5 research outputs found

    An r package and online resource for macroevolutionary studies using the ray‐finned fish tree of life

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    Comprehensive, time‐scaled phylogenies provide a critical resource for many questions in ecology, evolution and biodiversity. Methodological advances have increased the breadth of taxonomic coverage in phylogenetic data; however, accessing and reusing these data remain challenging.We introduce the Fish Tree of Life website and associated r package fishtree to provide convenient access to sequences, phylogenies, fossil calibrations and diversification rate estimates for the most diverse group of vertebrate organisms, the ray‐finned fishes. The Fish Tree of Life website presents subsets and visual summaries of phylogenetic and comparative data, and is complemented by the r package, which provides flexible programmatic access to the same underlying data source for advanced users wishing to extend or reanalyse the data.We demonstrate functionality with an overview of the website, and show three examples of advanced usage through the r package. First, we test for the presence of long branch attraction artefacts across the fish tree of life. The second example examines the effects of habitat on diversification rate in the pufferfishes. The final example demonstrates how a community phylogenetic analysis could be conducted with the package.This resource makes a large comparative vertebrate dataset easily accessible via the website, while the r package enables the rapid reuse and reproducibility of research results via its ability to easily integrate with other r packages and software for molecular biology and comparative methods.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149697/1/mee313182-sup-0001-Supinfo.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149697/2/mee313182_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149697/3/mee313182.pd

    Explanations Generation For Web Service Workflow

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    The motivation for the work is the challenge of providing textual explanations of automatically generated scientific workflows (e.g., paragraphs that scientists can include in their publications). The extended abstract presents a system which generates explanations for a web service workflow from sets of atoms derived from a collection of ontologies. The system, called nlgPhylogeny, demonstrates the feasibility of the task in the Phylotastic project, that aims at providing evolutionary biologists with a platform for automatic generation of phylogenetic trees given some suitable inputs

    Natural Language Generation From Ontologies Using Grammatical Framework

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    The paper addresses the problem of automatic generation of natural language descriptions for ontology-described artifacts. The motivation for the work is the challenge of providing textual descriptions of automatically generated scientific workflows (e.g., paragraphs that scientists can include in their publications). The extended abstract presents a system which generates descriptions of sets of atoms derived from a collection of ontologies. The system, called nlgPhylogeny, demonstrates the feasibility of the task in the Phylotastic project, that aims at providing evolutionary biologists with a platform for automatic generation of phylogenetic trees given some suitable inputs. nlgPhylogeny utilizes the fact that the Grammatical Framework (GF) is suitable for the natural language generation (NLG) task; the abstract shows how elements of the ontologies in Phylotastic, such as web services, inputs and outputs of web services, can be encoded in GF for the NLG task
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