cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/102345
title: Supporting data for "Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data"

description: Biological networks are often used to describe the relationships between relevant entities, in particular genes and proteins, and are a powerful tool for functional genomics. Many important biological problems can be investigated by comparing biological networks between different conditions, or networks obtained with different techniques. We show that contrast subgraphs, a recently introduced technique to identify the most important structural differences between two networks, provide a versatile tool for comparing gene and protein networks of diverse origin. We demonstrate the use of contrast subgraphs in the comparison of coexpression networks derived from different subtypes of breast cancer; of coexpression networks derived from transcriptomic and proteomic data; and of protein-protein interaction networks assayed in different cell lines. These examples demonstrate how contrast subgraphs can provide new insight in functional genomics by extracting the gene/protein modules whose connectivity is most altered between two conditions or experimental techniques.
DOI: 10.7303/syn1688369
title: METABRIC Data for Use in Independent Research
DOI: 10.5524/102340
title: Supporting data for "HTGQC and shinyHTGQC: an R package and shinyR application for quality controls of HTG EDGE-seq protocols"

description: We have developed HTGQC, a R package for the quality control of HTG Edge-Seq protocols, and shinyHTGQC, a shiny application for users without computing knowledge, that provides an easy-to-use interface for the the quality control of the data.<br>The quality check can be performed directly from the raw output of the sequencing machine, and provides summary, tables and plots for the assessment of the quality of the samples. Samples are flagged as FAIL or ALERT based on the expression levels of the positive and negative control genes. In the shiny application basic visualisation (PCA and heatmap) is provided for assessing the different pre vs post quality control. The code is freely available on the web at https://github.com/LodovicoTerzi/HTGQC (R package) and at https://lodovico.shinyapps.io/shinyHTGQC/ (shiny application), including test datasets.
DOI: 10.5524/102302
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 31 Q21 Development and temporal organization of compulsive checking induced by repeated injections of QNP (0.5 mg/kg)

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102303
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 32 Q21 Effect of separating pups from maternal nest for 15 or 180 min on postnatal days 2 to 15 on the development of compulsive checking induced by repeated injections of quinpirole in adult male rats

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102308
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 37 Q47 Effect of testing with the 4 objects removed from open field on the expression of sensitization and compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102309
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 38 Q31 Effect on performance in tests of depression and anxiety by rats expressing compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102311
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 40 Q40 Effects of NAc lesion plus 8OHDPAT (.0625 mg/kg on injections 1-4) or mCPP (0.625 mg/kg on injections 5-10) in producing compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102312
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 41 Q43 Effect of NAc lesion plus 8OHDPAT (0.0625 mg/kg on injections 1-4) in producing compulsive checking

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.
DOI: 10.5524/102316
title: Frictionless Data Handbook for Researchers

description: The Frictionless Data project is a open-source framework overseen by Datopian and Open Knowledge Foundation to make easier to work with data. The handbook covers an introduction to use Frictionless Data, an introduction to the specification, minimal working examples of creating your own data package, and long examples, based on published articles in GigaScience and GigaByte journals, illustrating the creation and use of Frictionless Data.
DOI: 10.5281/zenodo.4588969
title: LMAS Test Dataset

description: LMAS is an automated workflow enabling the benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. As proof of concept, the eight bacterial genomes and four plasmids, in tripled form, of the ZymoBIOMICS Microbial Community Standards are made available to be used as reference. Simulated raw sequence data of the mock communities with evenly distributed reads, generated from the reference genomes, with and without error, were obtained with inSilicoSeq. Project repository: https://github.com/cimendes/LMAS
DOI: 10.5281/zenodo.6623457
title: LMAS Supplemental Material

description: LMAS is an automated workflow enabling the benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. As proof of concept, the eight bacterial genomes and four plasmids, in tripled form, of the ZymoBIOMICS Microbial Community Standards are made available to be used as reference. Simulated raw sequence data of the mock communities with evenly distributed reads, generated from the reference genomes, with and without error, were obtained with inSilicoSeq. Project repository: https://github.com/cimendes/LMAS
DOI: 10.5281/zenodo.6783042
title: LMAS Figures

description: LMAS is an automated workflow enabling the benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. As proof of concept, the eight bacterial genomes and four plasmids, in tripled form, of the ZymoBIOMICS Microbial Community Standards are made available to be used as reference. Simulated raw sequence data of the mock communities with evenly distributed reads, generated from the reference genomes, with and without error, were obtained with inSilicoSeq. Project repository: https://github.com/cimendes/LMAS
DOI: 10.5281/zenodo.7088960
title: LMAS Test Dataset - ZymoBIOMICS Microbial Community Standards

description: The eight bacterial genomes and four plasmids of the ZymoBIOMICS Microbial Community Standards were used as reference. It contains tripled complete sequences for the following species: <em>Bacillus subtilis</em> <em>Enterococcus faecalis</em> <em>Escherichia coli</em> <em>Escherichia coli</em> plasmid <em>Lactobacillus fermentum</em> <em>Listeria monocytogenes</em> <em>Pseudomonas aeruginosa</em> <em>Salmonella enterica</em> <em>Staphylococcus aureus</em> <em>Staphylococcus aureus</em> plasmid 1 <em>Staphylococcus aureus</em> plasmid 2 <em>Staphylococcus aureus</em> plasmid 3 It also downloads the raw sequence data of the mock communities, with an even and logarithmic distribution of species: ERR2984773 - Evenly distributed real sample ERR2935805 - Log distributed real sample A set of simulated samples were generated from the genomes in the ZymoBIOMICS standard though the InSilicoSeq sequence simulator (version 1.5.2), including both even and logarithmic distribution, with and without Illumina error model. The number of read pairs generated matches the number of read pairs in the real data for each distribution. The following samples are available in Zenodo: <strong>ENN</strong> - Evenly distributed sample with no error model <strong>EMS</strong> - Evenly distributed sample with Illumina MiSeq error model <strong>LNN</strong> - Log distributed sample with no error model <strong>LHS</strong> - Log distributed sample with Illumina HiSeq error model DOI Dataset
DOI: 10.5281/zenodo.7092431
title: LMAS Test Dataset - BMock12 Community Standards

description: The twelve bacterial replicons of the BMock12 Community Standards were used as reference. It includes the following strains: Species Sample ID Depth of Coverage (x) Muricauda sp. ES.050 2615840527 618.76 Thioclava sp. ES.032 2615840533 78.32 Cohaesibacter sp. ES.047 2615840601 170.59 Propionibacteriaceae bacterium 2615840646 31.90 Marinobacter sp. LV10R510-8 2615840697 447.83 Marinobacter sp. LV10MA510-1 2616644829 135.05 Psychrobacter sp. LV10R520-6 2617270709 425.47 Micromonospora echinaurantiaca 2623620557 14.91 Micromonospora echinofusca 2623620567 18.19 Micromonospora coxensis 2623620609 0.02 Halomonas sp. HL-4 2623620617 507.08 Halomonas sp. HL-93 2623620618 579.87 The raw sequence data of the mock communities, with an even distribution of species, is available at: SRR8073716 For the sake of a less resource-intense evaluation we downsampled to have 20% of the reads available in the original sample and further processed only these. The main challenges of this data set are possibly to assemble the genomes of the three <em>Micromonospora</em> spp. and the two <em>Halomonas</em> spp. strains, which have an ANIb &gt;0.84 and 0.98, respectively. The two <em>Marinobacter</em> spp. have an ANIb of 0.78.
DOI: 10.5281/zenodo.7092693
title: LMAS Test Dataset - NIBSC Gut DNA Reference

description: The twenty bacterial replicons of the National Institute for Biological Standards and Control (NIBSC) Gut Community Standards were used as reference. It includes the following strains: Species Culture collection number Accession numbers Status Gut-Mix-RR Coverage (x) Gut-HiLo-RR Coverage (x) Akkermansia muciniphila DSM 22959 NC_010655 Complete genome 33.33 0.94 Alistipes finegoldii DSM 17242 NC_018011 Complete genome 16.94 4.85 Anaerostipes hadrus DSM 3319 NZ_KB290627 Complete genome 24.04 6.89 Bacteroides thetaiotaomicron DSM 2079 NC_004663 Complete genome 5.99 17.19 Bacteroides uniformis DSM 6597 GCF_000154205 Scaffold 10.81 3.10 Bifidobacterium longum subsp. infantis DSM 20088 NC_011593 Complete genome 29.52 84.63 Bifidobacterium longum subsp. longum DSM 20219 GCF_900104835 Contig 40.19 115.10 Blautia wexlerae DSM 19850 GCF_000484655 Scaffold 11.68 0.34 Clostridium butyricum DSM 10702 GCF_000409755 Contig 11.21 32.09 Collinsella aerofaciens DSM 13712 GCF_902501475 Contig 44.03 12.61 Escherichia coli DSM 1103 CP009072 Complete genome 8.86 25.34 Eubacterium hallii DSM 3353 GCF_000173975 Contig 21.79 6.25 Faecalibacterium prausnitzii DSM 17677 NZ_CP048437 Complete genome 24.66 0.72 Lactobacillus gasseri DSM 20077 NC_008530 Complete genome 66.00 1.91 Parabacteroides distasonis DSM 20701 NC_009615 Complete genome 10.20 29.26 Prevotella copri DSM 18205 GCF_000157935 Scaffold 19.23 55.11 Prevotella melaninogenica DSM 7089 NC_014370,1 and NC_014371,1 2 Chromosomes 23.49 6.73 Roseburia hominis DSM 16839 NC_015977 Complete genome 18.31 5.24 Roseburia intestinalis DSM 14610 NZ_LR027880 Complete genome 12.04 0.34 Ruminococcus gauvreauii DSM 19829 GCF_000425525 Scaffold 14.04 0.41 The raw sequence data of the mock communities, with an even and staggered distribution of species, is available at: SRR11487941 - Gut-Mix-RR Illumina MiSeq sample SRR11487935 - Gut-Mix-HiLo Illumina MiSeq sample
DOI: 10.5524/102286
title: A Virtual Library for Behavioral Performance in Standard Conditions – Experiment 15 Q46 Effect of 8OHDPAT dose (0 0.03125 0.0625 0.125 mg/kg) co-injected with a low dose of QNP (0.125 mg/kg) on the development of sensitization and compulsive checking (batch 1)

description: Beyond their specific experiment, video records of behavior have future value; for example, as inputs for new experiments or for yet unknown types of analysis of behaviorsimilar to tissue or blood sample banks in life sciences where clinically-derived or otherwise well-described experimental samples are stored to be available for some unknown potential future purpose. <br>Research using an animal model of obsessive-compulsive disorder employed a standardized paradigm where the behavior of rats in a large open field was video recorded for 55 min on each test. From 43 experiments, there are 19,976 such trials that amount to over 2 years of continuous recording. In addition to videos, there are two video-derived raw data objects: XY locomotion coordinates, and plots of animal trajectory. To motivate future use, the three raw data objects are annotated with a general schemaone that abstracts the data records from their particular experiment while providing, at the same time a detailed list of independent variables bearing on behavioral performance. The raw data objects are deposited as 43 datasets but constitute, functionally, a library containing one large dataset. <br>Size and annotation schema give the library high re-use potential: in applications using machine learning techniques, statistical evaluation of subtle factors, simulation of new experiments, or as educational resource. Ultimately, the library can serve both as the seed and the test bed to create a machine searchable virtual library of linked open datasets for behavioral performance in defined conditions.