cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3901741
title: A meta analysis of Wikipedia's coronavirus sources during the COVID-19 pandemic

description: At the height of the coronavirus pandemic, on the last day of March 2020, Wikipedia in all languages broke a record for most traffic in a single day. Since the breakout of the Covid-19 pandemic at the start of January, tens if not hundreds of millions of people have come to Wikipedia to read - and in some cases also contribute - knowledge, information and data about the virus to an ever-growing pool of articles. Our study focuses on the scientific backbone behind the content people across the world read: which sources informed Wikipedia’s coronavirus content, and how was the scientific research on this field represented on Wikipedia. Using citation as readout we try to map how COVID-19 related research was used in Wikipedia and analyse what happened to it before and during the pandemic. Understanding how scientific and medical information was integrated into Wikipedia, and what were the different sources that informed the Covid-19 content, is key to understanding the digital knowledge echosphere during the pandemic. To delimitate the corpus of Wikipedia articles containing Digital Object Identifier (DOI), we applied two different strategies. First we scraped every Wikipedia pages form the COVID-19 Wikipedia project (about 3000 pages) and we filtered them to keep only page containing DOI citations. For our second strategy, we made a search with EuroPMC on Covid-19, SARS-CoV2, SARS-nCoV19 (30’000 sci papers, reviews and preprints) and a selection on scientific papers form 2019 onwards that we compared to the Wikipedia extracted citations from the english Wikipedia dump of <strong>May 2020</strong> (2’000’000 DOIs). This search led to 231 Wikipedia articles containing at least one citation of the EuroPMC search or part of the wikipedia COVID-19 project pages containing DOIs. Next, from our 231 Wikipedia articles corpus we extracted DOIs, PMIDs, ISBNs, websites and URLs using a set of regular expressions. Subsequently, we computed several statistics for each wikipedia article and we retrive Atmetics, CrossRef and EuroPMC infromations for each DOI. Finally, our method allowed to produce tables of citations annotated and extracted infromations in each wikipadia articles such as books, websites, newspapers. Files used as input and extracted information on Wikipedia's COVID-19 sources are presented in this archive. See the WikiCitationHistoRy Github repository for the R codes, and other bash/python scripts utilities related to this project.
description: Analysis on Wikipedia sources during the first wave of the COVID-19 pandemics (up to May 2020)
DOI: 10.5281/zenodo.4293493
title: Training dataset: Generation of a spectral library from HEK-Ecoli Spike-in mass spectrometry data

description: The five raw files serve as a concise but meaningful training data set in the Galaxy training network (https://galaxyproject.github.io/training-material/). HEK and E.coli cell pellets were lysed with 5 % SDS, 50 mM triethylammonium bicarbonate (TEAB), pH 7.55. The obtained protein extracts were reduced by adding f.c. 5 mM TCEP and alkylated by the addition of f.c. 10 mM iodacetamide. Protein digestion and purification was performed on S-Trap columns. To ensure protein binding to the S-Trap columns, samples were acidified to a final concentration of 1.2 % phosphoric acid (~ pH 2). Six times the sample volume S-Trap buffer (90% aqueous methanol containing a final concentration of 100 mM TEAB, pH 7.1) was added to the samples which were then loaded on the columns and washed with S-Trap buffer. Protein digestion was performed with trypsin and LysC for one hour at 47 °C. Peptides were eluted in three steps with (1) 50 mM TEAB, (2) 0.2 % aqueous formic acid and (3) 50 % acetonitrile containing 0.2 % formic acid. Eluted peptides of HEK and E.coli were mixed in the following ratios (amount in µg): Sample HEK E.coli MS method<br> Sample1 2.5 0.00 DDA<br> Sample2 2.5 0.05 DDA<br> Sample3 2.5 0.15 DDA<br> Sample4 2.5 0.40 DDA<br> Sample5 2.5 0.80 DDA Additionally, iRT peptides were added and 1µg of each samples was measured with a Q-Exactive Plus mass spectrometer. Besides the five raw files, we uploaded two fasta files that serve as human and ecoli protein sequence databases, an transition list for the iRT peptides as well as an experimental design for the MaxQuant search.<br> Additionally, we uploaded the Galaxy MaxQuant training result files: protein groups, peptides, mqpar, msms, evidence and PTXQC.
DOI: 10.5281/zenodo.4307762
title: Training dataset: DIA data analysis of a HEK/Ecoli Spike-in dataset using OpenSwathWorkflow

description: The eight raw files serve as a concise but meaningful training data set in the Galaxy training network (https://galaxyproject.github.io/training-material/). HEK and E.coli cell pellets were lysed with 5 % SDS, 50 mM triethylammonium bicarbonate (TEAB), pH 7.55. The obtained protein extracts were reduced by adding f.c. 5 mM TCEP and alkylated by the addition of f.c. 10 mM iodacetamide. Protein digestion and purification was performed on S-Trap columns. To ensure protein binding to the S-Trap columns, samples were acidified to a final concentration of 1.2 % phosphoric acid (~ pH 2). Six times the sample volume S-Trap buffer (90% aqueous methanol containing a final concentration of 100 mM TEAB, pH 7.1) was added to the samples which were then loaded on the columns and washed with S-Trap buffer. Protein digestion was performed with trypsin and LysC for one hour at 47 °C. Peptides were eluted in three steps with (1) 50 mM TEAB, (2) 0.2 % aqueous formic acid and (3) 50 % acetonitrile containing 0.2 % formic acid. Eluted peptides of HEK and E.coli were mixed in two different ratios and four replicates of each Spike/in ratio were measured: Sample HEK E.coli MS method<br> Sample1 2.5 0.15 DIA<br> Sample2 2.5 0.15 DIA<br> Sample3 2.5 0.15 DIA<br> Sample4 2.5 0.15 DIA<br> Sample5 2.5 0.80 DIA<br> Sample6 2.5 0.80 DIA<br> Sample7 2.5 0.80 DIA<br> Sample8 2.5 0.80 DIA Additionally, iRT peptides were added and 1µg of each samples was measured using data independent acquisition with a Q-Exactive Plus mass spectrometer. Briefly, a scan range from 400-1000 m/Z was first covered by an MS1 scan followed by 25 consecutive MS2 scans (each 24 m/z broad). In the next cycle another MS1 scan was acquired followd by 26 MS2 scans (also 24m/z broad) in which the window centers were shifted by 50% compared to the previous cycle of MS2 scans. The resulting raw files contain overlapping MS2 scans. Besides the eight raw files, we uploaded a spectral library, a transition list for the iRT peptides as well as an sample annotation file.<br> Additionally, we uploaded the Galaxy PyProphet score training result files: PyProphet score report and PyProphet score.
DOI: 10.5281/zenodo.4616731
title: From partial to whole genome imputation of SARS-CoV-2 for epidemiological surveillance

description: Supplementary data for "From partial to whole genome imputation of SARS-CoV-2 for epidemiological surveillance".
DOI: 10.5524/100930
title: Chromosome-level genome assembly of <i>C. argus</i>

description: The northern snakehead (<i>Channa argus</i>) is a species of snakehead fish native to China, Russia, North Korea, and South Korea, ranging from the Amur River to Hainan.<br>The northern snakehead is a freshwater species and cannot tolerate salinity in excess of 10 parts per million. It is a facultative air breather; it uses a suprabranchial organ and a bifurcated ventral aorta that permits aquatic and aerial respiration. This unusual respiratory system allows it to live outside of water for several days; it can wriggle its way to other bodies of water or survive being transported by humans.<br><i>Channa argus</i> is one of the main cultured species of the family Channidae. In this study, we sequenced and assembled the whole genome of <i>C. argus</i> for the first time and obtained a chromosome-level genome assembly of 630.39 Mb. Contig N50 was 13.20 Mb, scaffold N50 was 28.37 Mb, with 28,054 coding genes annotated for <i>C. argus</i>.<br>This study provides a high-quality genome research platform for follow-up studies of Channidae.
DOI: 10.5524/100931
title: Chromosome-level genome assembly of <i>C. maculata</i>

description: The blotched snakehead (<i>Channa maculata</i>) is a species of snakehead. It is one of four species of the genus <i>Channa</i> native to China. It is also to native northern Vietnam and Taiwan, but has been widely introduced to other countries, where it is an invasive species. This predatory species typically grows to a length of 2030 cm (7.911.8 in), but it has been confirmed at 33 cm (13 in) and some suggest it may reach a far larger size.<br><i>Channa maculata</i> is one of the main cultured species of the family Channidae. In this study, we sequenced and assembled the whole genome of <i>C. maculata</i> for the first time and obtained a chromosome-level genome assembly of 618.82 Mb. Contig N50 was 21.73 Mb, scaffold N50 was 28.37 Mb, with 24,115 coding genes annotated for <i>C. maculata</i>.<br>This study provides a high-quality genome research platform for follow-up studies of Channidae.
DOI: 10.5524/100933
title: Supporting data for "Genome assembly and annotation of the tambaqui (<i>Colossoma macropomum</i>): an emblematic fish of the Amazon River basin"

description: <i>Colossoma macropomum</i> known as "tambaqui" is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and great adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina, Pac Bio and Hi-C sequencing technologies to generate a reference genome, assembled with 39X coverage of long reads and polished to a QV=36 with 169X coverage of short reads. The genome was assembled into 1,269 scaffolds to a total of 1,221,847,006 bases, with a scaffold N50 size of 40 Mb where 93% of all assembled bases were placed in the largest 54 scaffolds that corresponds to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced which benefits any groups interested in exploring unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for novel insights about ecological and evolutionary facets and is a helpful resource for aquaculture purposes.
DOI: 10.5524/100936
title: Supporting data for "Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects"

description: Organizing and annotating biological sample data is critical in data-intensive bioinformatics. Unfortunately, metadata formats from a data provider are often incompatible with requirements of a processing tool. There is no broadly accepted standard to organize metadata across biological projects and bioinformatics tools, restricting the portability and reusability of both annotated datasets and analysis software.<br>To address this, we present Portable Encapsulated Projects (PEP), a formal specification for biological sample metadata structure. The PEP specification accommodates typical features of data-intensive bioinformatics projects with many biological samples. In addition to standardization, the PEP specification provides descriptors and modifiers for project-level and sample-level metadata, which improve portability across both computing environments and data processing tools. PEP includes a schema validator framework, allowing formal definition of required metadata attributes for data analysis broadly. We have implemented packages for reading PEPs in both Python and R to provide a language-agnostic interface for organizing project metadata. PEP therefore presents an important step toward unifying data annotation and processing tools in data-intensive biological research projects. The formal PEP specification and links to associated tools and documentation are available at pep.databio.org.
DOI: 10.5524/100937
title: Supporting data for "<i>De novo</i> screening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation."

description: Mutants are important for the discovery of functional genes and creation of germplasm resources. Mutant acquisition depends on the efficiency of mutation technology and screening methods. CRISPR-Cas9 technology is an efficient gene editing technology mainly used for editing a few genes or target sites, which has not been applied for the construction of random mutant libraries and for the <i>de novo</i> discovery of functional genes.<br>In this study, we first sequenced and assembled the chromosome-level genome of wild-type rare minnow as a susceptible model of hemorrhagic disease, obtained a 956.05 M genome sequence, assembled the sequence into 25 chromosomes, and annotated 26,861 protein-coding genes. Thereafter, CRISPR-Cas9 technology was applied to randomly mutate the whole genome of rare minnow with the conserved bases (TATAWAW and ATG) of the promoter and coding regions as the target sites. The survival rate of hemorrhagic disease in the rare minnow gradually increased from 0% (the entire wild-type population died after infection) to 38.24% (F3 generation). Finally, seven susceptible genes were identified via genome comparative analysis and cell-level verification based on the rare minnow genome.<br>The results provided the genomic resources for wild-type rare minnow, and confirmed that the random mutation system designed using CRISPR-Cas9 technology in this study is simple and efficient, and is suitable for the <i>de novo</i> discovery of functional genes and creation of a germplasm related to quality traits.
DOI: 10.5524/100938
title: Supporting data for "CNVpytor: a tool for CNV detection and analysis from read depth and allele imbalance in whole genome sequencing"

description: Detecting copy number variations (CNVs) and copy number alterations (CNAs) based on whole genome sequencing data is important for personalized genomics and treatment. CNVnator is one of the most popular tools for CNV/CNA discovery and analysis based on read depth (RD).<br>Herein, we present an extension of CNVnator developed in Python called CNVpytor. CNVpytor inherits the reimplemented core engine of its predecessor and extends visualization, modularization, performance, and functionality. Additionally, CNVpytor uses B-allele frequency (BAF) likelihood information from single nucleotide polymorphism and small indels data as additional evidence for CNVs/CNAs and as primary information for copy number neutral losses of heterozygosity.<br>CNVpytor is significantly faster than CNVnator particularly for parsing alignment files (2 to 20 times faster) and has (20-50 times) smaller intermediate files. CNV calls can be filtered using several criteria, annotated, and merged over multiple samples. Modular architecture allows it to be used in shared and cloud environments such as Google Colab and Jupyter notebook. Data can be exported into JBrowse, while a lightweight plugin version of CNVpytor for JBrowse enables nearly instant and GUI-assisted analysis of CNVs by any user. CNVpytor release and the source code are available on GitHub under the MIT license.
DOI: 10.5524/100943
title: Supporting data for "De novo chromosome level assembly of the mule deer (Odocoileus hemionus) genome"

description: The mule deer <i>Odocoileus hemionus</i> is an ungulate species that ranges from western Canada to central Mexico. Mule deer are an essential source of food for many predators, are relatively abundant, and commonly make broad migration movements. A clearer understanding of the mule deer genome can help facilitate knowledge of its population genetics, movements, and demographic history, aiding in conservation efforts. While mule deer are excellent candidates for population genomic studies because of their large population size, continuous distribution, and diversity of habitat, few genomic resources are currently available for this species. Here, we sequence and assemble the mule deer genome into a highly contiguous chromosome-length assembly for use in future research using long-read sequencing and Hi-C. We also provide a genome annotation and compare demographic histories of the mule deer and white-tail deer using PSMC. We expect this assembly to be a valuable resource in the continued study and conservation of mule deer.
DOI: 10.5524/100944
title: Supporting data for "An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome"

description: The domestic sheep (<i>Ovis aries</i>) is an important agricultural species raised for meat, wool, and milk across the world. A high-quality reference genome for this species enhances the ability to discover genetic mechanisms influencing biological traits. Further, a high-quality reference genome allows for precise functional annotation of gene regulatory elements. The rapid advances in genome assembly algorithms and emergence of increasingly long sequence read length provide the opportunity for an improved <i>de novo</i> assembly of the sheep reference genome. <br>Short-read Illumina (55x coverage), long-read PacBio (75x coverage), and Hi-C data from this ewe retrieved from public databases were combined with an additional 50x coverage of Oxford Nanopore data and assembled with canu v1.9. The assembled contigs were scaffolded using Hi-C data with Salsa v2.2, gaps filled with PBsuitev 15.8.24, and polished with Nanopolish v0.12.5. After duplicate contig removal with PurgeDups v1.0.1, chromosomes were oriented and polished with two rounds of a pipeline which consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI_Ramb_v2.0 assembly has improved continuity (contig N50 of 43.18Mb) with a 19-fold and 38-fold decrease in the number of scaffolds compared with Oar_rambouillet_v1.0 and Oar_v4.0. ARS-UI_Ramb_v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies. <br>TheARS-UI_Ramb_v2.0 assembly is a substantial improvement that will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits in sheep.
DOI: 10.5524/100946
title: Supporting data for "Highly accurate whole genome imputation of SARS-CoV-2 from partial or low-quality sequences"

description: The current SARS-CoV-2 pandemic has emphasized the utility of viral whole genome sequencing (WGS) in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and therefore useless, sequences. Viral sequences evolve in the context of a complex phylogeny and different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data. <br> The impuSARS application, which takes advantage of the enormous number of SARS-CoV-2 genomes available, using a reference panel containing 239,301 sequences, to produce missing data imputation in viral genomes, has been developed. The impuSARS was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing) showing great fidelity when reconstructing the original sequences, recovering the lineage with a 100% precision for almost all the lineages, even in very poorly covered genomes (&lt; 20%). <br> Imputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. impuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 WGS.
DOI: 10.5524/100948
title: Supporting data for "A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles"

description: The increasing number of chromosome-level genome assemblies has advanced our knowledge and understanding of macroevolutionary processes. Here, we introduce the genome of the desert horned lizard, <i>Phrynosoma platyrhinos</i>, an iguanid lizard occupying extreme desert conditions of the American Southwest. We conduct analysis of the chromosomal structure and composition of this species and compare these features across genomes of 12 other reptiles (5 species of lizards, 3 snakes, 3 turtles, and 1 bird).<br>The desert horned lizard genome was sequenced using Illumina paired-end reads and assembled and scaffolded using Dovetail Genomics Hi-C and Chicago long-range contact data. The resulting genome assembly has a total length of 1,901.85 Mb, scaffold N50 length of 273.213 Mb, and includes 5,294 scaffolds. The chromosomel-evel assembly is composed of 6 macrochromosomes and 11 microchromosomes. A total of 20,764 genes were annotated in the assembly. GC content and gene density are higher for microchromosomes than macrochromosomes, while repeat element distributions show the opposite trend. Pathway analyses provide preliminary evidence that microchromosome and macrochromosome gene content are functionally distinct. Synteny analysis indicates that large microchromosome blocks are conserved among closely related species, whereas macrochromosomes show evidence of frequent fusion and fission events among reptiles, even between closely related species.<br>Our results demonstrate dynamic karyotypic evolution across Reptilia, with frequent inferred splits, fusions, and rearrangements that have resulted in shuffling of chromosomal blocks between macrochromosomes and microchromosomes. Our analyses also provide new evidence for distinct gene content and chromosomal structure between microchromosomes and macrochromosomes within reptiles.