Abstract:
:Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn's disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools.
journal_name
Sci Datajournal_title
Scientific dataauthors
Hahn AS,Altman T,Konwar KM,Hanson NW,Kim D,Relman DA,Dill DL,Hallam SJdoi
10.1038/sdata.2017.35subject
Has Abstractpub_date
2017-04-11 00:00:00pages
170035issn
2052-4463pii
sdata201735journal_volume
4pub_type
杂志文章相关文献
Scientific Data文献大全abstract::With the help of the bacteria in the rumen, ruminants can effectively convert human inedible plant fiber to edible food (meat and milk). However, the understanding of rumen bacteriome in dairy cows is still limited, especially in a large population under the same diet, breed, and milking period. Here we described the ...
journal_title:Scientific data
pub_type:
doi:10.1038/sdata.2018.301
更新日期:2019-01-22 00:00:00
abstract::In the last few decades, data-driven methods have come to dominate many fields of scientific inquiry. Open data and open-source software have enabled the rapid implementation of novel methods to manage and analyze the growing flood of data. However, it has become apparent that many scientific fields exhibit distressin...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2017.114
更新日期:2017-09-05 00:00:00
abstract::Tardigrades are ubiquitous microscopic animals that play an important role in the study of metazoan phylogeny. Most terrestrial tardigrades can withstand extreme environments by entering an ametabolic desiccated state termed anhydrobiosis. Due to their small size and the non-axenic nature of laboratory cultures, molec...
journal_title:Scientific data
pub_type: 评论,杂志文章
doi:10.1038/sdata.2016.63
更新日期:2016-08-16 00:00:00
abstract::Rett syndrome is an X-linked neurodevelopmental disorder caused by mutation in the methyl-CpG-binding protein 2 gene (MECP2) in the majority of cases. We describe an RNA sequencing dataset of postmortem brain tissue samples from four females clinically diagnosed with Rett syndrome and four age-matched female donors. T...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-0527-2
更新日期:2020-06-19 00:00:00
abstract::In Eco-Metabolomics interactions are studied of non-model organisms in their natural environment and relations are made between biochemistry and ecological function. Current challenges when processing such metabolomics data involve complex experiment designs which are often carried out in large field campaigns involvi...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2018.179
更新日期:2018-08-28 00:00:00
abstract::We introduce and make openly accessible a comprehensive, multivariate time series (MVTS) dataset extracted from solar photospheric vector magnetograms in Spaceweather HMI Active Region Patch (SHARP) series. Our dataset also includes a cross-checked NOAA solar flare catalog that immediately facilitates solar flare pred...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-0548-x
更新日期:2020-07-10 00:00:00
abstract::Land Use Information is a key dataset required to enable an understanding of the changing nature of our landscapes and the associated influences on natural resources and regional communities. The Victorian Land Use Information System (VLUIS) data product has been created within the State Government of Victoria to supp...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2015.70
更新日期:2015-11-24 00:00:00
abstract::With electric heat pumps substituting for fossil-fueled alternatives, the temporal variability of their power consumption becomes increasingly important to the electricity system. To easily include this variability in energy system analyses, this paper introduces the "When2Heat" dataset comprising synthetic national t...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0199-y
更新日期:2019-10-01 00:00:00
abstract::While tick-borne zoonoses, such as Lyme disease and tick-borne encephalitis, present an increasing global concern, knowledge of their vectors' distribution remains limited, especially for China. In this paper, we present the first comprehensive dataset of known tick species and their distributions in China, derived fr...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0115-5
更新日期:2019-07-01 00:00:00
abstract::Ticks carry pathogens that can cause disease in both animals and humans, and there is a need to monitor the distribution and abundance of ticks and the pathogens they carry to pinpoint potential high risk areas for tick-borne disease transmission. In a joint Scandinavian study, we measured Ixodes ricinus instar abunda...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-00579-y
更新日期:2020-07-16 00:00:00
abstract::We present the Tesco Grocery 1.0 dataset: a record of 420 M food items purchased by 1.6 M fidelity card owners who shopped at the 411 Tesco stores in Greater London over the course of the entire year of 2015, aggregated at the level of census areas to preserve anonymity. For each area, we report the number of transact...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-0397-7
更新日期:2020-02-18 00:00:00
abstract::The big-headed turtle, Platysternon megacephalum, as the sole member of the monotypic family Platysternidae, has a number of distinct characteristics including an extra-large head, long tail, flat carapace, and a preference for low water temperature environments. We performed whole genome sequencing, assembly, and gen...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0067-9
更新日期:2019-05-16 00:00:00
abstract::The experimental dataset presented was collected in an 18 m long and 1 m wide laboratory flume. Low to high flood flows through an urbanized floodplain were modelled. The floodplain bed is rough, modelled with dense artificial grass. A square cylinder array, representing house models, was set on the rough bed. The cyl...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-00791-w
更新日期:2021-01-11 00:00:00
abstract::While the GRACE (Gravity Recovery and Climate Experiment) satellite mission is of great significance in understanding various branches of Earth sciences, the quality of GRACE monthly products can be unsatisfactory due to strong longitudinal stripe-pattern errors and other flaws. Based on corrected GRACE Mascon (mass c...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0239-7
更新日期:2019-10-23 00:00:00
abstract::The silkmoth chorion was studied extensively by F.C. Kafatos' group for almost 40 years. However, the complete structure of the chorion locus was not obtained in the genome sequence of Bombyx mori published in 2008 due to repetitive sequences, resulting in gaps and an incomplete view of the locus. To obtain the comple...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2015.62
更新日期:2015-11-10 00:00:00
abstract::The nuclear receptor estrogen receptor 2 (ESR2, ERβ) modulates cancer cell proliferation and tumor growth, exerting an oncosuppressive role in breast cancer (BC). Interaction proteomics by tandem affinity purification coupled to mass spectrometry was previously applied in BC cells to identify proteins acting in concer...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2018.31
更新日期:2018-03-06 00:00:00
abstract::Today's scientific data are primarily stored and accessed via centralized Web-based infrastructure. Centralization has advantages but also carries risks such as link rot and content drift, which can hinder scientific progress. It is time to ask whether traditional, centralized Web architecture aligns with scholarly pr...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2018.221
更新日期:2018-10-23 00:00:00
abstract::We introduce the Precipitation Probability DISTribution (PPDIST) dataset, a collection of global high-resolution (0.1°) observation-based climatologies (1979-2018) of the occurrence and peak intensity of precipitation (P) at daily and 3-hourly time-scales. The climatologies were produced using neural networks trained ...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-00631-x
更新日期:2020-09-11 00:00:00
abstract::There is still limited information on the diversity of viruses co-circulating in humans and animals. Here, we report data obtained from a large field collection of enteric samples taken from humans, pigs, rodents and other mammal hosts in Vietnam between 2012 and 2016. Each of 2100 stool or rectal swab samples was sub...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0215-2
更新日期:2019-10-15 00:00:00
abstract::The detection, identification, and localization of illicit nuclear materials in urban environments is of utmost importance for national security. Most often, the process of performing these operations consists of a team of trained individuals equipped with radiation detection devices that have built-in algorithms to a...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-00672-2
更新日期:2020-10-05 00:00:00
abstract::Phase contrast time-lapse microscopy is a non-destructive technique that generates large volumes of image-based information to quantify the behaviour of individual cells or cell populations. To guide the development of algorithms for computer-aided cell tracking and analysis, 48 time-lapse image sequences, each spanni...
journal_title:Scientific data
pub_type:
doi:10.1038/sdata.2018.237
更新日期:2018-11-13 00:00:00
abstract::Brittle faults and fault zones are important fluid flow conduits through the upper part of Earth's crust that are involved in many well-known phenomena (e.g. earthquakes, thermal water and gas transport, or water leakage to underground tunnels). The permeability property, or the ability of porous materials to conduct ...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-0435-5
更新日期:2020-03-19 00:00:00
abstract::Sepsis is a syndrome with physiologic, pathologic, and biochemical abnormalities induced by infection. Sepsis can induce the dysregulation of systemic coagulation and fibrinolytic systems, resulting in disseminated intravascular coagulation (DIC), which is associated with a high mortality rate. Although there is no in...
journal_title:Scientific data
pub_type:
doi:10.1038/sdata.2018.243
更新日期:2018-12-11 00:00:00
abstract::The immune response to major trauma has been analysed mainly within post-hospital admission settings where the inflammatory response is already underway and the early drivers of clinical outcome cannot be readily determined. Thus, there is a need to better understand the immediate immune response to injury and how thi...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0337-6
更新日期:2019-12-19 00:00:00
abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title:Scientific data
pub_type: 杂志文章,已发布勘误
doi:10.1038/s41597-019-0348-3
更新日期:2020-01-06 00:00:00
abstract::East Africa is a drought prone, food and water insecure region with a highly variable climate. This complexity makes rainfall estimation challenging, and this challenge is compounded by low rain gauge densities and inhomogeneous monitoring networks. The dearth of observations is particularly problematic over the past ...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/sdata.2015.50
更新日期:2015-09-29 00:00:00
abstract::Structural studies of challenging targets such as G protein-coupled receptors (GPCRs) have accelerated during the last several years due to the development of new approaches, including small-wedge and serial crystallography. Here, we describe the deposition of seven datasets consisting of X-ray diffraction images acqu...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-020-00729-2
更新日期:2020-11-12 00:00:00
abstract::Chest radiography is an extremely powerful imaging modality, allowing for a detailed inspection of a patient's chest, but requires specialized training for proper interpretation. With the advent of high performance general purpose computer vision algorithms, the accurate automated analysis of chest radiographs is beco...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0322-0
更新日期:2019-12-12 00:00:00
abstract::The insights that historical evidence of human presence and man-made documents provide are unique. For example, using historical data may be critical to adequately understand the ecological requirements of species. However, historical information about freshwater species distribution remains largely a knowledge gap. I...
journal_title:Scientific data
pub_type: 历史文章,杂志文章
doi:10.1038/sdata.2018.163
更新日期:2018-08-14 00:00:00
abstract::The data record contains Material Intensity data for buildings (MI). MI coefficients are often used for different types of analysis of socio-economic systems and in particular for environmental assessments. Until now, MI values were compiled and reported ad-hoc with few cross-study comparisons. We extracted and conver...
journal_title:Scientific data
pub_type: 杂志文章
doi:10.1038/s41597-019-0021-x
更新日期:2019-04-09 00:00:00