cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100127
title: The genome of the saltwater crocodile (<em>Crocodylus porosus</em>).

description: Saltwater crocodiles (<em>Crocodylus porosus</em>) are the largest reptilian species alive today and as the name suggests they shows a high tolerance to salinity. <br>
Native to much of Australasia and parts of Asia, they are found mostly in coastal waters or around rivers. They are strong swimmers and can be found very far from land. <br>
These data have been produced as part of the Crocodilian Genomes Project. Genomic DNA was isolated using blood from "Errol", a 4.65 meter long male, sampled on the 25th October 2007 at Darwin Crocodile Farm, Noonamah, Northern Territory, Australia. Errol was relocated from the wild (Mud Island, Daly River, Northern Territory) after being deemed a problem crocodile in 1981, where he was housed individually within a purpose-built facility in the tourist section of the farm. He currently resides at the Fort Worth Zoo, Texas, USA. <br>
Briefly, the crocodile data consisted of Illumina reads from three libraries ranging from 21.6 to 90.2x coverage. These reads were assembled using AllPaths-LG with default parameters. Legacy sequence data from 360 MHC region BAC assemblies as well as RNASeq data were used to aid the assembly.
DOI: 10.5524/100130
title: 3-dimensional microCT reconstructions of brooding brittle stars

description: Brooding brittle stars have a special reproduction mode of retaining their eggs and juveniles inside respiratory body-sacs called bursae. In the past, studying this phenomenon required disturbance of the sample by dissecting the adult. This caused irreversible damage and made the sample unsuitable for future studies. Micro X-ray-computed tomography (µCT) is a promising technique, not only to visualise juveniles inside the bursae, but also retaining the sample intact and making the dataset of the scan available for future reference. <br>
Seven µCT scans of five freshly fixed (70% ethanol) individuals, representing three differently-sized brittle star species, provided adequate image quality to determine the numbers, sizes and postures of internally-brooded young, as well as anatomy and morphology of adults. No staining agents were necessary to achieve high-resolution, high-contrast images, which permitted visualisations of both calcified and soft tissue. The raw data (projection, reconstruction images and an additional volume file for easy viewing) are hereby made publicly available for download.
DOI: 10.5524/100131
title: Supporting materials for "Benchmark datasets for 3D MALDI- and DESI-Imaging Mass Spectrometry".

description: Three-dimensional imaging mass spectrometry (3D imaging MS) is a technique of analytical chemistry for three-dimensional molecular analysis of a tissue specimen, entire organ, or microbes on an agar plate. 3D imaging MS has unique advantages over existing 3D imaging techniques and offers novel perspectives for understanding the spatial organization of biological processes with possible applications in both biology and medicine. Due to the sheer quantity of data generated, visualization, analysis, and interpretation of big 3D imaging MS data remain a significant challenge. In this paper, we provide to the community selected high-quality 3D imaging MS datasets from different biological systems acquired at several labs with the aim to stimulate computational research in this field.
<br>
3D imaging MS data was collected from five different samples using two different types of 3D imaging MS. 3D Matrix-Assisted Laser Desorption/Ionization (MALDI) imaging MS data was collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D Desorption Electrospray Ionization (DESI) imaging MS data was collected from a human colorectal adenocarcinoma.
DOI: 10.5524/100132
title: Genomic data from the Tibetan Plateau frog (<em>Nanorana parkeri</em>).

description: <em>Nanorana parkeri</em> (also known as the high Himalaya frog, Xizang Plateau frog, Parker's slow frog, or mountain slow frog) is a common frog living across the Tibetan Plateau. It occurs at elevations ranging from 2,850 to 5,000m. Because this species lives at such high elevations, it provides an additional excellent biological model to study the frogs adaptations to extreme conditions. <br>
A female frog was collected from the Qinghai-Tibetan Plateau at an elevation of 4,900m, and genomic DNA was extracted from muscle tissue. Paired end DNA libraries with different insert-size lengths (170 bp to 20 kb) were
sequenced on the Illumina HiSeq 2000 platform. After performing filtering steps to remove artificial duplication, adapter
contamination and low-quality reads, 190 Gbp of high-quality data (83× genome coverage) was obtained. This was assembled using SOAPdenovo and SSPACE, producing a final draft assembly of 2.0Gb with an N50 scaffold size of 1.05Mb. More than 20,000 genes were predicted. The <em>Nanorana parkeri</em> genome should help offer new insights into the amphibian evolution and Tibetan high-altitude adaptation.
DOI: 10.5524/100134
title: Supporting materials for "Bacterial and viral identification and differentiation by amplicon7 sequencing on the MinION nanopore sequencer".

description: The MinION nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications. Recent reports have tested the ability of the MinION to act as a whole genome sequencer and have demonstrated that nanopore sequencing has tremendous potential utility. However, the current nanopore technology still has limitations with respect to error-rate, and this is problematic when attempting to assemble whole genomes without secondary rounds of sequencing to correct errors. In this study, we tested the ability of the MinION nanopore sequencer to accurately identify and differentiate bacterial and viral samples via directed sequencing of characteristic genes shared broadly across a target clade.
Using a 6 hour sequencing run time, sufficient data were generated to identify an E. coli sample down to the species level from 16S rDNA amplicons. Three poxviruses (cowpox, vaccinia-MVA, and vaccinia-Lister) were identified and differentiated down to the strain level, despite over 98% identity between the vaccinia strains.
DOI: 10.5524/100136
title: Supporting data and materials for "Large-scale analysis of evolutionary histories of phosphorylation motifs in the human genome".

description: Protein phosphorylation is a post-translational modification that is essential for a wide range of eukaryotic physiological processes, such as transcription, cytoskeletal regulation, cell metabolism, and signal transduction. In this study, we provide data for the assessments of functional phosphorylation signaling using comparative proteome analysis of phosphorylation motifs.
Data for 93,101 phosphosites and 1,003,756 potential phosphosites are described and provide an overview of evolutionary patterns of phosphomotif acquisition and indicate dependence on motif structures. By using these data, we described interaction networks of phosphoproteins, identified kinase substrates associated with phosphoproteins, and performed gene ontology enrichment analyses.
DOI: 10.5524/100141
title: Supporting material and data for "An Image Database of <i>Drosophila melanogaster</i> Wings for Phenomic and Biometric analysis".

description: Extracting important biological descriptors and features from images of biological specimens remains an important and open problem. In many biological disciplines, landmark and semi-landmark based approaches are used to define features. These features are determined a priori based on numerous
criteria such as homology, or some measure of biological significance. An alternative, widely used strategy uses computational pattern-recognition, in which features are acquired from the image denovo. Sub-sets of these features are then selected based on some objective criteria. Computational pattern-recognition has been extensively developed primarily for classification of samples into groups, while landmark methods have been broadly applied to biological inference.<br>
To address how these approaches compare, and to provide a general community resource, we have constructed an image database of Drosophila melanogaster wings, individually identifiable and organized by sex, genotype, and replicate imaging system, for the development and testing of measurement and classification tools for biological images.
DOI: 10.5524/100142
title: Supporting scripts and data for "Investigation into the annotation of protocol sequencing steps in the Sequence Read Archive".

description: The workflow for the production of high-throughput sequencing data from nucleic acid samples is complex. There are a series of protocol steps to be followed in the preparation of samples for next-generation sequencing. The quantification of bias in a number of protocol steps, namely DNA fractionation, blunting, phosphorylation, adapter ligation and library enrichment, remains to be determined. 
We examined the experimental metadata of the public repository Sequence Read Archive (SRA) in order to ascertain the level of annotation of important sequencing steps in submissions to the database.
DOI: 10.5524/100149
title: Supporting data and materials for "NCBI BLAST+ integrated into Galaxy".

description: The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST into Galaxy was a natural step for sequence comparison workflows. Here we provide the command line NCBI BLAST+ tool suite wrapped for use within Galaxy. <br>The integration of the BLAST+ tool suite into Galaxy has the goal of making common BLAST tasks easy and advanced tasks possible.
This project is an informal international collaborative effort, it is deployed and used on Galaxy servers worldwide.
DOI: 10.5524/100152
title: Supporting materials and software for "Tentacle: distributed quantification of genes in metagenomes".

description: In metagenomics, microbial communities are sequenced at increasingly high resolution generating data sets with billions of DNA fragments. Novel methods that can efficiently process the growing volumes of sequence data are necessary for accurate analysis and interpretation of existing and upcoming
metagenomes. Here we present Tentacle, a novel framework which uses distributed computational resources for gene quantification in metagenomes. Tentacle is implemented using a dynamic master-worker approach where DNA fragments are streamed via a network and processed in parallel on worker nodes. Tentacle is modular, extensible, and comes with support for six commonly used sequence aligners. It is easy to adapt to different applications in metagenomics and easy to integrate into existing workflows.
Evaluations show that Tentacle scales very well with increasing computing resources. We illustrate the versatility of Tentacle on three different use cases. Tentacle is written for Linux in Python 2.7 and is published as open source under the GNU General Public License (v3). Documentation, tutorials,
installation instructions, and source code is freely available online at:
http://bioinformatics.math.chalmers.se/tentacle.
DOI: 10.5524/100153
title: Supporting data for "A close look at protein function prediction evaluation protocols".

description: The recently held Critical Assessment of Functional Annotation challenge (CAFA2) required its participants to submit predictions for a large number of target proteins regardless of whether they have previous annotations or not. This is in contrast to the original CAFA challenge in which participants were asked to submit predictions for proteins with no existing annotations. The CAFA2 task is more realistic, in that it more closely mimics the accumulation of annotations over time. In this study we compare these tasks in terms of their difficulty, and determine if cross-validation provides a good estimate of performance.
The CAFA2 task is a combination of two sub-tasks: making predictions on annotated proteins and making predictions on previously unannotated proteins. In this study we analyze the performance of several function prediction methods in these two scenarios. Our results show that several methods (GOstruct, binary SVMs, and guilt by association) find it hard to achieve the same level of accuracy on these two tasks compared to cross-validation, and that predicting novel annotations for previously annotated proteins is a harder problem than predicting annotations for uncharacterized proteins. We also find that different methods have different performance characteristics in these tasks, and that cross-validation is not adequate at estimating performance and ranking methods.
DOI: 10.5524/100102
title: Bacterial whole-genome read data from the Oxford Nanopore Technologies MinION™ nanopore sequencer.

description: The MinION is a new, portable single-molecule sequencer developed by Oxford Nanopore Technologies. It measures four inches in length and is powered from the USB 3.0 port of a laptop computer. By measuring the change in resistance produced when DNA strands translocate through and interact with a protein nanopore the device is able to deduce the underlying nucleotide sequence.<br><br>Here we present a read dataset from whole-genome shotgun sequencing of the model organism Escherichia coli K-12 substr. MG1655 generated on a MinION device with R7 chemistry during the early-access MinION Access Program (MAP). <br> <br>Three sequencing runs of the MinION were performed using R7 chemistry. The first run produced 43,656 forward reads (272Mb), 23,338 (125Mb) reverse reads, 20,087 two-direction (2D) reads (131Mb), of which 8% (10Mb) were full 2D. Full 2D reads means that the complementary strand was successfully slowed through the pore.<br> <br>The R7 protocol has a modification to increase the relative number of full 2D reads (NONI). To exploit this, two new libraries were produced which included an overnight incubation stage (ONI-1 and ONI-2). Each library was run on an individual flow cell. This resulted in 6,534 & 8,260 forward reads, 2,171 & 2,945 reads and 1,740 & 2,394 2D reads (27%, 29%). In this case, 50% and 41.8% of reads were full 2D respectively. The mean fragment lengths for 2D reads from the three libraries were 6,543 (NONI) 6,907 (ONI-1) and 6,434 (ONI-2).<br> <br>A fourth run was performed using a further modified chemistry (R7.3), which resulted in 39819 forward reads, 18889 complement reads, of which 11823 and 9563 were 2D and full 2D respectively. <br> <br>Raw and assembled sequence data is provided to demonstrate the nature of data produced by the MinION platform and to encourage the development of customised methods for alignment and variant calling, de novo assembly and scaffolding. FAST5 files containing event data within the HDF5 container format are provided to assist with the development of improved base-calling methods.
DOI: 10.5524/100111
title: Supporting material for: "Event-related potential datasets based on three-stimulus paradigm".

description: The event-related potentials technique is widely used in cognitive neuroscience research. The P300 waveform has been explored in many research articles because of its wide applications including lie detection or brain-computer interfaces. However, a very few datasets are publicly available. Therefore, most researchers use only their private datasets for their analysis. This leads to hardly comparable results, particularly in brain-computer interfaces research.<br>This article presents the electroencephalography/event-related potentials (EEG/ERP) data. These were acquired using an odd-ball hardware stimulator. The visual stimulation was based on a three-stimulus paradigm and included target, non-target and distracter stimuli. The data were obtained from 20 healthy subjects.<br> The presented datasets together with their metadata provide researchers with an opportunity to study the P300 component from different perspectives. Furthermore, they can be used for BCI research.
DOI: 10.5524/100112
title: Supporting materials for: "Clinical outcome of preimplantation genetic diagnosis and screening using next generation sequencing".

description: A total of 395 couples were subjected to IVF-PGD treatment, including 129 couples with NGS-based test and 266 couples with SNP array based test for the detection of embryonic chromosomal abnormalities. The NGS test was performed using low coverage whole genome sequencing with HiSeq 2000 platform. And the SNP array test was using Affymetrix Gene Chip Mapping Nsp I 262K. The average age of patients was 32.1 years (age range 20-44 years).
<br><br>
Due to the sensitive nature of this dataset it is being hosted in the secure restricted access database European Genome-Phenome Archive at the EBI. It has been assigned the accession number EGAD00001001037.
<br>To gain access to this dataset you will need to apply for permission from the CITIC Xiangya Hospital and BGI PGD/PGS Data Access Committee (DAC). 
<br>There are <b>two</b> forms available to download from GigaDB FTP server (below), <b>both</b> should be completed and emailed to Dr Yueqiu Tan, who is the named representative of the CITIC Xiangya Hospital and BGI PGD/PGS DAC.
<br>After sending the forms to the DAC you will be contacted either by the DAC to decline your application or from the EGA with login details if your application is approved. This process can take several days.
DOI: 10.5524/100113
title: Supporting materials for: "VirAmp: A Galaxy-based viral genome assembly pipeline".

description: We have developed a multi-step viral genome assembly pipeline named VirAmp, that combines existing tools and techniques and presents them to end users via a web-enabled Galaxy interface. <br>Our pipeline allows users to assemble, analyze and interpret high coverage viral sequencing data with an ease and efficiency that was not possible previously. Our software makes a large number of genome assembly and related tools available to life scientists and automates the currently recommended best practices into a single, easy to use interface. We tested our pipeline with three different datasets from human herpes simplex virus (HSV). <br>VirAmp provides a user-friendly interface and a complete pipeline for viral genome analysis. We make our software available via an Amazon Elastic Cloud disk image that can be easily launched by anyone with an Amazon web service account. A demonstration version of our system can be found at http://viramp.com. We also maintain detailed documentation on each tool and methodology at http://docs.viramp.com. <br> Here in GigaDB you will find an archived version of the tools as they were published.
DOI: 10.5524/100117
title: RNA-Seq analysis and annotation of a draft blueberry genome assembly.

description: Blueberries are a popular and commercially important fruit, rich in antioxidants and other beneficial compounds that can protect against disease. To understand and identify genes involved in synthesis of bioactive compounds that could enable breeding berry varieties with enhanced health benefits, a draft blueberry genome assembly was produced using RNA-Seq data from five stages of berry fruit development and ripening. Libraries were prepared from samples of green and ripe fruit from plants of the ONeal variety of southern highbush blueberry (<em>Vaccinium corymbosum</em>). Genome-guided assembly of RNA-Seq read alignments combined with output from ab initio gene finders produced around 60,000 gene models, of which more than half were similar to proteins from other species, typically the grape <em>Vitis vinifera</em>. Homology-based annotation using Blast2GO and InterPro assigned Gene Ontology terms to around 15,000 genes. <br>
All sequence data are available in the Short Read Archive under accessions SRP039977 and SRP039971. Files containing alignments, RNA-Seq coverage graphs, and output from TopHat2 are also available from a publicly accessible IGBQuickLoad site configured to serve data for visualization in Integrated Genome Browser (see:http://www.igbquickload.org/blueberry). RNA-Seq data are freely available for visualization in Integrated Genome Browser. Archives of Visualization of read alignments, gene models, GeneModelAnalysis, counts file of numbers of single-mapping reads for each annotated blueberry gene, differentially expressed genes, Gene Ontology categories and Blastx Analysis files are available for download here. A snapshot of the R Markdown files, python scripts, and shell scripts used in data analysis and data processing are archived here as a set of static files representing those as publlished. For the current up-to-date scripts please visit the BitBucket repository.
DOI: 10.5524/100119
title: Anguidae lizard (Ophisaurus gracilis) genome assembly data.

description: The evolutionary transition from a lizard-like body to a snake-like body form is one
of the most important transformations in reptilian evolution. The increasing number of reptilian
genomes allows a deeper understanding of vertebrate evolution, although the genetic basis
underlying the loss of limbs in reptiles remains enigmatic. Here we report the sequencing,
assembly, and annotation of the genome of Asian glass lizard Ophisaurus gracilis, which is a
limbless lizard species with an elongated snake-like body form. <br> The sequencing of the O. gracilis genome using the Illumina HiSeq2000 platform
resulted in a total of 274.20 Gbp raw data, which was subsequently filtered and assembled to a
final assembly of 1.78 Gbp, comprising 6,717 scaffolds with N50=1.27 Mbp. Based on the k-mer
estimated genome size of 1.71 Gbp, the assembly appears to be near 100% complete. A total of
19,513 protein coding genes were predicted, and 884.06 Mbp repeat sequences (approximately
half of the genome) were annotated. The draft genome of O. gracilis shows similar characteristics
to both lizards and snakes, and represents a substantial addition to existing reptilian genomes
available for comparative analysis.
DOI: 10.5524/100125
title: Annotation and analysis of three crocodilian genomes.

description: Crocodilians are important model organisms in fields as diverse as developmental biology, osmoregulation, cardiophysiology, paleoclimatology, sex determination, population genetics, paleobiogeography, and functional morphology. Crocodilians, birds, dinosaurs, and pterosaurs comprise a monophyletic group known as the archosaurs. Crocodilians and birds are the only extant members and thus crocodilians (alligators, caimans, crocodiles, and gharials) are the closest living relatives of all birds. <br>
To provide context for the diversifications of archosaurs, we generated draft genomes of three crocodilians, <em>Alligator mississippiensis</em> (the American alligator), <em>Crocodylus porosus</em> (the saltwater crocodile), and <em>Gavialis gangeticus</em> (the Indian gharial). We generated high-coverage Illumina sequence data from paired-end and mate-pair libraries from each species. The assembly strategy for each taxon differed due to varying legacy data and developments in library preparation methods during the course of the project. Gene annotation was accomplished using a combination of RNASeq data and homology-based analyses. We identified 23,323 protein-coding genes in the alligator compared to 13,321 and 14,043 in crocodile and gharial, respectively. Transposable elements (TEs) were identified de novo in all three crocodilians and analyses resulted in a library of 1269 different TEs.