cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25345/c56q1sh64
title: MassIVE Reanalysis RMSV000000354.3578 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RARG [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5z60c292
title: MassIVE Reanalysis RMSV000000354.3575 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, COMMD8 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19158710.v1
title: Data of A Real-time Safe Path Planning System For Cooperative Robot

description: Data of A Real-time Safe Path Planning System For Cooperative Robot
DOI: 10.5281/zenodo.6205896
title: Datasets for the Carpentry-style RNA-seq lesson

description: <strong>Lesson files</strong> For all compressed files, go to the Shell and uncompress using `tar -xzvf myarchive.tar.gz`. <strong>1) Bioinformatic files: </strong>bioinformatic_tutorial_files.tar.gz This archive contains the following datasets: FASTQ files from Arabidopsis leaf RNA-seq: Arabidopsis_sample3.fq.gz Arabidopsis_sample1.fq.gz Arabidopsis_sample4.fq.gz Arabidopsis_sample2.fq.gz Arabidopsis thaliana genome assembly and genome annotation: AtChromosome1.fa.gz ath_annotation.gff3.gz The sequence of sequencing adapters in adapters.fasta. <strong>2) Gene counts usable with DESeq2 and R: </strong>tutorial.tar.gz This archive contains the following datasets: <strong>raw_counts.csv</strong>: a dataframe of the sample raw counts. It is a comma-separate values file therefore data are separated by commas ','. <strong>samples_to_conditions.csv</strong>: a dataframe that indicates the correspondence between samples and experimental conditions (e.g. control, treated). <strong>differential_genes.csv: </strong>a dataframe that contains the result of the DESeq2 analysis specifying this contrast in `DESEq2::results()` function: `<code class="language-plaintext">contrast = c("infected", "Pseudomonas_syringae_DC3000", "mock")</code> The<strong> raw_counts.csv </strong>file was obtained by running the `v0.1.1` version of a RNA-Seq bioinformatic pipeline on the mRNA-Seq sequencing files from Vogel et al. (2016): https://www.ebi.ac.uk/ena/data/view/PRJEB13938. Please read the original study (Vogel et al. 2016): https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.14036 ==== <strong>Exercise files</strong> <strong>1) NASA spaceflight</strong> The NASA GeneLab experiment GLDS-38 performed transcriptomics and proteomics of Arabidopsis seedlings in microgravity by sending seedlings to the International Space Station (ISS). The raw counts, scaled counts and sample to conditions files are available in the ZIP archive <strong>2) Deforges 2019 hormone-treatments: </strong>deforges_2019.tar.gz This archive contains: arabidopsis_root_hormones_raw_counts.csv arabidopsis_root_hormones_sample2condition.csv dataset01_IAA_arabidopsis_root_raw_counts.csv dataset02_ABA_arabidopsis_root_raw_counts.csv dataset03_ACC_arabidopsis_root_raw_counts.csv dataset04_MeJA_arabidopsis_root_raw_counts.csv The <em>arabidopsis_root_hormones_raw_counts.csv</em> file contains all gene counts from all hormones. Separate datasets were made for each hormone for convenience.
DOI: 10.5281/zenodo.6205320
title: Erythroxylum panamense SPAdes preassembly

description: .
DOI: 10.5281/zenodo.6205319
title: Erythroxylum panamense SPAdes preassembly

description: .
DOI: 10.25345/c5td9n85c
title: MassIVE Reanalysis RMSV000000354.3576 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, IFIT5 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.5281/zenodo.6206009
title: GIANI Paper - Supplemental File 4

description: GIANI settings used to produce the data in Fig 4
DOI: 10.5281/zenodo.6206008
title: GIANI Paper - Supplemental File 4

description: GIANI settings used to produce the data in Fig 4
DOI: 10.5281/zenodo.6205979
title: GIANI Paper - Supplemental File 3

description: GIANI settings used to produce the data in Fig 3
DOI: 10.5281/zenodo.6205978
title: GIANI Paper - Supplemental File 3

description: GIANI settings used to produce the data in Fig 3
DOI: 10.25345/c5pn8xg17
title: MassIVE Reanalysis RMSV000000354.3579 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C11orf67 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.5281/zenodo.6206023
title: GIANI Paper - Supplemental File 5

description: GIANI and Imaris settings used to produce the data in Fig 5
DOI: 10.5281/zenodo.6206022
title: GIANI Paper - Supplemental File 5

description: GIANI and Imaris settings used to produce the data in Fig 5
DOI: 10.25345/c5jw86n6c
title: MassIVE Reanalysis RMSV000000354.3583 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, BROX [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5f47gv2j
title: MassIVE Reanalysis RMSV000000354.3580 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, FBXO30 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.5281/zenodo.6206043
title: GIANI Paper - Supplemental File 6

description: GIANI and Imaris settings used to produce the data in Fig 6
DOI: 10.5281/zenodo.6206042
title: GIANI Paper - Supplemental File 6

description: GIANI and Imaris settings used to produce the data in Fig 6
DOI: 10.5281/zenodo.6206088
title: GIANI Paper - Supplemental File 7

description: GIANI and Imaris settings used to produce the data in Fig S1
DOI: 10.5281/zenodo.6206087
title: GIANI Paper - Supplemental File 7

description: GIANI and Imaris settings used to produce the data in Fig S1
DOI: 10.25345/c59g5gf0n
title: MassIVE Reanalysis RMSV000000354.3586 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TRPT1 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c55q4rm7c
title: MassIVE Reanalysis RMSV000000354.3584 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MECP2 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19188857.v1
title: Table 2: Growth of Streptococcus mutans colonies after consumption of test product

description: Table 2: Growth of Streptococcus mutans colonies after consumption of test product
DOI: 10.25345/c51z41t43
title: MassIVE Reanalysis RMSV000000354.3588 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GPD1 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5x63b59t
title: MassIVE Reanalysis RMSV000000354.3585 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C2orf27B [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5sf2mc46
title: MassIVE Reanalysis RMSV000000354.3587 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RNF14 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5np1wj9z
title: MassIVE Reanalysis RMSV000000354.3581 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, NOSIP [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5hx15r56
title: MassIVE Reanalysis RMSV000000354.3589 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, DHRS2 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5d795b51
title: MassIVE Reanalysis RMSV000000354.3592 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, LTBR [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.5281/zenodo.6188748
title: Classes of errors in DOI names: evaluation dataset

description: This dataset contains the results of the evaluation of the methodology presented in the article <em>Identifying and correcting invalid citations due to DOI errors in Crossref data</em> (https://arxiv.org/abs/2111.11263). The file named 10_random_citations_per_rule.csv contains 193 randomly selected citations from the corrected citations obtained by the process described in the article (10.5281/zenodo.4892551). They were extracted using the script called evaluation.py, which can be viewed in the GitHub repository <em>open-sci/2020-2021-grasshoppers-code </em>(10.5281/zenodo.4723983).
description: {"references": ["Peroni, Silvio. (2021). Citations to invalid DOI-identified entities obtained from processing DOI-to-DOI citations to add in COCI (Version 1.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4625300", "Cioffi, Alessia, Coppini, Sara, Massari, Arcangelo, Moretti, Arianna, Peroni, Silvio & Santini, Cristian. (2021). Identifying and correcting invalid citations due to DOI errors in Crossref data. https://doi.org/10.48550/arXiv.2111.11263"]}
DOI: 10.5281/zenodo.6188747
title: Classes of errors in DOI names: evaluation dataset

description: This dataset contains the results of the evaluation of the methodology presented in the article <em>Identifying and correcting invalid citations due to DOI errors in Crossref data</em> (https://arxiv.org/abs/2111.11263). The file named 10_random_citations_per_rule.csv contains 193 randomly selected citations from the corrected citations obtained by the process described in the article (10.5281/zenodo.4892551). They were extracted using the script called evaluation.py, which can be viewed in the GitHub repository <em>open-sci/2020-2021-grasshoppers-code </em>(10.5281/zenodo.4723983).
description: {"references": ["Peroni, Silvio. (2021). Citations to invalid DOI-identified entities obtained from processing DOI-to-DOI citations to add in COCI (Version 1.0) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.4625300", "Cioffi, Alessia, Coppini, Sara, Massari, Arcangelo, Moretti, Arianna, Peroni, Silvio & Santini, Cristian. (2021). Identifying and correcting invalid citations due to DOI errors in Crossref data. https://doi.org/10.48550/arXiv.2111.11263"]}
DOI: 10.25345/c58g8fj2c
title: MassIVE Reanalysis RMSV000000354.3594 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, MAGED2 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54q7qq8m
title: MassIVE Reanalysis RMSV000000354.3590 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RAPGEF5 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c50z70x4v
title: MassIVE Reanalysis RMSV000000354.3595 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C22orf43 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5w669883
title: MassIVE Reanalysis RMSV000000354.3591 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, WISP3 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5rf5kg3g
title: MassIVE Reanalysis RMSV000000354.3593 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, EMILIN1 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5mp4vn9q
title: MassIVE Reanalysis RMSV000000354.3597 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TMC6 [launched by fce971e5ede541cca3fc5307a73294d8]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.18822194
title: Data from "Comprehensive Quantitative Evaluation of Inter-observer Delineation Performance of MR-guided Delineation of Oropharyngeal Gross Tumor Volumes and High-risk Clinical Target Therapy: An R-IDEAL Stage 0 Prospective Study"

description: Pre-treatment T1-weighted (T1w), T1-weighted with Gadolinium contrast (T1w+C) and T2-weigted (T2w) MRI scans were retrospectively collected for 4 OPC patients under an IRB-approved protocol. The scans were provided to twenty-six radiation oncologists from seven international cancer centers who participated in this delineation study. In addition, each patient’s clinical history and physical examination findings along with a medical photographic image and radiological results were provided. The contours were compared using overlap and distance metrics using both STAPLE and pair-wise comparisons.