cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.tsmqt8
title: Occurrence Download

description: A dataset containing 29912 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "TaxonKey is Phyllomedusidae"
 ]
}

 The dataset includes 29912 records from 292 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003293-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.789nz3
title: Occurrence Download

description: A dataset containing 231 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Specimen, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is one of (Coordinate rounded, Geodetic datum assumed WGS84, Coordinate reprojected, Country derived from coordinates, Continent derived from coordinates)",
 "TaxonKey is Meliosma alba (Schltdl.) Walp."
 ]
}

 The dataset includes 231 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003295-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.su252r
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lepthoplosternum pectorale (Boulenger, 1895)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 177 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003296-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r5mxp6
title: Occurrence Download

description: A dataset containing 13770 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Persea americana Mill."
 ]
}

 The dataset includes 13770 records from 633 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003294-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.prxbgy
title: Occurrence Download

description: A dataset containing 3046 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Occurrence data for unidentified species and for species not yet listed in the species checklist of Seychelles"
 ]
}

 The dataset includes 3046 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003298-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hrwexq
title: Occurrence Download

description: A dataset containing 345 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Loricariichthys platymetopon Isbrücker & Nijssen, 1979",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 345 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003299-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.11583/dtu.28443050
title: Nudging tool to prevent rebound effects and promote secondary benefits of sustainable design

description: This data includes the nudging tool which is part of the MSc Thesis: "Using behavioural design to prevent rebound effects and promote secondary benefits of sustainable design"<br><br>The goal of the project is to develop a tool for designers that utilises behavioural design to prevent rebound effects and promote secondary benefits. The content of the tool is based on a comprehensive literature review on behavioural design and environmental sustainability. The tool was tested with various experts within the field and the industry.
DOI: 10.15468/dl.8q8gf6
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Loricariichthys rostratus Reis & Pereira, 2000",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 39 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003300-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10726573
title: Risk of bias assessments (RoB 2 and ROBINS-I) for the Cochrane review 'Vaccines for the prevention of infections in adults with haematological malignancies'

description: Risk of bias assessments and support for judgement with ROB 2 and ROBINS-I tool for the Cochrane Review: Vaccines for the prevention of infections in adults with haematological malignancies.
description: funded by the Federal Ministry of Education and Research, Germany (funding number: 01KG2104)
DOI: 10.5281/zenodo.14900503
title: Risk of bias assessments (RoB 2 and ROBINS-I) for the Cochrane review 'Vaccines for the prevention of infections in adults with haematological malignancies'

description: Risk of bias assessments and support for judgement with ROB 2 and ROBINS-I tool for the Cochrane Review: Vaccines for the prevention of infections in adults with haematological malignancies.
description: funded by the Federal Ministry of Education and Research, Germany (funding number: 01KG2104)
DOI: 10.15468/dl.vfrcv3
title: Occurrence Download

description: A dataset containing 1980 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Persea indica (L.) Spreng."
 ]
}

 The dataset includes 1980 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003301-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10650466
title: BioToFlow: a corpus annotated with bioinformatics workflows information

description: BioToFlow is a corpus describing bioinformatics workflows in English publications. These annotations are available in the BRAT Rapid Annotation Tool (BRAT) standoff format (https://brat.nlplab.org/standoff.html).


This corpus is composed of 52 articles (26 articles related to Nextflow workflows and 26 on Snakemake workflows, randomly selected from PubMed) with a total of 78 419 tokens 27 786 annotated tokens.

 

Repository organisation







The articles are separated into two directories:





one containing all the articles for the training phases (39) and

the other with 13 articles for test.




Papers
Please cite BioToFlow in any research that uses or extends it :

 





Sebe, C., Cohen-Boulakia, S., Ferret, O., Névéol, A.: Extracting information in a low-resource setting: Case study on bioinformatics workflows (2024), https://arxiv.org/abs/2411.19295



In this article accepted to IDA 2025 (in English), we present *BioToFlow* and experiments with few shot named entity recognition (NER) using an autoregressive language model, we also use a pre-existing corpus and test integration of workflow knowledge in NER models.


 





Clémence Sebe, Sarah Cohen-Boulakia, Olivier Ferret, Aurélie Névéol. Extraction d’entités nommées décrivant des chaînes de traitement bioinformatiques dans des articles scientifiques en anglais. 35emes Journées d’Études sur la Parole (JEP 2024) 31eme Conférence sur le Traitement Automatique des Langues Naturelles (TALN 2024) 26eme Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues (RECITAL 2024), Jul 2024, Toulouse, France. pp.422-434. hal-04623033.



In this article (in French), we present the second version of *BioToFlow*. The new articles are annotated with entities and attributes. We conduct preliminary experiments with NER with a specific focus on the memorization vs. generalization abilities of statistical and rule-based methods.






Sebe C., Névéol A., Cohen-Boulakia S. & Gaignard A. (2023). Extraction d’informations sur les workflows scientifiques à partir de la littérature. volume Extraction et Gestion des Connaissances, RNTI-E-39, p. 313.



In this article (in French), we present the first version of the corpus with 24 articles annotated with entities and relations. We show the feasibility of the task of NER.


 

Contact







Clémence Sebe, clemence.sebe@universite-paris-saclay.fr




Funding
This work received support from the National Research Agency under the France 2030 program, with reference to ANR-22-PESN-0007.
DOI: 10.5281/zenodo.10650467
title: BioToFlow Corpus

description: BioToFlow is a corpus describing bioinformatic workflows in publications. These annotations are available in the BRAT Rapid Annotation Tool (BRAT) standoff format.
DOI: 10.5281/zenodo.11204427
title: BioToFlow Corpus

description: BioToFlow is a corpus describing bioinformatic workflows in publications. These annotations are available in the BRAT Rapid Annotation Tool (BRAT) standoff format.
DOI: 10.5281/zenodo.14900544
title: BioToFlow: a corpus annotated with bioinformatics workflows information

description: BioToFlow is a corpus describing bioinformatics workflows in English publications. These annotations are available in the BRAT Rapid Annotation Tool (BRAT) standoff format (https://brat.nlplab.org/standoff.html).


This corpus is composed of 52 articles (26 articles related to Nextflow workflows and 26 on Snakemake workflows, randomly selected from PubMed) with a total of 78 419 tokens 27 786 annotated tokens.

 

Repository organisation







The articles are separated into two directories:





one containing all the articles for the training phases (39) and

the other with 13 articles for test.




Papers
Please cite BioToFlow in any research that uses or extends it :

 





Sebe, C., Cohen-Boulakia, S., Ferret, O., Névéol, A.: Extracting information in a low-resource setting: Case study on bioinformatics workflows (2024), https://arxiv.org/abs/2411.19295



In this article accepted to IDA 2025 (in English), we present *BioToFlow* and experiments with few shot named entity recognition (NER) using an autoregressive language model, we also use a pre-existing corpus and test integration of workflow knowledge in NER models.


 





Clémence Sebe, Sarah Cohen-Boulakia, Olivier Ferret, Aurélie Névéol. Extraction d’entités nommées décrivant des chaînes de traitement bioinformatiques dans des articles scientifiques en anglais. 35emes Journées d’Études sur la Parole (JEP 2024) 31eme Conférence sur le Traitement Automatique des Langues Naturelles (TALN 2024) 26eme Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues (RECITAL 2024), Jul 2024, Toulouse, France. pp.422-434. hal-04623033.



In this article (in French), we present the second version of *BioToFlow*. The new articles are annotated with entities and attributes. We conduct preliminary experiments with NER with a specific focus on the memorization vs. generalization abilities of statistical and rule-based methods.






Sebe C., Névéol A., Cohen-Boulakia S. & Gaignard A. (2023). Extraction d’informations sur les workflows scientifiques à partir de la littérature. volume Extraction et Gestion des Connaissances, RNTI-E-39, p. 313.



In this article (in French), we present the first version of the corpus with 24 articles annotated with entities and relations. We show the feasibility of the task of NER.


 

Contact







Clémence Sebe, clemence.sebe@universite-paris-saclay.fr




Funding
This work received support from the National Research Agency under the France 2030 program, with reference to ANR-22-PESN-0007.
DOI: 10.5281/zenodo.14900453
title: SIMULATED PHISAT-2 METHANE BENCHMARK DATASET

description: Simulation of PhiSat-2 images based on AVIRIS-NG hyperspectral data for methane detection.
DOI: 10.5281/zenodo.14900454
title: SIMULATED PHISAT-2 METHANE BENCHMARK DATASET

description: Simulation of PhiSat-2 images based on AVIRIS-NG hyperspectral data for methane detection.
DOI: 10.5281/zenodo.14900609
title: Test upload
DOI: 10.5281/zenodo.14900610
title: Test upload
DOI: 10.5281/zenodo.14900195
title: Novel approach to rectal cancer in inflammatory bowel disease: preliminary results from a hyperfractionated-accelerated chemoradiation protocol.
DOI: 10.5281/zenodo.14900196
title: Novel approach to rectal cancer in inflammatory bowel disease: preliminary results from a hyperfractionated-accelerated chemoradiation protocol.
DOI: 10.15468/dl.ffpgg4
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leporinus macrocephalus Garavello & Britski, 1988",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 126 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003302-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3v5asn
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ephedra distachya L.",
 "Geometry POLYGON((-4.57907617500001 39.884719509, -4.57907617500001 41.165844755, -3.05298331400002 41.165844755, -3.05298331400002 39.884719509, -4.57907617500001 39.884719509))"
 ]
}

 The dataset includes 58 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003303-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.11583/dtu.27835929
title: Updated Sea Ice Products for the NIMBUS 5 Electrically Scanning Microwave Radiometer data from 1972–1977

description: The Electrically Scanning Microwave Radiometer (ESMR) instrument onboard the NIMBUS 5 satellite was a one-channel microwave radiometer that measured the 19.35 GHz horizontally polarized brightness temperature (TB) from 11 December 1972 to 16 May 1977.Kolbe et. al. (2024) reprocessed this data in order to derive sea Ice concentration for the period and showed that sea ice extend and concentration was indeed recoverable, but one major challenge was that the implemented one-channel algorithm was unable to distinguish first year ice and multiyear ice, resulting in ambiguity between areas with multi-year ice, and areas with low sea ice concentration. Furthermore, since publishing, we have found the applied filtering to be removing too much data, especially after 1975, and on top of that, we have resolved minor data issues.Two datesets are uploaded here, split in to 4 files ;1) A reprocessed version of the data using the methods of Kolbe et. al. (2024), but with some corrections to the output and a new filtering scheme. This is a direct update to https://doi.org/10.5285/34a15b96f1134d9e95b9e486d74e49cf.2) A post processed dataset (LDTPcorrected) where a local dynamical tie point framework has been applied, which resolves the ambiguity by enforcing stability of tiepoints over time.For each dataset a file for each hemisphere (Northern Hemisphere, NH, and Southern Hemisphere (SH)) can be downloadet.The dataset is created using the code available in the referenced github repository https://github.com/EHTellefsen/N5ESMR-SIC-processing
DOI: 10.11583/dtu.27835929.v2
title: Updated Sea Ice Products for the NIMBUS 5 Electrically Scanning Microwave Radiometer data from 1972–1977

description: The Electrically Scanning Microwave Radiometer (ESMR) instrument onboard the NIMBUS 5 satellite was a one-channel microwave radiometer that measured the 19.35 GHz horizontally polarized brightness temperature (TB) from 11 December 1972 to 16 May 1977.Kolbe et. al. (2024) reprocessed this data in order to derive sea Ice concentration for the period and showed that sea ice extend and concentration was indeed recoverable, but one major challenge was that the implemented one-channel algorithm was unable to distinguish first year ice and multiyear ice, resulting in ambiguity between areas with multi-year ice, and areas with low sea ice concentration. Furthermore, since publishing, we have found the applied filtering to be removing too much data, especially after 1975, and on top of that, we have resolved minor data issues.Two datesets are uploaded here, split in to 4 files ;1) A reprocessed version of the data using the methods of Kolbe et. al. (2024), but with some corrections to the output and a new filtering scheme. This is a direct update to https://doi.org/10.5285/34a15b96f1134d9e95b9e486d74e49cf.2) A post processed dataset (LDTPcorrected) where a local dynamical tie point framework has been applied, which resolves the ambiguity by enforcing stability of tiepoints over time.For each dataset a file for each hemisphere (Northern Hemisphere, NH, and Southern Hemisphere (SH)) can be downloadet.The dataset is created using the code available in the referenced github repository https://github.com/EHTellefsen/N5ESMR-SIC-processing
DOI: 10.11583/dtu.27835929.v1
title: Updated Sea Ice Products for the NIMBUS 5 Electrically Scanning Microwave Radiometer data from 1972–1977

description: The Electrically Scanning Microwave Radiometer (ESMR) instrument onboard the NIMBUS 5 satellite was a one-channel microwave radiometer that measured the 19.35 GHz horizontally polarized brightness temperature (TB) from 11 December 1972 to 16 May 1977.Kolbe et. al. (2024) reprocessed this data in order to derive sea Ice concentration for the period and showed that sea ice extend and concentration was indeed recoverable, but one major challenge was that the implemented one-channel algorithm was unable to distinguish first year ice and multiyear ice, resulting in ambiguity between areas with multi-year ice, and areas with low sea ice concentration. Furthermore, since publishing, we have found the applied filtering to be removing too much data, especially after 1975, and on top of that, we have resolved minor data issues.Two datesets are uploaded here, split in to 4 files ;1) A reprocessed version of the data using the methods of Kolbe et. al. (2024), but with some corrections to the output and a new filtering scheme. This is a direct update to https://doi.org/10.5285/34a15b96f1134d9e95b9e486d74e49cf.2) A post processed dataset (LDTPcorrected) where a local dynamical tie point framework has been applied, which resolves the ambiguity by enforcing stability of tiepoints over time.For each dataset a file for each hemisphere (Northern Hemisphere, NH, and Southern Hemisphere (SH)) can be downloadet.The dataset is created using the code available in the referenced github repository https://github.com/EHTellefsen/N5ESMR-SIC-processing
DOI: 10.15468/dl.6uu4aw
title: Occurrence Download

description: A dataset containing 616 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leporinus obtusidens (Valenciennes, 1837)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 616 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003304-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6xxr33
title: Occurrence Download

description: A dataset containing 136 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ephedra fragilis Desf.",
 "Geometry POLYGON((-4.57907617500001 39.884719509, -4.57907617500001 41.165844755, -3.05298331400002 41.165844755, -3.05298331400002 39.884719509, -4.57907617500001 39.884719509))"
 ]
}

 The dataset includes 136 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003305-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60656/4bf05f409abe47d4
title: Custom collection of categorize, and classification data from Jülich on 22 Jul 2021
DOI: 10.21961/mdm:45851
title: DZG-Basisdatensatz

description: Deutsch: Die Deutsche Zentren der Gesundheitsforschung (DZG) haben sich dazu verpflichtet, die Standardisierung und Harmonisierung ihrer Daten und Prozesse voranzutreiben, um die Zusammenarbeit und Forschungskapazitäten zu stärken. In diesem Zusammenhang wurde der DZG Basisdatensatz von klinisch Forschendern aller DZG entwickelt, der prospektiv in DZG geförderten Studien zu erheben ist.
Der DZG-übergreifende Basisdatensatz ermöglicht es Forschenden, mit den erhobenen Daten in offenen Projekten zu arbeiten und trägt so zur Stärkung der Forschungskapazitäten bei.
English: The German Centers for Health Research (DZG) have committed to advancing the standardization and harmonization of their data and processes to strengthen collaboration and research capabilities. In this context, the DZG core dataset was developed by clinical researchers from all DZG, which is to be collected prospectively in DZG-funded studies.
The DZG basic dataset allows researchers to work with the collected data in open projects and thus contributes to strengthening research capacities.
DOI: 10.15468/dl.nd3ac4
title: Occurrence Download

description: A dataset containing 123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leporinus piavussu Britski, Birindelli & Garavello, 2012",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 123 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003306-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mftaqk
title: Occurrence Download

description: A dataset containing 3490453 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Living Specimen, Human Observation, Observation)",
 "Country is Kenya",
 "Year is one of (2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024, 2025)"
 ]
}

 The dataset includes 3490453 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003292-250218110819086/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.