cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10075671
title: Bin-assembled Escherichia coli genomes from a study in Punjab, Pakistan

description: Bin-assembled Escherichia coli genomes from Punjab, Pakistan
These assemblies are a part of a cross-sectional study conducted in Punjab, Pakistan aimed at investigating E. coli colonisation diversity in healthy carriage with the use of CLED enrichment plates.
About
Version history
v0.1.0 (current version)

Added brief description with a few missing parts.
Distribution
These assemblies are made available under a CC-BY 4.0 license. If you use these assemblies in your study please cite the source as appropriate (study will be added in a later version).
Methods briefly
Species identification
Sequencing data from the ENA project PRJEB36642 was error-corrected with fastp and pseudoaligned with Themisto against a species-level index (available from https://doi.org/10.5281/zenodo.6656881). Reads were assigned to species using the mSWEEP/mGEMS pipeline as described in https://www.nature.com/articles/s41467-022-35178-5.
Lineage identification
Read from the species-level bins were again pseudoaligned with Themisto against an E. coli index (will be made available in a later version). Lineage-level assignment was performed using mSWEEP and mGEMS at the level of PopPUNK sequence clusters. The created bins were screened with demix_check and bins that received a score of 1 or 2 were kept. Data in the kept bins were assembled with shovill and the bin-assembled genomes (BAGs) were quality controlled with checkm for >= 90% completeness and <= 10% contamination. Finally, BAGs shorter than 4 Mb or longer than 6 Mb were removed.
Contact
Tommi Mäklin <tommi'at'maklin.fi>.
DOI: 10.60600/yu/clawet/qmlcso
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DOI: 10.15468/dl.yqqznm
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
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 "HasCoordinate is true"
 ]
}

 The dataset includes 61 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092439-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
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DOI: 10.6084/m9.figshare.26096410
title: Data.xlsx

description: Serum samples from patients with benign and malignant breast lesions and healthy subjects were analyzed using gas chromatography-mass spectrometry.We found that amino acid metabolism was significantly altered in breast cancer patients.
DOI: 10.6084/m9.figshare.26096410.v1
title: Data.xlsx

description: Serum samples from patients with benign and malignant breast lesions and healthy subjects were analyzed using gas chromatography-mass spectrometry.We found that amino acid metabolism was significantly altered in breast cancer patients.
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DOI: 10.15468/dl.2e2amq
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
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}

 The dataset includes 86 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092441-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/scvadh
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DOI: 10.60600/yu/clawet/odawmf
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DOI: 10.5284/1119906
title: Data from a Building Survey at the Old Oak Common Carriage Sheds and a Railway Turntable, Hammersmith and Fulham, 2019 (HS2 Phase One)

description: This collection comprises images, site records, documents, reports, spreadsheets, CAD files and a laser scan from a building survey carried out by MOLA Headland Infrastructure and MOLA Northampton at the Old Oak Common Carriage Sheds, Hammersmith and Fulham during October and November 2019.
DOI: 10.60600/yu/clawet/bndqnr
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DOI: 10.57967/hf/2614
title: SpeechInterviewBERT
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DOI: 10.57745/w2sgjn
title: Supplementary tables-V2.docx

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DOI: 10.15468/dl.grefrc
title: Occurrence Download

description: A dataset containing 4070 species occurrences available in GBIF matching the query:
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}

 The dataset includes 4070 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092440-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/ozyyje
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DOI: 10.15468/dl.x5ebkh
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
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 The dataset includes 20 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092442-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
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DOI: 10.15468/dl.4m8vcw
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
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 The dataset includes 3 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092443-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/fthw7f
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DOI: 10.60600/yu/clawet/ndkbo3
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DOI: 10.15468/dl.g6f53r
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
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 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (April, May)",
 "OccurrenceStatus is Present",
 "TaxonKey is Lepidoptera",
 "Year 1990-2024"
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}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092445-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/t2bt0e
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DOI: 10.60600/yu/clawet/pmzkgz
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DOI: 10.60600/yu/clawet/nlwd5e
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DOI: 10.60600/yu/clawet/2oijoe
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DOI: 10.15468/dl.ku3z5j
title: Occurrence Download

description: A dataset containing 363862 species occurrences available in GBIF matching the query:
{
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 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Senecio vulgaris L."
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 The dataset includes 363862 records from 2397 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092438-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/thskfkcyvh.1
title: Formalisation and Centralisation of Street Vendors in the Surabaya Culinary Centre, Indonesia
DOI: 10.6084/m9.figshare.28869920
title: Impacts of aspect ratio on task accuracy in parallel coordinates - Supplementary (revised 20240425)

description: Supplementary material for 'Impacts of aspect ratio on task accuracy in parallel coordinates' (revised 20240425)
DOI: 10.6084/m9.figshare.28869920.v1
title: Impacts of aspect ratio on task accuracy in parallel coordinates - Supplementary (revised 20240425)

description: Supplementary material for 'Impacts of aspect ratio on task accuracy in parallel coordinates' (revised 20240425)
DOI: 10.15156/bio/sh1374678.10fu
title: SH1374678.10FU

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/sh1374679.10fu
title: SH1374679.10FU

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/sh1374684.10fu
title: SH1374684.10FU

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/sh1374685.10fu
title: SH1374685.10FU

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/sh1374686.10fu
title: SH1374686.10FU

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/sh1374687.10fu
title: SH1374687.10FU

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/sh1374692.10fu
title: SH1374692.10FU

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/sh1374694.10fu
title: SH1374694.10FU

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/sh1374696.10fu
title: SH1374696.10FU

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.