for diseases, medications and professions created by the experts who annotated the corpora mentioned above, using the same guidelines and annottaion criteria. It can this be considered the first clinical Gold Standard corpus for diseases, medications and processions in Catalan.


It is noteworthy that the MEDDOPROF-related data includes annotations for two labels, PROFESION and SITUACION_LABORAL, but only the former was used for training and evaluation in the paper.

These are the 10 languages included in the repository (along with their language codes):



Spanish (`es-gs`, with `gs` standing for Gold Standard)

Catalan (`cat`)

English (`en`)

French (`fr`)

Italian (`it`)

Dutch (`nl`)

Portuguese (`pt`)

Romanian (`ro`)

Swedish (`sv`)

Czech (`cz`)


Related Links



Validation and Correction Guidelines for the Multilingual Annotation Projection of Gold Standard Corpora

MultiCardioNER Shared Task 


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: 10.5281/zenodo.13133124
title: Datasets for "Exploring the potential of neural machine translation for cross-language clinical NLP resource generation through annotation projection"

description: This repository contains the data and additional resources used for the paper:

"Exploring the Potential of Neural Machine Translation for Cross-Language Clinical NLP Resource Generation through Annotation Projection. Rodriguez Miret et al. Information (2024)".

There are four different datasets included, namely:



The (1)  DisTEMIST, (2)  DrugTEMIST and (3) MEDDOPROF Spanish corpora and corresponding versions in 10 different languages, created through Machine Translation and annotation projection techniques. The Catalan annotations, used in the paper's experiments, were validated by bilingual expert annotators, who also provided alternative translations for the annotated terms in case they were wrongly translated. Thus, for Catalan we provide two different versions of the data: (i) the output of the annotation projection process as is, without any further validation, and (ii) the validated version of the data. For the rest of the languages (with the exception of the DrugTEMIST English and Italian data, used for the MultiCardioNER shared task), only an unvalidated version is provided.

The (4) Catalan Clinical Case Corpus (CataCCC), a collection of 200 clinical case reports in originally written in Catalan covering a variety of clinical specialties. This corpus includes manually validated annotations for diseases, medications and professions created by the experts who annotated the corpora mentioned above, using the same guidelines and annottaion criteria. It can this be considered the first clinical Gold Standard corpus for diseases, medications and processions in Catalan.


It is noteworthy that the MEDDOPROF-related data includes annotations for two labels, PROFESION and SITUACION_LABORAL, but only the former was used for training and evaluation in the paper.

These are the 10 languages included in the repository (along with their language codes):



Spanish (`es-gs`, with `gs` standing for Gold Standard)

Catalan (`cat`)

English (`en`)

French (`fr`)

Italian (`it`)

Dutch (`nl`)

Portuguese (`pt`)

Romanian (`ro`)

Swedish (`sv`)

Czech (`cz`)


Related Links



Validation and Correction Guidelines for the Multilingual Annotation Projection of Gold Standard Corpora

MultiCardioNER Shared Task 


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: 10.5281/zenodo.12092908
title: The Role of Climate on the Emergence of Giant Caimaninae from the Miocene Western Amazonian Region

description: Supplementary Material of the manuscript "The Role of Climate on the Emergence of Giant Caimaninae from the Miocene Western Amazonian Region". The zip folder contains six subfolders with data and code, and a README file with the instructions to perform all the analyses.
DOI: 10.5281/zenodo.12092907
title: The Role of Climate on the Emergence of Giant Caimanines (Crocodylia, Alligatoroidea) from the Miocene Western Amazonian Region

description: Supplementary Material of the manuscript "The Role of Climate on the Emergence of Giant Caimanines (Crocodylia, Alligatoroidea) from the Miocene Western Amazonian Region". The zip folder contains six subfolders with data and code, and a README file with the instructions to perform all the analyses.
DOI: 10.5281/zenodo.13735700
title: The Role of Climate on the Emergence of Giant Caimanines (Crocodylia, Alligatoroidea) from the Miocene Western Amazonian Region

description: Supplementary Material of the manuscript "The Role of Climate on the Emergence of Giant Caimanines (Crocodylia, Alligatoroidea) from the Miocene Western Amazonian Region". The zip folder contains six subfolders with data and code, and a README file with the instructions to perform all the analyses.