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  1. Article ; Online: The Coastal Carbon Library and Atlas: Open source soil data and tools supporting blue carbon research and policy.

    Holmquist, James R / Klinges, David / Lonneman, Michael / Wolfe, Jaxine / Boyd, Brandon / Eagle, Meagan / Sanderman, Jonathan / Todd-Brown, Kathe / Belshe, E Fay / Brown, Lauren N / Chapman, Samantha / Corstanje, Ron / Janousek, Christopher / Morris, James T / Noe, Gregory / Rovai, André / Spivak, Amanda / Vahsen, Megan / Windham-Myers, Lisamarie /
    Kroeger, Kevin / Megonigal, J Patrick

    Global change biology

    2024  Volume 30, Issue 1, Page(s) e17098

    Abstract: Quantifying carbon fluxes into and out of coastal soils is critical to meeting greenhouse gas reduction and coastal resiliency goals. Numerous 'blue carbon' studies have generated, or benefitted from, synthetic datasets. However, the community those ... ...

    Abstract Quantifying carbon fluxes into and out of coastal soils is critical to meeting greenhouse gas reduction and coastal resiliency goals. Numerous 'blue carbon' studies have generated, or benefitted from, synthetic datasets. However, the community those efforts inspired does not have a centralized, standardized database of disaggregated data used to estimate carbon stocks and fluxes. In this paper, we describe a data structure designed to standardize data reporting, maximize reuse, and maintain a chain of credit from synthesis to original source. We introduce version 1.0.0. of the Coastal Carbon Library, a global database of 6723 soil profiles representing blue carbon-storing systems including marshes, mangroves, tidal freshwater forests, and seagrasses. We also present the Coastal Carbon Atlas, an R-shiny application that can be used to visualize, query, and download portions of the Coastal Carbon Library. The majority (4815) of entries in the database can be used for carbon stock assessments without the need for interpolating missing soil variables, 533 are available for estimating carbon burial rate, and 326 are useful for fitting dynamic soil formation models. Organic matter density significantly varied by habitat with tidal freshwater forests having the highest density, and seagrasses having the lowest. Future work could involve expansion of the synthesis to include more deep stock assessments, increasing the representation of data outside of the U.S., and increasing the amount of data available for mangroves and seagrasses, especially carbon burial rate data. We present proposed best practices for blue carbon data including an emphasis on disaggregation, data publication, dataset documentation, and use of standardized vocabulary and templates whenever appropriate. To conclude, the Coastal Carbon Library and Atlas serve as a general example of a grassroots F.A.I.R. (Findable, Accessible, Interoperable, and Reusable) data effort demonstrating how data producers can coordinate to develop tools relevant to policy and decision-making.
    MeSH term(s) Carbon/chemistry ; Soil/chemistry ; Ecosystem ; Wetlands ; Policy
    Chemical Substances Carbon (7440-44-0) ; Soil
    Language English
    Publishing date 2024-01-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 1281439-8
    ISSN 1365-2486 ; 1354-1013
    ISSN (online) 1365-2486
    ISSN 1354-1013
    DOI 10.1111/gcb.17098
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: PLINK: a tool set for whole-genome association and population-based linkage analyses.

    Purcell, Shaun / Neale, Benjamin / Todd-Brown, Kathe / Thomas, Lori / Ferreira, Manuel A R / Bender, David / Maller, Julian / Sklar, Pamela / de Bakker, Paul I W / Daly, Mark J / Sham, Pak C

    American journal of human genetics

    2007  Volume 81, Issue 3, Page(s) 559–575

    Abstract: Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit ... ...

    Abstract Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.
    MeSH term(s) Genetic Linkage/genetics ; Genome, Human/genetics ; Humans ; Polymorphism, Single Nucleotide ; Population/genetics ; Software
    Language English
    Publishing date 2007-07-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 219384-x
    ISSN 1537-6605 ; 0002-9297
    ISSN (online) 1537-6605
    ISSN 0002-9297
    DOI 10.1086/519795
    Database MEDical Literature Analysis and Retrieval System OnLINE

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