cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17241697
title: MacSyDB/Secreton

description: Secreton raw data

This set of data was used to build MacSyDB/Secreton (http://macsydb.web.pasteur.fr/secreton/ The service is discontinuted).

The information presented was originally obtained using a protoptype of MacSyFinder program, eventually with some subsequent curation (check the literature references below).

Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial flagellum,which allow direct injection of bacterial effectors from bacterial cytoplasm to eukaryotic cells via a molecular needle (cf. schema above).NF-T3SS are found in animal and plant pathogens (*Yersinia pestis*, *Escherichia coli*, *Burkholderia*,...),but also in plant and insect symbionts (e.g., Rhizobiales).

This  dataset contains 216 NF-T3SS retrieved from 1385 complete genome sequences.These systems were detected with proteic profiles of NF-T3SS core genes (sctC, sctN, sctJ, sctQ, sctR, sctS, sctT, sctU, sctV),and with an analysis of the genomic context of the hits obtained.

(This data set is partly superseded by TXSSdb)

The data set in this archive is out of date, it is provided for reproducibility reasons.If you need updated data, visit our tools on galaxy server (http://galaxy.pasteur.fr)(https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr/repos/odoppelt/txsscan/TXSScan/)Content

data set content 2 data files in "tabulated separated value" (tsv) format.The first line of each files is the header.



info_replicon.tsv contains informations about the replicon.



Replicon: the identifier of the replicon

Taxid: the identifier of the taxa

Strain: The name of the strain

Taxonomy: The taxonomy each level is separate by ;

Replicon_type: The type of replicon 'plasmid' or 'Chromosome'



info_syst_annot.tsv contains informations about the systems themselves



Gene_cod:e  unique gene identifier

Gene_ID: The NCBI gene id

Protein_length: The lenght of the protein

Strand: The strand 'D' for direct 'C' for complement

Begin: the begining of gene on the replicon

End: the end of the gene on the replicon

Match: the name of the profil which match

Full-score: The hmm score

E-value: the hmm evalue

Best-domain-score: the hmm score of the best domain

Best-domain-evalue the hmm evalue of the best domain

C-value:

Coverage-profile: coverage

Match_begin: The start of trhe match in the protein

Match_end: The end of the match in the protein

Replicon: The name of the replicon

Predicted_system: The name of the predicted system

System_code: The unique identifier of this system occurrence

T3SS-familly: The name of T3SS secretion system

Gene_name: The name of the gene

Description: The description of the gene



README.md this file
DOI: 10.5281/zenodo.17241698
title: MacSyDB/Secreton

description: Secreton raw data

This set of data was used to build MacSyDB/Secreton (http://macsydb.web.pasteur.fr/secreton/ The service is discontinuted).

The information presented was originally obtained using a protoptype of MacSyFinder program, eventually with some subsequent curation (check the literature references below).

Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial flagellum,which allow direct injection of bacterial effectors from bacterial cytoplasm to eukaryotic cells via a molecular needle (cf. schema above).NF-T3SS are found in animal and plant pathogens (*Yersinia pestis*, *Escherichia coli*, *Burkholderia*,...),but also in plant and insect symbionts (e.g., Rhizobiales).

This  dataset contains 216 NF-T3SS retrieved from 1385 complete genome sequences.These systems were detected with proteic profiles of NF-T3SS core genes (sctC, sctN, sctJ, sctQ, sctR, sctS, sctT, sctU, sctV),and with an analysis of the genomic context of the hits obtained.

(This data set is partly superseded by TXSSdb)

The data set in this archive is out of date, it is provided for reproducibility reasons.If you need updated data, visit our tools on galaxy server (http://galaxy.pasteur.fr)(https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr/repos/odoppelt/txsscan/TXSScan/)Content

data set content 2 data files in "tabulated separated value" (tsv) format.The first line of each files is the header.



info_replicon.tsv contains informations about the replicon.



Replicon: the identifier of the replicon

Taxid: the identifier of the taxa

Strain: The name of the strain

Taxonomy: The taxonomy each level is separate by ;

Replicon_type: The type of replicon 'plasmid' or 'Chromosome'



info_syst_annot.tsv contains informations about the systems themselves



Gene_cod:e  unique gene identifier

Gene_ID: The NCBI gene id

Protein_length: The lenght of the protein

Strand: The strand 'D' for direct 'C' for complement

Begin: the begining of gene on the replicon

End: the end of the gene on the replicon

Match: the name of the profil which match

Full-score: The hmm score

E-value: the hmm evalue

Best-domain-score: the hmm score of the best domain

Best-domain-evalue the hmm evalue of the best domain

C-value:

Coverage-profile: coverage

Match_begin: The start of trhe match in the protein

Match_end: The end of the match in the protein

Replicon: The name of the replicon

Predicted_system: The name of the predicted system

System_code: The unique identifier of this system occurrence

T3SS-familly: The name of T3SS secretion system

Gene_name: The name of the gene

Description: The description of the gene



README.md this file
DOI: 10.13120/84b18605-cd31-48cb-ab08-75f2c9595b75
title: Black Sea - Eutrophication and Acidity aggregated datasets 1935/2024 v2025
title: Black_Sea_-_Eutrophication_and_Acidity_aggregated_datasets_1935/2024_v2025

description: EMODnet Chemistry aims to provide access to marine chemistry datasets and derived data products concerning eutrophication, acidity and contaminants. The importance of the selected substances and other parameters relates to the Marine Strategy Framework Directive (MSFD). This aggregated dataset contains all unrestricted EMODnet Chemistry data on eutrophication and acidity, and covers the Black Sea, Marmara Sea and Sea of Azov. Data were aggregated and quality controlled by the 'National Institute for Marine Research and Development 'Grigore Antipa' in Romania.
ITS-90 water temperature and water body salinity variables have also been included ('as are') to complete the eutrophication and acidity data. If you use these variables for calculations, please refer to SeaDataNet for the quality flags: https://www.seadatanet.org/Products/Aggregated-datasets .
Regional datasets concerning eutrophication and acidity are automatically harvested, and the resulting collections are aggregated and quality controlled using ODV Software and following a common methodology for all sea regions ( https://doi.org/10.13120/8xm0-5m67 ). Parameter names are based on P35 vocabulary, which relates to EMODnet Chemistry aggregated parameter names and is available at: https://vocab.nerc.ac.uk/search_nvs/P35/
When not present in original data, water body nitrate plus nitrite was calculated by summing all nitrate and nitrite parameters. The same procedure was applied for water body dissolved inorganic nitrogen (DIN), which was calculated by summing all nitrate, nitrite, and ammonium parameters. Concentrations per unit mass were converted to a unit volume using a constant density of 1.25 kg/L.
The aggregated dataset can also be downloaded as an ODV collection and spreadsheet, which is composed of a metadata header followed by tab separated values. This spreadsheet can be imported to ODV Software for visualisation (more information can be found at: https://www.seadatanet.org/Software/ODV ).
DOI: 10.13140/2.1.3358.8802
title: Supplementary research presentation to Cooling meat products in foodservice: Time, temperature, and growth of Clostridium perfringens ATCC 10388
DOI: 10.13120/13d2a552-ee18-49a0-abdf-ac7936bc070f
title: Mediterranean Sea - Eutrophication and Acidity aggregated datasets 1911/2024 v2025
title: Mediterranean_Sea_-_Eutrophication_and_Acidity_aggregated_datasets_1911/2024_v2025

description: EMODnet Chemistry aims to provide access to marine chemistry datasets and derived data products concerning eutrophication, acidity and contaminants. The importance of the selected substances and other parameters relates to the Marine Strategy Framework Directive (MSFD). This aggregated dataset contains all unrestricted EMODnet Chemistry data on eutrophication and acidity, and covers the Mediterranean Sea. Data were aggregated and quality controlled by the 'Hellenic Centre for Marine Research, Hellenic National Oceanographic Data Centre (HCMR/HNODC)' in Greece. 
ITS-90 water temperature and water body salinity variables have also been included ('as are') to complete the eutrophication and acidity data. If you use these variables for calculations, please refer to SeaDataNet for the quality flags: https://www.seadatanet.org/Products/Aggregated-datasets. 
Regional datasets concerning eutrophication and acidity are automatically harvested, and the resulting collections are aggregated and quality controlled using ODV Software and following a common methodology for all sea regions (https://doi.org/10.13120/8xm0-5m67 ) Parameter names are based on P35 vocabulary, which relates to EMODnet Chemistry aggregated parameter names and is available at: https://vocab.nerc.ac.uk/search_nvs/P35/.
When not present in original data, water body nitrate plus nitrite was calculated by summing all nitrate and nitrite parameters. The same procedure was applied for water body dissolved inorganic nitrogen (DIN), which was calculated by summing all nitrate, nitrite, and ammonium parameters. Concentrations per unit mass were converted to a unit volume using a constant density of 1.25 kg/L.
The aggregated dataset can also be downloaded as an ODV collection and spreadsheet, which is composed of a metadata header followed by tab separated values. This spreadsheet can be imported to ODV Software for visualisation (more information can be found at: https://www.seadatanet.org/Software/ODV ).
DOI: 10.15468/dl.pf6ju2
title: Occurrence Download

description: A dataset containing 533 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((3.29803 42.87428,4.59248 42.87428,4.59248 43.6837,3.29803 43.6837,3.29803 42.87428))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cetacea",
 "Year 2010-2025"
 ]
}

 The dataset includes 533 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040029-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8axhvr
title: Occurrence Download

description: A dataset containing 2028 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Moss occurrences of the Great Vasyugan Bog system"
 ]
}

 The dataset includes 2028 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040030-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3thmwj
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is UWS Flanders Moss Meiofauna Records 2015"
 ]
}

 The dataset includes 15 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040027-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.suqtuk
title: Occurrence Download

description: A dataset containing 1481 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-74.42414 40.76388,-74.43156 40.7615,-74.43146 40.75743,-74.42623 40.7563,-74.42135 40.75913,-74.42105 40.76211,-74.42414 40.76388))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1481 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040033-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13120/12bee998-56b5-4576-b1bb-37df1b3c1d6c
title: North East Atlantic Ocean - Contaminants aggregated datasets 1966/2023 v2025
title: North_East_Atlantic_Ocean_Contaminants_aggregated_datasets_1966/2023_v2025

description: EMODnet Chemistry aims to provide access to marine chemistry datasets and derived data products concerning eutrophication, acidity and contaminants. The importance of the selected substances and other parameters relates to the Marine Strategy Framework Directive (MSFD). This aggregated dataset contains all unrestricted EMODnet Chemistry data on potential hazardous substances, despite the fact that some data might not be related to pollution (e.g. collected by deep corer). Temperature, salinity and additional parameters are included when available. It covers the Northeast Atlantic Ocean (40W). Data were harmonised and validated by '‘IFREMER / IDM / SISMER - Scientific Information Systems for the SEA’ in France.
The dataset contains water (profiles), sediment (profiles and timeseries) and biota (timeseries). The temporal coverage is 1974–2018 for water measurements, 1966–2022 for sediment measurements and 1979–2023 for biota measurements.
Regional datasets concerning contaminants are automatically harvested and the resulting collections are harmonised and validated using ODV Software and following a common methodology for all sea regions ( https://doi.org/10.6092/8b52e8d7-dc92-4305-9337-7634a5cae3f4 ). Parameter names are based on P01 vocabulary, which relates to BODC Parameter Usage Vocabulary and is available at: https://vocab.nerc.ac.uk/search_nvs/P01/ .
The harmonised dataset can be downloaded as as an ODV spreadsheet, which is composed of a metadata header followed by tab separated values. This spreadsheet can be imported into ODV Software for visualisation (more information can be found at: https://www.seadatanet.org/Software/ODV ). In addition, the same dataset is offered also as a txt file in a long/vertical format, in which each P01 measurement is a record line. Additionally, there are a series of columns that split P01 terms into subcomponents (substance, CAS number, matrix...).This transposed format is more adapted to worksheet applications (e.g. LibreOffice Calc).
DOI: 10.5281/zenodo.17207521
title: Detecting Gender Stereotypes in Scratch Programming Tutorials

description: Artefact for our paper at Koli Calling 2025: 'Detecting Gender Stereotypes in Scratch Programming Tutorials' (doi:10.1145/3769994.3770019)

 

Projects in the `data` subdirectory are licensed under a Creative Commons Attribution-ShareAlike 2.0 license as described in the Scratch Terms of Use (Section 4.3). Projects in `data/projects/rpifoundation-tutorials` were published by Scratch user CodeClubRik/the Raspberry Pi Foundation, the ones in `data/projects/scratch-starter` by Scratch user Scratchteam.
DOI: 10.5281/zenodo.17207522
title: Detecting Gender Stereotypes in Scratch Programming Tutorials

description: Artefact for our paper at Koli Calling 2025: 'Detecting Gender Stereotypes in Scratch Programming Tutorials' (doi:10.1145/3769994.3770019)

 

Projects in the `data` subdirectory are licensed under a Creative Commons Attribution-ShareAlike 2.0 license as described in the Scratch Terms of Use (Section 4.3). Projects in `data/projects/rpifoundation-tutorials` were published by Scratch user CodeClubRik/the Raspberry Pi Foundation, the ones in `data/projects/scratch-starter` by Scratch user Scratchteam.
DOI: 10.15468/dl.m85kw2
title: Occurrence Download

description: A dataset containing 1721 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cissus quadrangularis"
 ]
}

 The dataset includes 1721 records from 120 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040034-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h7759f
title: Occurrence Download

description: A dataset containing 11634 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pheidole megacephala"
 ]
}

 The dataset includes 11634 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038839-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13120/8ee6c1fb-da30-45a7-baaa-3ebce46770b9
title: Arctic region - Contaminants aggregated datasets 1974/2022 v2025
title: Arctic_region_Contaminants_aggregated_datasets_1974/2022_v2025

description: EMODnet Chemistry aims to provide access to marine chemistry datasets and derived data products concerning eutrophication, acidity and contaminants. The importance of the selected substances and other parameters relates to the Marine Strategy Framework Directive (MSFD). This aggregated dataset contains all unrestricted EMODnet Chemistry data on potential hazardous substances, despite the fact that some data might not be related to pollution (e.g. collected by deep corer). Temperature, salinity and additional parameters are included when available. It covers the Norwegian Sea, Barents Sea, Greenland Sea and Icelandic Waters. Data were harmonised and validated by the 'Institute of Marine Research - Norwegian Marine Data Centre (NMD)' in Norway.
The dataset contains water and sediment profiles. The temporal coverage is 1974–2011 for water measurements and 1974–2022 for sediment measurements.
Regional datasets concerning contaminants are automatically harvested and the resulting collections are harmonised and validated using ODV Software and following a common methodology for all sea regions ( https://doi.org/10.6092/8b52e8d7-dc92-4305-9337-7634a5cae3f4 ). Parameter names are based on P01 vocabulary, which relates to BODC Parameter Usage Vocabulary and is available at: https://vocab.nerc.ac.uk/search_nvs/P01/ .
The harmonised dataset can be downloaded as as an ODV spreadsheet, which is composed of a metadata header followed by tab separated values. This spreadsheet can be imported into ODV Software for visualisation (more information can be found at: https://www.seadatanet.org/Software/ODV ). In addition, the same dataset is offered also as a txt file in a long/vertical format, in which each P01 measurement is a record line. Additionally, there are a series of columns that split P01 terms into subcomponents (substance, CAS number, matrix...).This transposed format is more adapted to worksheet applications (e.g. LibreOffice Calc).
DOI: 10.13120/7aa27f48-c63d-417c-ac82-f18fd33782a4
title: North East Atlantic Ocean - Eutrophication and Acidity aggregated datasets 1921/2024 v2025
title: North_East_Atlantic_Ocean_-_Eutrophication_and_Acidity_aggregated_datasets_1921/2024_v2025

description: EMODnet Chemistry aims to provide access to marine chemistry datasets and derived data products concerning eutrophication, acidity and contaminants. The importance of the selected substances and other parameters relates to the Marine Strategy Framework Directive (MSFD). This aggregated dataset contains all unrestricted EMODnet Chemistry data on eutrophication and acidity, and covers the Northeast Atlantic Ocean (40W). Data were aggregated and quality controlled by 'IFREMER / IDM / SISMER - Scientific Information Systems for the SEA' in France.
ITS-90 water temperature and water body salinity variables have also been included ('as are') to complete the eutrophication and acidity data. If you use these variables for calculations, please refer to SeaDataNet for the quality flags: https://www.seadatanet.org/Products/Aggregated-datasets .
Regional datasets concerning eutrophication and acidity are automatically harvested, and the resulting collections are aggregated and quality controlled using ODV Software and following a common methodology for all sea regions ( https://doi.org/10.13120/8xm0-5m67 ). Parameter names are based on P35 vocabulary, which relates to EMODnet Chemistry aggregated parameter names and is available at: https://vocab.nerc.ac.uk/search_nvs/P35/ .
When not present in original data, water body nitrate plus nitrite was calculated by summing all nitrate and nitrite parameters. The same procedure was applied for water body dissolved inorganic nitrogen (DIN), which was calculated by summing all nitrate, nitrite, and ammonium parameters. Concentrations per unit mass were converted to a unit volume using a constant density of 1.25 kg/L.
The aggregated dataset can also be downloaded as an ODV collection and spreadsheet, which is composed of a metadata header followed by tab separated values. This spreadsheet can be imported to ODV Software for visualisation (more information can be found at: https://www.seadatanet.org/Software/ODV ).
DOI: 10.13120/4db2d213-fb18-4ac5-85be-7184f844d595
title: Black Sea - Contaminants aggregated datasets 1974/2023 v2025
title: Black_Sea_Contaminants_aggregated_datasets_1974/2023_v2025

description: EMODnet Chemistry aims to provide access to marine chemistry datasets and derived data products concerning eutrophication, acidity and contaminants. The importance of the selected substances and other parameters relates to the Marine Strategy Framework Directive (MSFD). This aggregated dataset contains all unrestricted EMODnet Chemistry data on potential hazardous substances, despite the fact that some data might not be related to pollution (e.g. collected by deep corer). Temperature, salinity and additional parameters are included when available. It covers the Black Sea. Data were harmonised and validated by the ‘National Institute for Marine Research and Development "Grigore Antipa" in Romania. 
The dataset contains water, sediment and biota profiles. The temporal coverage is 1974–2023 for water measurements, 1990–2023 for sediment measurements and 2008–2019 for biota measurements.
Regional datasets concerning contaminants are automatically harvested and the resulting collections are harmonised and validated using ODV Software and following a common methodology for all sea regions ( https://doi.org/10.6092/8b52e8d7-dc92-4305-9337-7634a5cae3f4 ). Parameter names are based on P01 vocabulary, which relates to BODC Parameter Usage Vocabulary and is available at: https://vocab.nerc.ac.uk/search_nvs/P01/ .
The harmonised dataset can be downloaded as as an ODV spreadsheet, which is composed of a metadata header followed by tab separated values. This spreadsheet can be imported into ODV Software for visualisation (more information can be found at: https://www.seadatanet.org/Software/ODV ). In addition, the same dataset is offered also as a txt file in a long/vertical format, in which each P01 measurement is a record line. Additionally, there are a series of columns that split P01 terms into subcomponents (substance, CAS number, matrix...).This transposed format is more adapted to worksheet applications (e.g. LibreOffice Calc).
DOI: 10.15468/dl.r729zq
title: Occurrence Download

description: A dataset containing 168 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-114.18739 50.93358,-113.91464 50.93358,-113.91464 51.17869,-114.18739 51.17869,-114.18739 50.93358))",
 "OccurrenceStatus is Present",
 "TaxonKey is Squamata",
 "Year 2015-2025"
 ]
}

 The dataset includes 168 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0040036-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.