The Experts below are selected from a list of 2715 Experts worldwide ranked by ideXlab platform
Michael Mcclennen - One of the best experts on this subject based on the ideXlab platform.
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the Paleobiology database application programming interface
Paleobiology, 2016Co-Authors: Shanan E Peters, Michael McclennenAbstract:The Paleobiology Database (PBDB; https://paleobiodb.org) consists of geographically and temporally explicit, taxonomically identified fossil occurrence data. The taxonomy utilized by the PBDB is not static, but is instead dynamically generated using an algorithm applied to separately managed taxonomic authority and opinion data. The PBDB owes its existence to many individuals, some of whom have entered more than 1.26 million fossil occurrences and over 570,000 taxonomic opinions, and some of whom have developed and maintained supporting infrastructure and analysis tools. Here, we provide an overview of the data model currently used by the PBDB and then briefly describe how this model is exposed via an Application Programming Interface (API). Our objective is to outline how PBDB data can now be accessed within individual scientific workflows, used to develop independently managed educational and scientific applications, and accessed to forge dynamic, near real-time connections to other data resources.
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the Paleobiology database application programming interface
Paleobiology, 2016Co-Authors: Shanan E Peters, Michael McclennenAbstract:Abstract. The Paleobiology Database (PBDB; https://paleobiodb.org) consists of geographically and temporally explicit, taxonomically identified fossil occurrence data. The taxonomy utilized by the PBDB is not static, but is instead dynamically generated using an algorithm applied to separately managed taxonomic authority and opinion data. The PBDB owes its existence to many individuals, some of whom have entered more than 1.26 million fossil occurrences and over 570,000 taxonomic opinions, and some of whom have developed and maintained supporting infrastructure and analysis tools. Here, we provide an overview of the data model currently used by the PBDB and then briefly describe how this model is exposed via an Application Programming Interface (API). Our objective is to outline how PBDB data can now be accessed within individual scientific workflows, used to develop independently managed educational and scientific applications, and accessed to forge dynamic, near real-time connections to other data resou...
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paleobiodb an r package for downloading visualizing and processing data from the Paleobiology database
Ecography, 2015Co-Authors: Sara Varela, Luciano Fabris Sgarbi, Shanan E Peters, Juan Gonzalezhernandez, Mark D. Uhen, Charles R. Marshall, Michael McclennenAbstract:The fossil record acts as a time machine, providing data on the morphology, ecology and biogeography of ancient species. Therefore, ideally, fossil data should be included in evolutionary, macroecological and biogeographical studies. However, paleontological data are often not used in biological research, in part because of the difficulty of extracting occurrence records from the primary literature. The goal of the Paleobiology Database is to make these records generally accessible, but unlike databases such as Genbank and GBIF, a ready-made interface to the R computing environment has not been available. We have developed paleobioDB, an R package designed to perform easy and flexible queries of the Paleobiology Database, including visualization, downloading and processing of selected data. This package facilitates access to paleontological data in a way that should allow further analysis using other packages and libraries available in R. The paleobioDB package should facilitate the integration of paleontological and neontological datasets, so that data from the deep past can be used to help inform our understanding of living biota, and vice versa.
Shanan E Peters - One of the best experts on this subject based on the ideXlab platform.
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the Paleobiology database application programming interface
Paleobiology, 2016Co-Authors: Shanan E Peters, Michael McclennenAbstract:The Paleobiology Database (PBDB; https://paleobiodb.org) consists of geographically and temporally explicit, taxonomically identified fossil occurrence data. The taxonomy utilized by the PBDB is not static, but is instead dynamically generated using an algorithm applied to separately managed taxonomic authority and opinion data. The PBDB owes its existence to many individuals, some of whom have entered more than 1.26 million fossil occurrences and over 570,000 taxonomic opinions, and some of whom have developed and maintained supporting infrastructure and analysis tools. Here, we provide an overview of the data model currently used by the PBDB and then briefly describe how this model is exposed via an Application Programming Interface (API). Our objective is to outline how PBDB data can now be accessed within individual scientific workflows, used to develop independently managed educational and scientific applications, and accessed to forge dynamic, near real-time connections to other data resources.
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the Paleobiology database application programming interface
Paleobiology, 2016Co-Authors: Shanan E Peters, Michael McclennenAbstract:Abstract. The Paleobiology Database (PBDB; https://paleobiodb.org) consists of geographically and temporally explicit, taxonomically identified fossil occurrence data. The taxonomy utilized by the PBDB is not static, but is instead dynamically generated using an algorithm applied to separately managed taxonomic authority and opinion data. The PBDB owes its existence to many individuals, some of whom have entered more than 1.26 million fossil occurrences and over 570,000 taxonomic opinions, and some of whom have developed and maintained supporting infrastructure and analysis tools. Here, we provide an overview of the data model currently used by the PBDB and then briefly describe how this model is exposed via an Application Programming Interface (API). Our objective is to outline how PBDB data can now be accessed within individual scientific workflows, used to develop independently managed educational and scientific applications, and accessed to forge dynamic, near real-time connections to other data resou...
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paleobiodb an r package for downloading visualizing and processing data from the Paleobiology database
Ecography, 2015Co-Authors: Sara Varela, Luciano Fabris Sgarbi, Shanan E Peters, Juan Gonzalezhernandez, Mark D. Uhen, Charles R. Marshall, Michael McclennenAbstract:The fossil record acts as a time machine, providing data on the morphology, ecology and biogeography of ancient species. Therefore, ideally, fossil data should be included in evolutionary, macroecological and biogeographical studies. However, paleontological data are often not used in biological research, in part because of the difficulty of extracting occurrence records from the primary literature. The goal of the Paleobiology Database is to make these records generally accessible, but unlike databases such as Genbank and GBIF, a ready-made interface to the R computing environment has not been available. We have developed paleobioDB, an R package designed to perform easy and flexible queries of the Paleobiology Database, including visualization, downloading and processing of selected data. This package facilitates access to paleontological data in a way that should allow further analysis using other packages and libraries available in R. The paleobioDB package should facilitate the integration of paleontological and neontological datasets, so that data from the deep past can be used to help inform our understanding of living biota, and vice versa.
Sergio Almecija - One of the best experts on this subject based on the ideXlab platform.
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pitfalls reconstructing the last common ancestor of chimpanzees and humans
Proceedings of the National Academy of Sciences of the United States of America, 2016Co-Authors: Sergio AlmecijaAbstract:The morphological nature of the last common ancestor (LCA) of chimpanzees/bonobos and humans is a fascinating topic in human evolution. Available evidence suggests that both lineages share a LCA that lived in Africa ∼8–6 Myr. However, the hominoid fossil record of this time period is inadequate, prompting the use of novel methodological approaches to reconstruct the anatomy of this key ancestor. In a recent example, Young et al. (1) claim that “fossil hominin shoulders support an African ape-like last common ancestor of humans and chimpanzees.” Although I applaud these authors for implementing novel comparative methods to paleoanthropology, fundamental aspects of the experimental design were disregarded, leading to biased conclusions. Herein I provide constructive criticisms on that study, also addressing recurrent pitfalls in the field, to help redirect future research on human Paleobiology.
Qun Yang - One of the best experts on this subject based on the ideXlab platform.
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Molecular Paleobiology - Progress and perspectives
Palaeoworld, 2014Co-Authors: Gert W??rheide, Martin Dohrmann, Qun YangAbstract:Molecular Paleobiology is a subfield of paleontology that uses molecular biological methods on extant organisms to address geoscientifically relevant questions. Progress in the field was last reviewed in 2007, and here we highlight some of the more recent developments, with a focus on ancient animal evolution, in areas such as the application of molecular clocks to estimate clade ages, the evolution of biomineralization, and the evolution of key traits. We argue that molecular Paleobiology has much to offer and will be central to paleontological research and evolutionary biology in general, but we also discuss some remaining challenges and future directions of the discipline.
Karl W. Flessa - One of the best experts on this subject based on the ideXlab platform.
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conservation Paleobiology putting the dead to work
Trends in Ecology and Evolution, 2011Co-Authors: Gregory P. Dietl, Karl W. FlessaAbstract:Geohistorical data and analyses are playing an increasingly important role in conservation biology practice and policy. In this review, we discuss examples of how the near-time and deep-time fossil record can be used to understand the ecological and evolutionary responses of species to changes in their environment. We show that beyond providing crucial baseline data, the conservation Paleobiology perspective helps us to identify which species will be most vulnerable and what kinds of responses will be most common. We stress that inclusion of geohistorical data in our decision-making process provides a more scientifically robust basis for conservation policies than those dependent on short-term observations alone.
