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55 results for “Validation collection”
Dataset and Scripts for: RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs (v.20200528_415)
<p><strong>RefPlantNLR v.20200528_415</strong></p> <p><strong>See </strong>bioRxiv 2020.07.08.193961; doi: <a href="https://doi.org/10.1101/2020.07.08.193961">https://doi.org/10.1101/2020.07.08.193961</a></p> <p>SUPPLEMENTAL DATA</p> <p>Table S1: Description of RefPlantNLR.</p> <p>Table S2: Plant orders represented in RefPlantNLR.</p> <p>Supplemental dataset 1: Amino acid sequences of RefPlantNLR entries (fasta format). This file contains 415 amino acid sequences.</p> <p>Supplemental dataset 2: CDS sequences of RefPlantNLR entries (fasta format). This file contains 400 CDS sequences. CDS sequences could not be retrieved for 15 RefPlantNLR entries.</p> <p>Supplemental dataset 3: Annotated genomic sequences of RefPlantNLR entries (GenBank flat file format). This file contains 329 genomic loci containing the gene models of 344 RefPlantNLR entries and 56 RefPlantNLR mRNA entries lacking genomic information.</p> <p>Supplemental dataset 4: InterProScan annotation of the RefPlantNLR amino acid sequences (GFF3 format). This file contains the InterProScan annotation of 415 amino acid sequences.</p> <p>Supplemental dataset 5: InterProScan annotation of the RefPlantNLR CDS sequences (GFF3 format). This file contains the InterProScan annotation of the 400 CDS sequences.</p> <p>Supplemental dataset 6: Amino acid sequences of the extracted RefPlantNLR NB-ARC domains (fasta format). This file contains 424 NB-ARC domain (SUPERFAMILY signature SSF52540) amino acid sequences belonging to 415 RefPlantNLR entries.</p> <p>Supplemental dataset 7: Amino acid sequences of the unique RefPlantNLR extracted NB-ARC domains (fasta format). This file contains 347 unique NB-ARC domain (SUPERFAMILY signature SSF52540) amino acid sequences.</p> <p>Supplemental dataset 8: Clustal Omega alignment of the unique RefPlantNLR extracted NB-ARC domains (PHYLIP format). This file contains the Clustal Omega alignment of 346 unique NB-ARC domains (SUPERFAMILY signature SSF52540) with all positions with less than 95% coverage removed. Pb1 was omitted from this alignment.</p> <p>Supplemental dataset 9: NB-ARC domain phylogeny of the RefPlantNLR entries using the Maximum likelihood method (Newick format). This file contains the phylogenetic analysis of the NB-ARC domain of the RefPlantNLR entries using the JTT method.</p> <p>Supplemental dataset 10: Amino acid sequences of the non-redundant RefPlantNLR entries (fasta format). This file contains 235 amino acid sequences representing the non-redundant RefPlantNLR entries at a 90% amino acid identity threshold per genus according to the NB-ARC domain.</p> <p>Supplemental dataset 11: Amino acid sequences of the NB-ARC domains of the non-redundant RefPlantNLR entries (fasta format). This file contains 241 amino acid sequences representing the extracted NB-ARC domains of the 235 non-redundant RefPlantNLR.</p> <p>Appendix S1: R script used to generate annotations and figures.</p> <p>Appendix S2: InterProScan descriptions used for generating annotations.</p>
The Red Queen in the Repository: metadata quality in an ever-changing environment (preprint of paper, presentation slides and dataset collection with validation schemas to IDCC2019 conference paper)
<p>This fileset contains a preprint version of the conference paper (.pdf), presentation slides (as .pptx) and the dataset(s) and validation schema(s) for the IDCC 2019 (Melbourne) conference paper: <em>The Red Queen in the Repository: metadata quality in an ever-changing environment. </em>Datasets and schemas are in .xml, .xsd , Excel (.xlsx) and .csv (two files representing two different sheets in the .xslx -file). The <em>validationSchemas.zip</em> holds the additional validation schemas (.xsd), that were not found in the schemaLocations of the metadata xml-files to be validated. The schemas must all be placed in the same folder, and are to be used for validating the Dataverse <em>dcterms</em> records (with <em>metadataDCT.xsd</em>) and the Zenodo <em>oai_datacite</em> feeds respectively (<em>schema.datacite.org_oai_oai-1.0_oai.xsd</em>). In the latter case, a simpler way of doing it might be to replace the incorrect URL "<em>http://schema.datacite.org/oai/oai-1.0/ oai_datacite.xsd</em>" in the <em>schemaLocation </em>of these xml-files by the CORRECT: <em>schemaLocation="http://schema.datacite.org/oai/oai-1.0/ http://schema.datacite.org/oai/oai-1.0/oai.xsd"</em> as has been done already in the sample files here. The sample file folders <em>testDVNcoll.zip </em>(Dataverse), <em>testFigColl.zip </em>(Figshare)<em> </em>and <em>testZenColl.zip </em>(Zenodo)<em> </em>contain all the metadata files tested and validated that are registered in the spreadsheet with objectIDs.<br> In the case of Zenodo, one original file feed,<br> <em>zen2018oai_datacite3orig-https%20_zenodo.org_oai2d%20verb=ListRecords%26metadata<br> Prefix=oai_datacite%26from=2018-11-29%26until=2018-11-30.xml</em> ,<br> is also supplied to show what was necessary to change in order to perform validation as indicated in the paper.</p> <p>For Dataverse, a corrected version of a file,<br> <em>dvn2014ddi-27595<strong>Corr</strong>_https%20_dataverse.harvard.edu_api_datasets_export%20<br> exporter=ddi%26persistentId=doi%253A10.7910_DVN_27595<strong>Corr</strong>.xml</em> ,<br> is also supplied in order to show the changes it would take to make the file validate without error.</p>
Construction, validation and application of nocturnal pollen transport networks in an agro-ecosystem: datasets collected using light microscopy and DNA metabarcoding
<p>This dataset contains all data required to reproduce the analyses conducted in Macgregor <em>et al. </em>(2018), using the R Notebook archived at doi: <a href="https://dx.doi.org/10.5281/zenodo.1322712">10.5281/zenodo.1322712</a>.</p> <p>Specifically, the dataset contains details of pollen transport detected on two matched samples, each containing 311 moths of 41 species, using two methods: a traditional light microscopy approach and a novel DNA metabarcoding approach. Both raw and manually-curated versions of each dataset are archived for full clarity. The dataset additionally contains all metadata required to fully interpret these data, including the RGB tables used to prepare Fig 4 in Macgregor <em>et al. </em>(2018).</p> <p>Macgregor <em>et al. </em>(2018) Construction, validation and application of nocturnal pollen transport networks in an agro-ecosystem: a comparison using light microscopy and DNA metabarcoding. <em>Ecological Entomology</em>, doi: <a href="https://dx.doi.org/10.1111/een.12674">10.1111/een.12674</a>.</p>
TBValid collection: Pulmonary tuberculosis validation collection
<p>The TBValid dataset comprises 870 digital patients with different profiles, each with fixed Age, BMI and MtbSputum. Each is identified by a vector of features involving biological and pathophysiological parameters to roughly represent different profiles in the population and initial bacterial load. Individual patient data collected during a clinical trial have been transformed into aggregated data, which are already irreversibly anonymised. Subsequently, these aggregated data have been sampled through the procedure described in “Generation of digital patients for the simulation of tuberculosis with UISS-TB”, doi: 10.1186/s12859-020-03776-z. The obtained derivative dataset, owned by its creators, does not constitute sensitive data according to European laws, and it is impossible with this dataset to re-establish the identity of the patients enrolled in the original clinical trial.</p>
Data for the Article: Cross-validation of a semantic segmentation network for natural history collection specimens
<p>This deposit contains six datasets which were used for testing and validating a semantic segmentation network. The purpose was to evaluate the suitability of the segmentation network for use in the processing of images from Natural History Collections.</p>
DP1577 – Carex ornithopoda Willd. (Cyperaceae) – Détermination valide. in L'herbier Daniel Pellé (DP) - La collection d'un botaniste amateur de l'Aube (France)
DP1577 – Carex ornithopoda Willd. (Cyperaceae) – Détermination valide.
DP0690 – Malva alcea L. (Malvaceae) – Détermination valide. in L'herbier Daniel Pellé (DP) - La collection d'un botaniste amateur de l'Aube (France)
DP0690 – Malva alcea L. (Malvaceae) – Détermination valide.
DP0539 – Rosa pendulina L. (Rosaceae) – Détermination valide. in L'herbier Daniel Pellé (DP) - La collection d'un botaniste amateur de l'Aube (France)
DP0539 – Rosa pendulina L. (Rosaceae) – Détermination valide.
DP0033 – Aconitum napellus L. (Ranunculaceae) – Détermination valide. in L'herbier Daniel Pellé (DP) - La collection d'un botaniste amateur de l'Aube (France)
DP0033 – Aconitum napellus L. (Ranunculaceae) – Détermination valide.
DP1845 – Phegopteris dryopteris (L.) Fée (Cystopteridaceae) – Détermination valide. in L'herbier Daniel Pellé (DP) - La collection d'un botaniste amateur de l'Aube (France)
DP1845 – Phegopteris dryopteris (L.) Fée (Cystopteridaceae) – Détermination valide.
DP1290 – Lysimachia nummularia L. (Primulaceae) – Détermination valide. in L'herbier Daniel Pellé (DP) - La collection d'un botaniste amateur de l'Aube (France)
DP1290 – Lysimachia nummularia L. (Primulaceae) – Détermination valide.
DP0410 – Physalis alkekengi L. (Solanaceae) – Détermination valide. in L'herbier Daniel Pellé (DP) - La collection d'un botaniste amateur de l'Aube (France)
DP0410 – Physalis alkekengi L. (Solanaceae) – Détermination valide.
FIGURE 3 in Re-description of two spiny clam shrimps (Crustacea: Branchiopoda: Spinicaudata) of the Indian subcontinent from Daday de Dees's collection at MNHN with new insights on the validity of Eulimnadia compressa (Baird, 1860) and Eulimnadia chaperi (Simon, 1886)
FIGURE 3. Leptestheria sarsi (Daday, 1923). A, male head. B, female head. C, telson and cercopod (male). D, telson (female). E, dorsal armature. Scale bars: A & B: 0.5 mm; C & D: 0.75 mm; E: 0.05mm.
FIGURE 2. Eocyzicus bouvieri Daday, 1913. A, male head. B. female head. C in Re-description of two spiny clam shrimps (Crustacea: Branchiopoda: Spinicaudata) of the Indian subcontinent from Daday de Dees's collection at MNHN with new insights on the validity of Eulimnadia compressa (Baird, 1860) and Eulimnadia chaperi (Simon, 1886)
FIGURE 2. Eocyzicus bouvieri Daday, 1913. A, male head. B. female head. C, gripping area of the palm of the clasper 2. D, telson and cercopod (female) (arrow indicating the posteriormost spine, taken from second female). E, dorsal armature. Scale bars: A & B: 0.5mm; C & D: 0.2 mm; E: 0.05 mm.
FIGURE 1. Eocyzicus bouvieri Daday, 1913. A, carapace. B in Re-description of two spiny clam shrimps (Crustacea: Branchiopoda: Spinicaudata) of the Indian subcontinent from Daday de Dees's collection at MNHN with new insights on the validity of Eulimnadia compressa (Baird, 1860) and Eulimnadia chaperi (Simon, 1886)
FIGURE 1. Eocyzicus bouvieri Daday, 1913. A, carapace. B, second antenna (part). C, spine on the cercopod. D, telson (male; broken). Scale bars: A:1 mm; B: 0.05mm; C: 0.1mm; D: 0.5 mm.
FIGURE 5 in Re-description of two spiny clam shrimps (Crustacea: Branchiopoda: Spinicaudata) of the Indian subcontinent from Daday de Dees's collection at MNHN with new insights on the validity of Eulimnadia compressa (Baird, 1860) and Eulimnadia chaperi (Simon, 1886)
FIGURE 5. Eulimnadia chaperi (Simon, 1886). A, habitus. B, head with second sntenna. C, telson. Scale bars: A: 1 mm; B: 0.5 mm; C: 0.2mm.
FIGURE 4 in Re-description of two spiny clam shrimps (Crustacea: Branchiopoda: Spinicaudata) of the Indian subcontinent from Daday de Dees's collection at MNHN with new insights on the validity of Eulimnadia compressa (Baird, 1860) and Eulimnadia chaperi (Simon, 1886)
FIGURE 4. Leptestheria sarsi (Daday, 1923). A, carapace. B, spines on postero-lateral ridge of telson. C, first antenna (male). D, clasper 1. E, clasper 2. F, single antennomere of second antenna. Scale bars: A: 1 mm; B: 0.05 mm; C–F: 0.2 mm.
A Sample Collection Study to Validate the Astute Medical NephroCheck Test in Critically Ill Subjects at Risk for Acute Kidney Injury
ClinicalTrials.gov study NCT01573962. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Study to Collect Imaging Data for the Validation of the Intelligent Ultrasound's ScanNav Anatomy Peripheral Nerve Block (PNB) - US v1.0
ClinicalTrials.gov study NCT04906018. IPD Sharing: NO. Countries: 1. Publications: 1.
Validation of Human Papillomavirus Assays and Collection Devices for Self-samples and Urine Samples
ClinicalTrials.gov study NCT03064087. IPD Sharing: NO. Countries: 1. Publications: 9.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.