cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102550
title: Supporting data for "Deepdefense: Annotation of immune systems in prokaryotes using DeepLearning"

description: Due to a constant evolutionary arms race, archaea and bacteria have evolved an abundance and diversity of immune responses to protect themselves against phages. Since the discovery and application of CRISPR-Cas adaptive immune systems, numerous novel candidates for immune systems have been identified. Previous approaches to identifying these new immune systems rely on HMM-based homolog searches or use labor-intensive and costly wet-lab experiments. To aid in finding and classifying immune systems, we use machine learning to classify already known immune system proteins and discover potential candidates in the genome. Neural networks have shown promising results in classifying and predicting protein functionality in recent years. However, these approaches frequently rely on the assumption of a closed world, which is often different in practice. <br>In this work, we explore neural networks for immune protein classification and deal with different methods for rejecting unrelated proteins in a genome-wide search, and establish a benchmark. Then, we optimize our approach for accuracy. Based on this, we develop an algorithm called Deepdefense to predict immune cassette classes based on a genome. Finally, we test our approach for detecting immune systems in the genome against an HMM-based method. <br>Deepdefense can automatically detect genes and define cassette annotations and classifications using two model classifications. This is achieved by creating an optimized deep learning model to annotate immune systems, in combination with calibration methods, and a second model to enable the scanning of an entire genome
DOI: 10.5524/102557
title: Supporting data for "Dual-Alpha: A Large EEG Study for Dual-Frequency SSVEP Brain-Computer Interface"

description: The domain of brain-computer interface (BCI) technology has experienced significant expansion in recent years. However, the field continues to face a pivotal challenge due to the dearth of high-quality datasets. This lack of robust datasets serves as a bottleneck, constraining the progression of algorithmic innovations and, by extension, the maturation of the BCI field. <br>This study details the acquisition and compilation of electroencephalogram (EEG) data across three distinct dual-frequency steady-state visual evoked potential (SSVEP) paradigms, encompassing over one hundred participants. Each experimental condition featured 40 individual targets with 5 repetitions per target, culminating in a comprehensive dataset consisting of 21,000 trials of dual-frequency SSVEP recordings. We performed an exhaustive validation of the dataset through signal-to-noise ratio (SNR) analyses and Task-related Component Analysis (TRCA), thereby substantiating its reliability and effectiveness for classification tasks. <br>The extensive dataset presented is set to be a catalyst for the accelerated development of BCI technologies. Its significance extends beyond the BCI sphere and holds considerable promise for propelling research in psychology and neuroscience. The dataset is particularly invaluable for discerning the complex dynamics of binocular visual resource distribution.
DOI: 10.34740/kaggle/dsv/11960899
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5524/102543
title: The genomic data for Clitoria ternatea

description: <i>Clitoria ternatea</i>, commonly known as Asian pigeonwings, bluebellvine, blue pea, butterfly pea, cordofan pea or Darwin pea, is a plant species belonging to the family Fabaceae, endemic and native to the Indonesian island of Ternate. In this study, a chromosome-level reference genomes of <i>Clitoria ternatea</i>has been generated, as the genome size is 1.7Gb, contig N50 is 126 Mb, scaffold N50 is 169Mb.
DOI: 10.5524/102510
title: Supporting data for "PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata"

description: As biological data increases, we need additional infrastructure to share it and promote interoperability. While major effort has been put into sharing data, relatively less emphasis is placed on sharing metadata. Yet, sharing metadata is also important, and in some ways has a wider scope than sharing data itself. <br>Here, we present PEPhub, an approach to improve sharing and interoperability of biological metadata. PEPhub provides an API, natural language search, and user-friendly web-based sharing and editing of sample metadata tables. We used PEPhub to process more than 100,000 published biological research projects and index them with fast semantic natural language search. PEPhub thus provides a fast and user-friendly way to finding existing biological research data, or to share new data.
DOI: 10.5524/102517
title: Supporting data for "Snakemake workflows for long-read bacterial genome assembly and evaluation"

description: With the advancement of long-read sequencing technologies and their more widespread use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also the need for measuring completeness and accuracy of such assemblies, for which, again, several evaluation methods implemented in various programs are available. In order to automatically run multiple genome assembly and evaluation programs at once, I developed two workflows for the workflow management system Snakemake, which provide end users with an easy-to-run solution for testing various genome assemblies from their sequencing data. Both workflows use the conda packaging system, so that there is no need for manual installation of each program.
DOI: 10.5524/102522
title: Supporting data for "A Qualitative Assessment of Using ChatGPT as Large Language Model for Scientific Workflow Development"

description: Scientific workflow systems are increasingly popular for expressing and executing complex data analysis pipelines over large datasets, as they offer reproducibility, dependability, and scalability of analyses by automatic parallelization on large compute clusters. However, implementing workflows is difficult due to the involvement of many black-box tools and the deep infrastructure stack necessary for their execution. Simultaneously, user-supporting tools are rare, and the number of available examples is much lower than in classical programming languages. <br>To address these challenges, we investigate the efficiency of Large Language Models (LLMs), specifically ChatGPT, to support users when dealing with scientific workflows. We performed three user studies in two scientific domains to evaluate ChatGPT for comprehending, adapting, and extending workflows. Our results indicate that LLMs efficiently interpret workflows but achieve lower performance for exchanging components or purposeful workflow extensions. We characterize their limitations in these challenging scenarios and suggest future research directions. <br>Our results show a high accuracy for comprehending and explaining scientific workflows while achieving a reduced performance for modifying and extending workflow descriptions. These findings clearly illustrate the need for further research in this area.
DOI: 10.5524/102539
title: Supporting data for "Kinship analysis and pedigree reconstruction by RAD sequencing in cattle"

description: Kinship and pedigree information, used for estimating inbreeding, heritability, selection, and gene flow, is useful for breeding and animal conservation. However, as the size of the crossbred population increases, inaccurate generation and parentage recoding in livestock farms increases. Restriction-site-associated DNA sequencing (RAD-Seq) is a cost-effective platform for single nucleotide polymorphism (SNP) discovery and genotyping. Here, we performed a kinship analysis and pedigree reconstruction for Angus and Xiangxi yellow cattle, which benefit from good meat quality and yields, providing a basis for livestock management. A total of 975 cattle, including 923 offspring with 24 known sires and 28 known dams, were sampled and subjected to SNP discovery and genotyping. The identified SNPs panel included 7305 SNPs capturing the maximum difference between paternal and maternal genome information allowing us to distinguish between the F1 and F2 generation with 90% accuracy. In addition, parentage assignment software based on different strategies verified that the cross-assignments. In conclusion, we provided a low-cost and efficient SNP panel for kinship analyses and the improvement of local genetic resources, which are valuable for breed improvement, local resource utilization, and conservation.
DOI: 10.5524/102541
title: Supporting data for "CAT – A Computational Anatomy Toolbox for the Analysis of Structural MRI Data"

description: A large range of sophisticated brain image analysis tools have been developed by the neuroscience community, greatly advancing the field of human brain mapping. Here we introduce the iComputational Anatomy Toolbox/i (CAT) a powerful suite of tools for brain morphometric analyses with an intuitive graphical user interface, but also usable as a shell script. CAT is suitable for beginners, casual users, experts, and developers alike providing a comprehensive set of analysis options, workflows, and integrated pipelines. The available analysis streams illustrated on an example dataset allow for voxel-based, surface-based, as well as region-based morphometric analyses. Notably, CAT incorporates multiple quality control options and covers the entire analysis workflow, including the preprocessing of cross-sectional and longitudinal data, statistical analysis, and the visualization of results. The overarching aim of this article is to provide a complete description and evaluation of CAT, while offering a citable standard for the neuroscience community
DOI: 10.5524/102544
title: The genomic data for Crotalaria pallida

description: <i>Crotalaria pallida</i>, commonly known as the smooth crotalaria, is a species of flowering plant within the family Fabaceae. In this study, a chromosome-level reference genomes of <i>Crotalaria pallida</i> has been generated, as the genome size is 1.2Gb, contig N50 is 101 Mb, scaffold N50 is 142 Mb.
DOI: 10.5281/zenodo.8300413
title: Molecular Property Diagnostic Suite Compound Library (MPDS-CL): A Structure based Classification of the Chemical Space

description: Molecular Property Diagnostic Suite-Compound Library (MPDS-CL), is an open-source galaxy-based cheminformatics web-portal which presents a structure-based classification of the molecules. A structure-based classification of nearly 150 million unique compounds, which are obtained from 42 publicly available databases were curated for redundancy removal through 97 hierarchically well-defined atom composition-based portions. These are further subjected to 56-bit fingerprint-based classification algorithm which led to a formation of 56 structurally well-defined classes. The classes thus obtained were further divided into clusters based on their molecular weight. Thus, the entire set of molecules was put in 56 different classes and 625 clusters. This led to the assignment of a unique ID, named as <em>MPDS AadharID</em>, for each of these 149 169 443 molecules. <em>MPDS AadharID</em> is akin to the unique number given to citizens in India (similar to the SSN in US, NINO in UK). MPDS-CL unique features are: a) several search options, such as exact structure search, substructure search, property-based search, fingerprint-based search, using SMILES, InChIKey and key-in; b) automatic generation of information for the processing for MPDS and other galaxy tools; c) providing the class and cluster of a molecule which makes it easier and fast to search for similar molecules and d) information related to the presence of the molecules in multiple databases. The MPDS-CL can be accessed at http://mpds.neist.res.in:8086/.
DOI: 10.5524/102493
title: Supporting data for "Near chromosome-level and highly-repetitive genome assembly of the snake pipefish <i>Entelurus aequoreus</i> (Syngnathiformes: Syngnathidae)"

description: The snake pipefish, iEntelurus aequoreus/i (Linnaeus, 1758), is a slender, up to 60 cm long, northern Atlantic fish that dwells in open seagrass habitats and has recently expanded its distribution range. The snake pipefish is part of the family Syngnathidae (seahorses and pipefish) that has undergone several characteristic morphological changes, such as loss of pelvic fins and elongated snout. Here, we present a highly contiguous, near chromosome-scale genome of the snake pipefish assembled as part of a university masters course. The final assembly has a length of 1.6 Gbp in 7,391 scaffolds, a scaffold and contig N50 of 62.3 Mbp and 45.0 Mbp and L50 of 12 and 14, respectively. The largest 28 scaffolds (21 Mbp) span 89.7% of the assembly length. A BUSCO completeness score of 94.1% and a mapping rate above 98% suggest a high assembly completeness. Repetitive elements cover 74.93% of the genome, one of the highest proportions so far identified in vertebrate genomes. Demographic modeling using the PSMC framework indicates a peak in effective population size (50 100 kya) during the last interglacial period and suggests that the species might largely benefit from warmer water conditions, as seen today. Our updated snake pipefish assembly forms an important foundation for further analysis of the morphological and molecular changes unique to the family Syngnathidae.
DOI: 10.5524/102504
title: Supporting data for "Large-scale Genomic Survey with Deep Learning-based Method Reveals Strain-Level Phage Specificity Determinants"

description: Phage therapy, re-emerging as a promising approach to counter antimicrobial-resistant infections, relies on a comprehensive understanding of the specificity of individual phages. Yet the significant diversity within phage populations presents a considerable challenge. Currently, theres a notable lack of tools designed for large-scale characterization of phage receptor-binding proteins, which are crucial in determining the phage host range. <br>In this study, we present SpikeHunter, a deep learning method based on the ESM-2 protein language model. With SpikeHunter, we identified 231,965 diverse phage-encoded tailspike proteins, a crucial determinant of phage specificity that targets bacterial polysaccharide receptors, across 787,566 bacterial genomes from five virulent, antibiotic-resistant pathogens. Notably, 86.60% (143,200) of these proteins exhibited strong associations with specific bacterial polysaccharides. We discovered that phages with identical tailspike proteins can infect different bacterial species with similar polysaccharide receptors, underscoring the pivotal role of tailspike proteins in determining host range. The specificity is mainly attributed to the proteins C-terminal domain, which strictly correlates with host specificity during domain-swapping in tailspike proteins. Importantly, our dataset-driven predictions of phage-host specificity closely match the phage-host pairs observed in real-world phage therapy cases we studied. <br>Our research provides a rich resource, including both the method and a database derived from a large-scale genomics survey. This substantially enhances understanding of phage specificity determinants at the strain level and offers a valuable framework for guiding phage selection in therapeutic applications.
DOI: 10.5524/102506
title: Supporting data for "Hecatomb: An Integrated Software Platform for Viral Metagenomics"

description: Modern sequencing technologies offer extraordinary opportunities for virus discovery and virome analysis. Annotation of viral sequences from metagenomic data requires a complex series of steps to ensure accurate annotation of individual reads and assembled contigs. In addition, varying study designs will require project specific statistical analyses.<br> Here we introduce Hecatomb, a bioinformatic platform coordinating commonly used tasks required for virome analysis. Hecatomb means a great sacrifice. In this setting, Hecatomb is sacrificing false-positive viral annotations using extensive quality control and tiered-database searches. Hecatomb processes metagenomic data obtained from both short and long read sequencing technologies, providing annotations to individual sequences and assembled contigs. Results are provided in commonly used data formats useful for downstream analysis. Here we demonstrate the functionality of Hecatomb through the reanalysis of a primate enteric and a novel coral reef virome.<br> Hecatomb provides an integrated platform to manage many commonly used steps for virome characterization including rigorous quality control, host removal and both read- and contig-based analysis. Each step is managed using the Snakemake workflow manager with dependency management using Conda. Hecatomb outputs several tables properly formatted for immediate use within popular data analysis and visualization tools enabling effective data interpretation for a variety of study designs.
DOI: 10.5524/102508
title: Supporting data for "Improved integration of single cell transcriptome data demonstrates common and unique signatures of heart failure in mice and humans"

description: Cardiovascular research heavily relies on mouse (<i>Mus musculus</i>) models to study disease mechanisms and to test novel biomarkers and medications. Yet, applying these results to patients remains a major challenge and often results in non-effective drugs. Therefore, it is an open challenge of translational science to develop models with high similarities and predictive value. This requires a comparison of disease models in mice with diseased tissue derived from humans. <br>To compare the transcriptional signatures at single cell resolution, we implemented an integration pipeline called <i>OrthoIntegrate</i> which uniquely assigns orthologs and therewith merges single cell data (scRNA-SEQ) of different species. The pipeline has been designed to be as easy to use and is fully integrable in the standard Seurat workflow. <br>We applied <i>OrthoIntegrate</i> on scRNA-SEQ from cardiac tissue of heart failure patients with reduced ejection fraction (HFrEF) and scRNA-SEQ from the mice after chronic infarction, which is a commonly used mouse model to mimic HFrEF. We discovered shared and distinct regulatory pathways between human HFrEF patients and the corresponding mouse model. Overall, 54% of genes were commonly regulated including major changes in cardiomyocyte energy metabolism. However, several regulatory pathways, e.g. angiogenesis, were specifically regulated in humans. <br>The demonstration of unique pathways occurring in humans indicate limitations on the comparability between mice models and human HFrEF and show that results from the mice model should be validated carefully. <i>OrthoIntegrate</i> is publicly accessible (https://github.com/MarianoRuzJurado/OrthoIntegrate) and can be used to integrate other large data sets to provide a general comparison of models with patients data.
DOI: 10.5524/102509
title: Supporting data for "Molecular Property Diagnostic Suite for COVID-19 (MPDS<sup>COVID-19</sup>): An open-source disease-specific drug discovery portal"

description: Molecular Property Diagnostic Suite (MPDS) was conceived and developed as an open-source disease-specific web portal based on Galaxy. MPDS<sup>COVID-19</sup> was developed for COVID-19 as a one-stop solution for drug discovery research. Galaxy platforms enable the creation of customized workflows connecting various modules in the web server. The architecture of MPDS<sup>COVID-19</sup> effectively employs Galaxy v22.04 features, which are ported on CentOS 7.8 and Python 3.7. MPDS<sup>COVID-19</sup> provides significant updates and the addition of several new tools updated after six years. Tools developed by our group in Perl/Python and open-source tools are collated and integrated into MPDS<sup>COVID-19</sup> using XML scripts. Our MPDS suite aims to facilitate transparent and open innovation. This approach significantly helps bring inclusiveness in the community while promoting free access and participation in software development.
DOI: 10.5524/102511
title: Supporting data for "An effective strategy for assembling the sex-limited chromosome"

description: Most available reference genomes lack the sequence map of sex-limited (such as Y and W) chromosomes, which make the assemblies incomplete and difficult to conduct further research on sex chromosomes. Recent advances in long reads sequencing and population sequencing raise the opportunity to assemble sex-limited chromosomes without the traditional complicated experimental efforts. We introduced the first computational method, Sorting long Reads of Y or other sex-limited chromosome (SRY), which achieved improved assembly results compared to flow sorting. Specifically, SRY outperformed in the heterochromatic region and demonstrated comparable performance in other regions. Furthermore, we observed that SRY enhanced the capabilities of the hybrid assembly software, as evidenced by improved continuity and accuracy. Our method can realize true complete genome assembly and facilitate downstream research of sex-limited chromosomes.
DOI: 10.5524/102520
title: Supporting data for "The telomere-to-telomere (T2T) genome of <i>Peucedanum praeruptorum</i> Dunn provides insights into the genome evolution and coumarin biosynthesis"

description: <i>Peucedanum praeruptorum</i> Dunn (Apiaceae) has been used in traditional Chinese medicine for a long time. Various coumarins including the major root constituents Praeruptorin (A-D) are the active constituents of the dried roots of <i>P. praeruptorum</i>. Previous transcriptomic and metabolomic studies attempted to elucidate the distribution and biosynthetic network for these medicinal valuable compounds. However, the lack of a high-quality reference genome impedes in-depth understanding of genetic traits and thus development of better breeding strategies. <br>A telomere-to-telomere genome was assembled by the combination of PacBio HiFi, ONT ultra-long, and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes, and genome completeness &gt;98%. Comparative genomic analysis suggested that <i>P. praeruptorum</i> experienced two WGD events as the ones in the Apiaceae family. By the transcriptomic and metabolomic analysis of coumarin metabolic pathway, we presented the spatial and temporal distribution of coumarins as well as the expression patterns of key genes for its biosynthesis. Notably, the COSY genes and cytochrome P450 genes showed tandem duplications on several chromosomes which may be responsible for the high accumulations of coumarins. <br>A T2T genome for <i>P. praeruptorum</i> was obtained which provides molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome serves as an important resource for designing engineering strategies for improving the production of these valuable compounds.