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Scientific data 122건

  1. [해외논문]   Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice  

    Tang, Xing (Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine , Columbus, Ohio 43210, USA ) , Liu, Huayang (Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine , Columbus, Ohio 43210, USA ) , Srivastava, Arunima (Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine , Columbus, Ohio 43210, USA ) , Pé (Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine , Columbus, Ohio 43210, USA ) , cot, Thierry (Department of Molecular and Cellular Biochemistry , Columbus, Ohio 43210, USA ) , Chen, Zhong (Department of Molecular and Cellular Biochemistry , Columbus, Ohio 43210, USA ) , Wang, Qianben (Department of Biomedical Informatics, The Ohio State University , Columbus, Ohio 43210, USA ) , Huang, Kun (Department of Biological Sciences, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, USA ) , Sá , enz-Robles, Maria Teresa , Cantalupo, Paul , Pipas, James , Leone, Gustavo
    Scientific data v.3 ,pp. 160008 , 2016 ,

    초록

    E2F3 and MYC are transcription factors that control cellular proliferation. To study their mechanism of action in the context of a regenerating tissue, we isolated both proliferating (crypts) and non-dividing (villi) cells from wild-type and Rb depleted small intestines of mice and performed ChIP-exo-seq (chromatin immunoprecipitation combined with lambda exonuclease digestion followed by high-throughput sequencing). The genome-wide chromatin occupancy of E2F3 and MYC was determined by mapping sequence reads to the genome and predicting preferred binding sites (peaks). Binding sites could be accurately identified within small regions of only 24 bp-28 bp long, highlighting the precision to which binding peaks can be identified by ChIP-exo-seq. Forty randomly selected E2F3- and MYC-specific binding sites were validated by ChIP-PCR. In addition, we also presented gene expression data sets from wild type, Rb-, E2f3- and Myc -depleted crypts and villi within this manuscript. These represent comprehensive and validated datasets that can be integrated to identify putative direct targets of E2F3 and MYC involved in the control of cellular proliferation in normal and Rb -deficient small intestines.

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  2. [해외논문]   First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids  

    Ropo, Matti (Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany ) , Schneider, Markus (Department of Physics, Tampere University of Technology, 33720 Tampere, Finland ) , Baldauf, Carsten (COMP, Department of Applied Physics, Aalto University, 00076 Aalto, Finland ) , Blum, Volker (Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany )
    Scientific data v.3 ,pp. 160009 , 2016 ,

    초록

    We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca 2+ , Ba 2+ , Sr 2+ , Cd 2+ , Pb 2+ , and Hg 2+ ). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.

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  3. [해외논문]   An open access pilot freely sharing cancer genomic data from participants in Texas  

    Becnel, Lauren B. (Dan L. Duncan Cancer Center, Baylor College of Medicine , Houston, Texas 77030, USA ) , Pereira, Stacey (Center for Medical Ethics and Health Policy, Baylor College of Medicine , Houston, Texas 77030, USA ) , Drummond, Jennifer A. (Human Genome Sequencing Center, Baylor College of Medicine , Houston, Texas 77030, USA ) , Gingras, Marie-Claude (Human Genome Sequencing Center, Baylor College of Medicine , Houston, Texas 77030, USA ) , Covington, Kyle R. (Human Genome Sequencing Center, Baylor College of Medicine , Houston, Texas 77030, USA ) , Kovar, Christie L. (Human Genome Sequencing Center, Baylor College of Medicine , Houston, Texas 77030, USA ) , Doddapaneni, Harsha Vardhan (Human Genome Sequencing Center, Baylor College of Medicine , Houston, Texas 77030, USA ) , Hu, Jianhong (Human Genome Sequencing Center, Baylor College of Medicine , Houston, Texas 77030, USA ) , Muzny, Donna (Human Genome Sequencing Center, Baylor College of Medicine , Houston, Texas 77030, USA) , McGuire, Amy L. , Wheeler, David A. , Gibbs, Richard A.
    Scientific data v.3 ,pp. 160010 , 2016 ,

    초록

    Genomic data sharing in cancer has been restricted to aggregate or controlled-access initiatives to protect the privacy of research participants. By limiting access to these data, it has been argued that the autonomy of individuals who decide to participate in data sharing efforts has been superseded and the utility of the data as research and educational tools reduced. In a pilot Open Access (OA) project from the CPRIT-funded Texas Cancer Research Biobank, many Texas cancer patients were willing to openly share genomic data from tumor and normal matched pair specimens. For the first time, genetic data from 7 human cancer cases with matched normal are freely available without requirement for data use agreements nor any major restriction except that end users cannot attempt to re-identify the participants (http://txcrb.org/open.html).

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    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  4. [해외논문]   The mPower study, Parkinson disease mobile data collected using ResearchKit  

    Bot, Brian M. (Sage Bionetworks , Seattle, Washington 98109, USA ) , Suver, Christine (Sage Bionetworks , Seattle, Washington 98109, USA ) , Neto, Elias Chaibub (Sage Bionetworks , Seattle, Washington 98109, USA ) , Kellen, Michael (Sage Bionetworks , Seattle, Washington 98109, USA ) , Klein, Arno (Sage Bionetworks , Seattle, Washington 98109, USA ) , Bare, Christopher (Sage Bionetworks , Seattle, Washington 98109, USA ) , Doerr, Megan (Sage Bionetworks , Seattle, Washington 98109, USA ) , Pratap, Abhishek (Sage Bionetworks , Seattle, Washington 98109, USA ) , Wilbanks, John (Sage Bionetworks , Seattle, Washington 98109, USA ) , Dorsey, E. Ray (Center for Human Experimental Therapeutics, University of Rochester Medical Center , Rochester, New York 14642, USA ) , Friend, Stephen H. (Sage Bionetworks , Seattle, Washington 98109, USA ) , Trister, Andrew D. (Sage Bionetworks , Seattle, Washington 98109, USA )
    Scientific data v.3 ,pp. 160011 , 2016 ,

    초록

    Current measures of health and disease are often insensitive, episodic, and subjective. Further, these measures generally are not designed to provide meaningful feedback to individuals. The impact of high-resolution activity data collected from mobile phones is only beginning to be explored. Here we present data from mPower, a clinical observational study about Parkinson disease conducted purely through an iPhone app interface. The study interrogated aspects of this movement disorder through surveys and frequent sensor-based recordings from participants with and without Parkinson disease. Benefitting from large enrollment and repeated measurements on many individuals, these data may help establish baseline variability of real-world activity measurement collected via mobile phones, and ultimately may lead to quantification of the ebbs-and-flows of Parkinson symptoms. App source code for these data collection modules are available through an open source license for use in studies of other conditions. We hope that releasing data contributed by engaged research participants will seed a new community of analysts working collaboratively on understanding mobile health data to advance human health.

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  5. [해외논문]   A polymer dataset for accelerated property prediction and design  

    Huan, Tran Doan (Institute of Materials Science, University of Connecticut , 97 North Eagleville Rd., Unit 3136, Storrs, Connecticut 06269, USA ) , Mannodi-Kanakkithodi, Arun (Institute of Materials Science, University of Connecticut , 97 North Eagleville Rd., Unit 3136, Storrs, Connecticut 06269, USA ) , Kim, Chiho (Institute of Materials Science, University of Connecticut , 97 North Eagleville Rd., Unit 3136, Storrs, Connecticut 06269, USA ) , Sharma, Vinit (Institute of Materials Science, University of Connecticut , 97 North Eagleville Rd., Unit 3136, Storrs, Connecticut 06269, USA ) , Pilania, Ghanshyam (Materials Science and Technology Division, Los Alamos National Laboratory , Los Alamos, 87545, New Mexico USA ) , Ramprasad, Rampi (Institute of Materials Science, University of Connecticut , 97 North Eagleville Rd., Unit 3136, Storrs, Connecticut 06269, USA )
    Scientific data v.3 ,pp. 160012 , 2016 ,

    초록

    Emerging computation- and data-driven approaches are particularly useful for rationally designing materials with targeted properties. Generally, these approaches rely on identifying structure-property relationships by learning from a dataset of sufficiently large number of relevant materials. The learned information can then be used to predict the properties of materials not already in the dataset, thus accelerating the materials design. Herein, we develop a dataset of 1,073 polymers and related materials and make it available at http://khazana.uconn.edu/. This dataset is uniformly prepared using first-principles calculations with structures obtained either from other sources or by using structure search methods. Because the immediate target of this work is to assist the design of high dielectric constant polymers, it is initially designed to include the optimized structures, atomization energies, band gaps, and dielectric constants. It will be progressively expanded by accumulating new materials and including additional properties calculated for the optimized structures provided.

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  6. [해외논문]   Blended sea level anomaly fields with enhanced coastal coverage along the U.S. West Coast  

    Risien, C.M. (College of Earth, Ocean and Atmospheric Sciences, Oregon State University , 104 CEOAS Administration Building, Corvallis, Oregon 97331-5503, USA ) , Strub, P.T. (College of Earth, Ocean and Atmospheric Sciences, Oregon State University , 104 CEOAS Administration Building, Corvallis, Oregon 97331-5503, USA )
    Scientific data v.3 ,pp. 160013 , 2016 ,

    초록

    We form a new 'blended' data set of sea level anomaly (SLA) fields by combining gridded daily fields derived from altimeter data with coastal tide gauge data. Within approximately 55–70 km of the coast, the altimeter data are discarded and replaced by a linear interpolation between the tide gauge and remaining offshore altimeter data. To create a common reference height for altimeter and tide gauge data, a 20-year mean is subtracted from each time series (from each tide gauge and altimeter grid point) before combining the data sets to form a blended mean sea level anomaly (SLA) data set. Daily mean fields are produced for the 22-year period 1 January 1993–31 December 2014. The primary validation compares geostrophic velocities calculated from the height fields and velocities measured at four moorings covering the north-south range of the new data set. The blended data set improves the alongshore (meridional) component of the currents, indicating an improvement in the cross-shelf gradient of the mean SLA data set.

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  7. [해외논문]   A global bionomic database for the dominant vectors of human malaria  

    Massey, N. Claire (Spatial Ecology & Epidemiology Group, Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, UK ) , Garrod, Gala (Spatial Ecology & Epidemiology Group, Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, UK ) , Wiebe, Antoinette (Spatial Ecology & Epidemiology Group, Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, UK ) , Henry, Andrew J. (Spatial Ecology & Epidemiology Group, Department of Zoology, University of Oxford , Oxford, OX1 3PS, UK ) , Huang, Zhi (Spatial Ecology & Epidemiology Group, Department of Zoology, University of Oxford , Oxford, OX1 3PS, UK ) , Moyes, Catherine L. (Spatial Ecology & Epidemiology Group, Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, UK ) , Sinka, Marianne E. (Spatial Ecology & Epidemiology Group, Wellcome Trust Centre for Human Genetics, University of Oxford , Oxford, OX3 7BN, UK )
    Scientific data v.3 ,pp. 160014 , 2016 ,

    초록

    Anopheles mosquitoes were first recognised as the transmitters of human malaria in the late 19th Century and have been subject to a huge amount of research ever since. Yet there is still much that is unknown regarding the ecology, behaviour (collectively 'bionomics') and sometimes even the identity of many of the world's most prominent disease vectors, much less the within-species variation in their bionomics. Whilst malaria elimination remains an ambitious goal, it is becoming increasingly clear that knowledge of vector behaviour is needed to effectively target control measures. A database of bionomics data for the dominant vector species of malaria worldwide has been compiled from published peer-reviewed literature. The data identification and collation processes are described, together with the geo-positioning and quality control methods. This is the only such dataset in existence and provides a valuable resource to researchers and policy makers in this field.

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  8. [해외논문]   A large dataset of protein dynamics in the mammalian heart proteome  

    Lau, Edward (The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles , California 90095, USA ) , Cao, Quan (The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles , California 90095, USA ) , Ng, Dominic C.M. (The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles , California 90095, USA ) , Bleakley, Brian J. (The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles , California 90095, USA ) , Dincer, T. Umut (The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles , California 90095, USA ) , Bot, Brian M. (The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles , California 90095, USA ) , Wang, Ding (The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing) , Liem, David A. , Lam, Maggie P.Y. , Ge, Junbo , Ping, Peipei
    Scientific data v.3 ,pp. 160015 , 2016 ,

    초록

    Protein stability is a major regulatory principle of protein function and cellular homeostasis. Despite limited understanding on mechanisms, disruption of protein turnover is widely implicated in diverse pathologies from heart failure to neurodegenerations. Information on global protein dynamics therefore has the potential to expand the depth and scope of disease phenotyping and therapeutic strategies. Using an integrated platform of metabolic labeling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the in vivo half-life of 3,228 and the expression of 8,064 cardiac proteins, quantified under healthy and hypertrophic conditions across six mouse genetic strains commonly employed in biomedical research. We anticipate these data will aid in understanding key mitochondrial and metabolic pathways in heart diseases, and further serve as a reference for methodology development in dynamics studies in multiple organ systems.

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  9. [해외논문]   A test-retest dataset for assessing long-term reliability of brain morphology and resting-state brain activity  

    Huang, Lijie (State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University , Beijing 100875, China ) , Huang, Taicheng (State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University , Beijing 100875, China ) , Zhen, Zonglei (State Key Laboratory of Cognitive Neuroscience and Learning & IDG/McGovern Institute for Brain Research, Beijing Normal University , Beijing 100875, China ) , Liu, Jia (Beijing Key Laboratory of Applied Experimental Psychology, School of Psychology, Beijing Normal University , Beijing 100875, China )
    Scientific data v.3 ,pp. 160016 , 2016 ,

    초록

    We present a test-retest dataset for evaluation of long-term reliability of measures from structural and resting-state functional magnetic resonance imaging (sMRI and rfMRI) scans. The repeated scan dataset was collected from 61 healthy adults in two sessions using highly similar imaging parameters at an interval of 103–189 days. However, as the imaging parameters were not completely identical, the reliability estimated from this dataset shall reflect the lower bounds of the true reliability of sMRI/rfMRI measures. Furthermore, in conjunction with other test-retest datasets, our dataset may help explore the impact of different imaging parameters on reliability of sMRI/rfMRI measures, which is especially critical for assessing datasets collected from multiple centers. In addition, intelligence quotient (IQ) was measured for each participant using Raven's Advanced Progressive Matrices. The data can thus be used for purposes other than assessing reliability of sMRI/rfMRI alone. For example, data from each single session could be used to associate structural and functional measures of the brain with the IQ metrics to explore brain-IQ association.

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  10. [해외논문]   The Coral Trait Database, a curated database of trait information for coral species from the global oceans  

    Madin, Joshua S. (Department of Biological Sciences, Macquarie University , New South Wales 2109, Australia ) , Anderson, Kristen D. (Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4811, Australia ) , Andreasen, Magnus Heide (Center for Macroecology, Evolution & Climate, Natural History Museum of Denmark, University of Copenhagen , Copenhagen DK-2100, Denmark ) , Bridge, Tom C.L. (Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4811, Australia ) , Cairns, Stephen D. (Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian , Washington, District Of Columbia 20013, USA ) , Connolly, Sean R. (Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University , Townsville 4811, Australia ) , Darling, Emily S. (Marine Program, Wildlife Conservation Society , Bronx, New York 10460, USA ) , Diaz, Marcela , Falster, Daniel S. , Franklin, Erik C. , Gates, Ruth D. , Hoogenboom, Mia O. , Huang, Danwei , Keith, Sally A. , Kosnik, Matthew A. , Kuo, Chao-Yang , Lough, Janice M. , Lovelock, Catherine E. , Luiz, Osmar , Martinelli, Julieta , Mizerek, Toni , Pandolfi, John M. , Pochon, Xavier , Pratchett, Morgan S. , Putnam, Hollie M. , Roberts, T. Edward , Stat, Michael , Wallace, Carden C. , Widman, Elizabeth , Baird, Andrew H.
    Scientific data v.3 ,pp. 160017 , 2016 ,

    초록

    Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism's function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.

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