The Experts below are selected from a list of 5325 Experts worldwide ranked by ideXlab platform
H. Hermjakob - One of the best experts on this subject based on the ideXlab platform.
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The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple Source Databases
BMC Bioinformatics, 2007Co-Authors: Richard G. Côté, S. Kerrien, Philip Jones, Lennart Martens, Florian Reisinger, Rasko Leinonen, Rolf Apweiler, H. HermjakobAbstract:Background Each major protein Database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data Sources or querying data providers with one flavour of protein identifiers when the Source Database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of Databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs.
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IntAct: an open Source molecular interaction Database
Nucleic Acids Research, 2004Co-Authors: H. HermjakobAbstract:IntAct provides an open Source Database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains approximately 2200 binary and complex interactions imported from the literature and curated in collaboration with the Swiss-Prot team, making intensive use of controlled vocabularies to ensure data consistency. All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.
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intact an open Source molecular interaction Database
Nucleic Acids Research, 2004Co-Authors: H. Hermjakob, S. Kerrien, Luisa Montecchipalazzi, Chris Lewington, Sugath Mudali, Sandra Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso ValenciaAbstract:IntAct provides an open Source Database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains ∼2200 binary and complex interactions imported from the literature and curated in collaboration with the Swiss-Prot team, making intensive use of controlled vocabularies to ensure data consistency. All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.
Shamil Maksyutov - One of the best experts on this subject based on the ideXlab platform.
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a very high resolution 1 km 1 km global fossil fuel co 2 emission inventory derived using a point Source Database and satellite observations of nighttime lights
Atmospheric Chemistry and Physics, 2011Co-Authors: Shamil MaksyutovAbstract:Abstract. Emissions of CO 2 from fossil fuel combustion are a critical quantity that must be accurately given in established flux inversion frameworks. Work with emerging satellite-based inversions requires spatiotemporally-detailed inventories that permit analysis of regional natural Sources and sinks. Conventional approaches for disaggregating national emissions beyond the country and city levels based on population distribution have certain difficulties in their application. We developed a global 1 km×1 km annual fossil fuel CO 2 emission inventory for the years 1980–2007 by combining a worldwide point Source Database and satellite observations of the global nightlight distribution. In addition to estimating the national emissions using global energy consumption statistics, emissions from point Sources were estimated separately and were spatially allocated to exact locations indicated by the point Source Database. Emissions from other Sources were distributed using a special nightlight dataset that had fewer saturated pixels compared with regular nightlight datasets. The resulting spatial distributions differed in several ways from those derived using conventional population-based approaches. Because of the inherent characteristics of the nightlight distribution, Source regions corresponding to human settlements and land transportation were well articulated. Our distributions showed good agreement with a high-resolution inventory across the US at spatial resolutions that were adequate for regional flux inversions. The inventory can be extended to the future using updated data, and is expected to be incorporated into models for operational flux inversions that use observational data from the Japanese Greenhouse Gases Observing SATellite (GOSAT).
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A very high-resolution global fossil fuel CO2 emission inventory derived using a point Source Database and satellite observations of nighttime lights, 1980–2007
Atmospheric Chemistry and Physics, 2010Co-Authors: Shamil MaksyutovAbstract:Abstract. Emissions of CO2 from fossil fuel combustion are a critical quantity that must be accurately given in established flux inversion frameworks. Work with emerging satellite-based inversions requires spatiotemporally-detailed inventories that permit analysis of regional Sources and sinks. Conventional approaches for disaggregating national emissions beyond the country and city levels based on population distribution have certain difficulties in their application. We developed a global 1 km×1 km fossil fuel CO2 emission inventory for the years 1980–2007 by combining a worldwide point Source Database and satellite observations of the global nightlight distribution. In addition to estimating the national emissions using global energy consumption statistics, emissions from point Sources were estimated separately and were spatially allocated to exact locations indicated by the point Source Database. Emissions from other Sources were distributed using a special nightlight dataset that had fewer saturated pixels compared with regular nightlight datasets. The resulting spatial distributions differed in several ways from those derived using conventional population-based approaches. Because of the inherent characteristics of the nightlight distribution, Source regions corresponding to human settlements and land transportation were well articulated. Our distributions showed good agreement with a high-resolution inventory across the US at spatial resolutions that were adequate for regional flux inversions. The inventory will be incorporated into models for operational flux inversions that use observational data from the Japanese Greenhouse Gases Observing SATellite (GOSAT).
S. Kerrien - One of the best experts on this subject based on the ideXlab platform.
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The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple Source Databases
BMC Bioinformatics, 2007Co-Authors: Richard G. Côté, S. Kerrien, Philip Jones, Lennart Martens, Florian Reisinger, Rasko Leinonen, Rolf Apweiler, H. HermjakobAbstract:Background Each major protein Database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data Sources or querying data providers with one flavour of protein identifiers when the Source Database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of Databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs.
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IntAct - Open Source reSource for molecular interaction data
Nucleic Acids Research, 2007Co-Authors: S. Kerrien, Y. Alam-faruque, B. Aranda, I. Bancarz, C. Derow, E. Dimmer, M. Feuermann, A. Friedrichsen, Alan Bridge, Rajesh HuntleyAbstract:IntAct is an open Source Database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the Database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The Database features over 126,000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct Source code and data are freely available from http://www.ebi.ac.uk/intact.
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intact an open Source molecular interaction Database
Nucleic Acids Research, 2004Co-Authors: H. Hermjakob, S. Kerrien, Luisa Montecchipalazzi, Chris Lewington, Sugath Mudali, Sandra Orchard, Martin Vingron, Bernd Roechert, Peter Roepstorff, Alfonso ValenciaAbstract:IntAct provides an open Source Database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of protein interactions, and allows exploring interaction networks in the context of the GO annotations of the interacting proteins. A web service allows direct computational access to retrieve interaction networks in XML format. IntAct currently contains ∼2200 binary and complex interactions imported from the literature and curated in collaboration with the Swiss-Prot team, making intensive use of controlled vocabularies to ensure data consistency. All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.
Carlos A Sierra - One of the best experts on this subject based on the ideXlab platform.
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an open Source Database for the synthesis of soil radiocarbon data international soil radiocarbon Database israd version 1 0
Earth System Science Data, 2020Co-Authors: Corey R Lawrence, Jeffery Beemmiller, Alison M Hoyt, Grey Monroe, Carlos A Sierra, Shane Stoner, Katherine Heckman, Joseph C Blankinship, Susan E Crow, Gavin McnicolAbstract:Abstract. Radiocarbon is a critical constraint on our estimates of the timescales of soil carbon cycling that can aid in identifying mechanisms of carbon stabilization and destabilization and improve the forecast of soil carbon response to management or environmental change. Despite the wealth of soil radiocarbon data that have been reported over the past 75 years, the ability to apply these data to global-scale questions is limited by our capacity to synthesize and compare measurements generated using a variety of methods. Here, we present the International Soil Radiocarbon Database (ISRaD; http://soilradiocarbon.org , last access: 16 December 2019), an open-Source archive of soil data that include reported measurements from bulk soils, distinct soil carbon pools isolated in the laboratory by a variety of soil fractionation methods, samples of soil gas or water collected interstitially from within an intact soil profile, CO2 gas isolated from laboratory soil incubations, and fluxes collected in situ from a soil profile. The core of ISRaD is a relational Database structured around individual datasets (entries) and organized hierarchically to report soil radiocarbon data, measured at different physical and temporal scales as well as other soil or environmental properties that may also be measured and may assist with interpretation and context. Anyone may contribute their own data to the Database by entering it into the ISRaD template and subjecting it to quality assurance protocols. ISRaD can be accessed through (1) a web-based interface, (2) an R package (ISRaD), or (3) direct access to code and data through the GitHub repository, which hosts both code and data. The design of ISRaD allows for participants to become directly involved in the management, design, and application of ISRaD data. The synthesized dataset is available in two forms: the original data as reported by the authors of the datasets and an enhanced dataset that includes ancillary geospatial data calculated within the ISRaD framework. ISRaD also provides data management tools in the ISRaD-R package that provide a starting point for data analysis; as an open-Source project, the broader soil community is invited and encouraged to add data, tools, and ideas for improvement. As a whole, ISRaD provides reSources to aid our evaluation of soil dynamics across a range of spatial and temporal scales. The ISRaD v1.0 dataset is archived and freely available at https://doi.org/10.5281/zenodo.2613911 (Lawrence et al., 2019).
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an open Source Database for the synthesis of soil radiocarbon data israd version 1 0
Earth System Science Data Discussions, 2019Co-Authors: Corey R Lawrence, Jeffery Beemmiller, Alison M Hoyt, Grey Monroe, Carlos A SierraAbstract:Abstract. Radiocarbon is a critical constraint on our estimates of the timescales of soil carbon cycling that can aid in identifying mechanisms of carbon stabilization and destabilization, and improve forecast of soil carbon response to management or environmental change. Despite the wealth of soil radiocarbon data that has been reported over the past 75 years, the ability to apply these data to global scale questions is limited by our capacity to synthesis and compare measurements generated using a variety of methods. Here we describe the International Soil Radiocarbon Database (ISRaD, soilradiocarbon.org ), an open-Source archive of soils data that include data from bulk soils, or whole-soils ; distinct soil carbon pools isolated in the laboratory by a variety of soil fractionation methods; samples of soil gas or water collected interstitially from within an intact soil profile; CO2 gas isolated from laboratory soil incubations; and fluxes collected in situ from a soil surface. The core of ISRaD is a relational Database structured around individual datasets (entries) and organized hierarchically to report soil radiocarbon data, measured at different physical and temporal scales, as well as other soil or environmental properties that may also be measured at one or more levels of the hierarchy that may assist with interpretation and context. Anyone may contribute their own data to the Database by entering it into the ISRaD template and subjecting it to quality assurance protocols. ISRaD can be accessed through: (1) a web-based interface, (2) an R package (ISRaD), or (3) direct access to code and data through the GitHub repository, which hosts both code and data. The design of ISRaD allows for participants to become directly involved in the management, design, and application of ISRaD data. The synthesized dataset is available in two forms: the original data as reported by the authors of the datasets; and an enhanced dataset that includes ancillary geospatial data calculated within the ISRaD framework. ISRaD also provides data management tools in the ISRaD-R package that provide a starting point for data analysis. This community-based dataset and platform for soil radiocarbon and a wide array of additional soils data information in soils where data are easy to contribute and the community is invited to add tools and ideas for improvement. As a whole, ISRaD provides reSources that can aid our evaluation of soil dynamics and improve our understanding of controls on soil carbon dynamics across a range of spatial and temporal scales. The ISRaD v1.0 dataset (Lawrence et al., 2019) is archived and freely available at https://doi.org/10.5281/zenodo.2613911 .
Gavin Mcnicol - One of the best experts on this subject based on the ideXlab platform.
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an open Source Database for the synthesis of soil radiocarbon data international soil radiocarbon Database israd version 1 0
Earth System Science Data, 2020Co-Authors: Corey R Lawrence, Jeffery Beemmiller, Alison M Hoyt, Grey Monroe, Carlos A Sierra, Shane Stoner, Katherine Heckman, Joseph C Blankinship, Susan E Crow, Gavin McnicolAbstract:Abstract. Radiocarbon is a critical constraint on our estimates of the timescales of soil carbon cycling that can aid in identifying mechanisms of carbon stabilization and destabilization and improve the forecast of soil carbon response to management or environmental change. Despite the wealth of soil radiocarbon data that have been reported over the past 75 years, the ability to apply these data to global-scale questions is limited by our capacity to synthesize and compare measurements generated using a variety of methods. Here, we present the International Soil Radiocarbon Database (ISRaD; http://soilradiocarbon.org , last access: 16 December 2019), an open-Source archive of soil data that include reported measurements from bulk soils, distinct soil carbon pools isolated in the laboratory by a variety of soil fractionation methods, samples of soil gas or water collected interstitially from within an intact soil profile, CO2 gas isolated from laboratory soil incubations, and fluxes collected in situ from a soil profile. The core of ISRaD is a relational Database structured around individual datasets (entries) and organized hierarchically to report soil radiocarbon data, measured at different physical and temporal scales as well as other soil or environmental properties that may also be measured and may assist with interpretation and context. Anyone may contribute their own data to the Database by entering it into the ISRaD template and subjecting it to quality assurance protocols. ISRaD can be accessed through (1) a web-based interface, (2) an R package (ISRaD), or (3) direct access to code and data through the GitHub repository, which hosts both code and data. The design of ISRaD allows for participants to become directly involved in the management, design, and application of ISRaD data. The synthesized dataset is available in two forms: the original data as reported by the authors of the datasets and an enhanced dataset that includes ancillary geospatial data calculated within the ISRaD framework. ISRaD also provides data management tools in the ISRaD-R package that provide a starting point for data analysis; as an open-Source project, the broader soil community is invited and encouraged to add data, tools, and ideas for improvement. As a whole, ISRaD provides reSources to aid our evaluation of soil dynamics across a range of spatial and temporal scales. The ISRaD v1.0 dataset is archived and freely available at https://doi.org/10.5281/zenodo.2613911 (Lawrence et al., 2019).
