cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh0202700.10fu
title: SH0202700.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0202701.10fu
title: SH0202701.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0202702.10fu
title: SH0202702.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0202703.10fu
title: SH0202703.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0202704.10fu
title: SH0202704.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh0202705.10fu
title: SH0202705.10FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5281/zenodo.15656720
title: MALDI-TOF raw spectra data and taxonomy identification reports to benchmark maldipickr

description: This dataset was acquired to mimick an isolation campaign when microbiologists want to reduce the expected redundancy of bacterial isolates. We used it to benchmark our R package maldipickr. We grew 80 isolates in anaerobic conditions and acquired MALDI-TOF spectra and identification reports. Isolates were selected from in-house collections (HiBC, PiBAC), including 8 replicates of each 9 species and a novel species.



230328-1404-1001000371.zip: Raw spectra data in the form of a folders and acqu files

230328-1404-1001000371.csv: Identification report in the form of a semi-colon separated csv file

TableS1_isolates.csv: List of isolates taxonomy and identifiers.


UPDATE v3: Add spectra identifier column and exclude the low biomass isolates for clarity in  TableS1_isolates.csv

UPDATE v2: Fix a typo in the column name of TableS1_isolates.csv
description: Cultivation of strains

Selected bacterial strains (Table S1) were reactivated from cryo-stocks in 9 ml of their respective culture media. To generate sufficient biomass for downstream analysis, 1 ml of the reactivated culture was subcultured into 9 ml of fresh medium in Hungate tubes and incubated for 24 hours at 37 °C.

Preparation for MALDI-TOF analysis

Following cultivation, 50 µl of each bacterial culture was transferred into individual wells of a 96-well V-bottom plate (Thermo Fisher Scientific; Cat. No. 277143). Each sample was diluted with 100 µl of sterile water and centrifuged at 6000g for 30 minutes using a Hettich Rotanta 460 centrifuge. The supernatant was carefully discarded, and the resulting pellet was resuspended in 20 µl of sterile water.

Subsequently, 1 µl of resuspended sample was transferred onto a MALDI target plate. After air-drying, each spot was overlaid sequentially with 1 µl of 70% formic acid (Sigma-Aldrich; F0507) and 1 µl of HCCA matrix solution, prepared by dissolving 2.5 mg α-Cyano-4-hydroxycinnamic acid (Sigma-Aldrich; 900666) in 250 µl of organic solvent (Bruker Daltonics; 8255344). Mass spectra were acquired using a MALDI Biotyper Sirius system (Bruker Daltonics) following the manufacturer’s protocol, with an adapted accumulation method summing 800 satisfactory laser shots per spot.

Valid spectra could not be obtained for two strains, Faecalibacterium duncaniae (CLA-AA-H223) and Gallintestinimicrobium propionicum (CLA-AA-H176), likely due to low biomass yield under the tested cultivation conditions.
DOI: 10.5281/zenodo.15744631
title: MALDI-TOF raw spectra data and taxonomy identification reports to benchmark maldipickr

description: This dataset was acquired to mimick an isolation campaign when microbiologists want to reduce the expected redundancy of bacterial isolates. We used it to benchmark our R package maldipickr. We grew 80 isolates in anaerobic conditions and acquired MALDI-TOF spectra and identification reports. Isolates were selected from in-house collections (HiBC, PiBAC), including 8 replicates of each 9 species and a novel species.



230328-1404-1001000371.zip: Raw spectra data in the form of a folders and acqu files

230328-1404-1001000371.csv: Identification report in the form of a semi-colon separated csv file

TableS1_isolates.csv: List of isolates taxonomy and identifiers.


UPDATE v3: Add spectra identifier column and exclude the low biomass isolates for clarity in  TableS1_isolates.csv

UPDATE v2: Fix a typo in the column name of TableS1_isolates.csv
description: Cultivation of strains

Selected bacterial strains (Table S1) were reactivated from cryo-stocks in 9 ml of their respective culture media. To generate sufficient biomass for downstream analysis, 1 ml of the reactivated culture was subcultured into 9 ml of fresh medium in Hungate tubes and incubated for 24 hours at 37 °C.

Preparation for MALDI-TOF analysis

Following cultivation, 50 µl of each bacterial culture was transferred into individual wells of a 96-well V-bottom plate (Thermo Fisher Scientific; Cat. No. 277143). Each sample was diluted with 100 µl of sterile water and centrifuged at 6000g for 30 minutes using a Hettich Rotanta 460 centrifuge. The supernatant was carefully discarded, and the resulting pellet was resuspended in 20 µl of sterile water.

Subsequently, 1 µl of resuspended sample was transferred onto a MALDI target plate. After air-drying, each spot was overlaid sequentially with 1 µl of 70% formic acid (Sigma-Aldrich; F0507) and 1 µl of HCCA matrix solution, prepared by dissolving 2.5 mg α-Cyano-4-hydroxycinnamic acid (Sigma-Aldrich; 900666) in 250 µl of organic solvent (Bruker Daltonics; 8255344). Mass spectra were acquired using a MALDI Biotyper Sirius system (Bruker Daltonics) following the manufacturer’s protocol, with an adapted accumulation method summing 800 satisfactory laser shots per spot.

Valid spectra could not be obtained for two strains, Faecalibacterium duncaniae (CLA-AA-H223) and Gallintestinimicrobium propionicum (CLA-AA-H176), likely due to low biomass yield under the tested cultivation conditions.
DOI: 10.15468/dl.pgnasb
title: Occurrence Download

description: A dataset containing 211854 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lucanus cervus (Linnaeus, 1758), Lucanus scapulodonta Weinreich, 1963, Platycerus cervus (Linnaeus, 1758), Scarabaeus cervus Linnaeus, 1758)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Machine Observation)"
 ]
 }
 },
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 211854 records from 1627 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069684-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxd8eq
title: Occurrence Download

description: A dataset containing 3025 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lablab purpureus (L.) Sweet",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Human Observation, Living Specimen, Occurrence evidence)"
 ]
}

 The dataset includes 3025 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020016-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccsmyq1
title: CCDC 734164: Experimental Crystal Structure Determination

description: Related Article: S.Naskar, P.Paira, R.Paira, S.Mondal, A.Maity, A.Hazra, K.B.Sahu, P.Saha, S.Banerjee, P.Luger, M.Webe, N.B.Mondal|2010|Tetrahedron|66|5196|doi:10.1016/j.tet.2010.04.084
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccts2sf
title: CCDC 767925: Experimental Crystal Structure Determination

description: Related Article: M.Tori, K.Otose, H.Fukuyama, J.Murata, Y.Shiotani, S.Takaoka, K.Nakashima, M.Sono, M.Tanaka|2010|Tetrahedron|66|5235|doi:10.1016/j.tet.2010.04.079
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.39esk6
title: Occurrence Download

description: A dataset containing 158394 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Fungi)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((37.5 37.5,45 37.5,45 45,37.5 45,37.5 37.5))"
 ]
}

 The dataset includes 158394 records from 79 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044094-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nky5f4
title: Occurrence Download

description: A dataset containing 5992 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Fungi)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((-45 -30,-37.5 -30,-37.5 -22.5,-45 -22.5,-45 -30))"
 ]
}

 The dataset includes 5992 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044140-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccsmyr2
title: CCDC 734165: Experimental Crystal Structure Determination

description: Related Article: S.Naskar, P.Paira, R.Paira, S.Mondal, A.Maity, A.Hazra, K.B.Sahu, P.Saha, S.Banerjee, P.Luger, M.Webe, N.B.Mondal|2010|Tetrahedron|66|5196|doi:10.1016/j.tet.2010.04.084
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.k8cqww
title: Occurrence Download

description: A dataset containing 46099 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Fungi)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((-52.5 -30,-45 -30,-45 -22.5,-52.5 -22.5,-52.5 -30))"
 ]
}

 The dataset includes 46099 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044141-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cct1230
title: CCDC 745801: Experimental Crystal Structure Determination

description: Related Article: O.A.Attanasi, S.Bartoccini, G.Giorgi, F.Mantellini, F.R.Perrulli, S.Santeusanio|2010|Tetrahedron|66|5121|doi:10.1016/j.tet.2010.04.108
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cct1241
title: CCDC 745802: Experimental Crystal Structure Determination

description: Related Article: O.A.Attanasi, S.Bartoccini, G.Giorgi, F.Mantellini, F.R.Perrulli, S.Santeusanio|2010|Tetrahedron|66|5121|doi:10.1016/j.tet.2010.04.108
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cct7ltf
title: CCDC 752085: Experimental Crystal Structure Determination

description: Related Article: S.Naskar, P.Paira, R.Paira, S.Mondal, A.Maity, A.Hazra, K.B.Sahu, P.Saha, S.Banerjee, P.Luger, M.Webe, N.B.Mondal|2010|Tetrahedron|66|5196|doi:10.1016/j.tet.2010.04.084
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.h4rsug
title: Occurrence Download

description: A dataset containing 822770 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Fungi)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Geometry POLYGON((135 -37.5,142.5 -37.5,142.5 -30,135 -30,135 -37.5))"
 ]
}

 The dataset includes 822770 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044081-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cct1252
title: CCDC 745803: Experimental Crystal Structure Determination

description: Related Article: O.A.Attanasi, S.Bartoccini, G.Giorgi, F.Mantellini, F.R.Perrulli, S.Santeusanio|2010|Tetrahedron|66|5121|doi:10.1016/j.tet.2010.04.108
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cct2tk7
title: CCDC 747489: Experimental Crystal Structure Determination

description: Related Article: S.A.Bentley, S.G.Davies, J.A.Lee, P.M.Roberts, A.J.Russell, J.E.Thomson, S.M.Toms|2010|Tetrahedron|66|4604|doi:10.1016/j.tet.2010.04.027
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/cct2tl8
title: CCDC 747490: Experimental Crystal Structure Determination

description: Related Article: S.A.Bentley, S.G.Davies, J.A.Lee, P.M.Roberts, A.J.Russell, J.E.Thomson, S.M.Toms|2010|Tetrahedron|66|4604|doi:10.1016/j.tet.2010.04.027
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.xgrmdt
title: Occurrence Download

description: A dataset containing 6102958 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sylvia atricapilla",
 "Year 1980-2025"
 ]
}

 The dataset includes 6102958 records from 5803 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0044072-251009101135966/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qt6f3u
title: Occurrence Download

description: A dataset containing 22166 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cuscuta europaea L.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 22166 records from 369 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009665-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.33cptv
title: Occurrence Download

description: A dataset containing 5412 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Crocodylus moreletii (Duméril & Bibron, 1851)"
 ]
}

 The dataset includes 5412 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009666-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.