The Distributed Ontology Language (DOL): Use Cases, Syntax, and Extensibility

The Distributed Ontology Language (DOL) is currently being standardized within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3. It aims at providing a unified framework for (1) ontologies formalized in heterogeneous logics, (2) modular ontologies, (3) links between ontologies, and (4) annotation of ontologies. This paper presents the current state of DOL's standardization. It focuses on use cases where distributed ontologies enable interoperability and reusability. We demonstrate relevant features of the DOL syntax and semantics and explain how these integrate into existing knowledge engineering environments.Comment: Terminology and Knowledge Engineering Conference (TKE) 2012-06-20 to 2012-06-21 Madrid, Spai

An automatically curated first-principles database of ferroelectrics.

Ferroelectric materials have technological applications in information storage and electronic devices. The ferroelectric polar phase can be controlled with external fields, chemical substitution and size-effects in bulk and ultrathin film form, providing a platform for future technologies and for exploratory research. In this work, we integrate spin-polarized density functional theory (DFT) calculations, crystal structure databases, symmetry tools, workflow software, and a custom analysis toolkit to build a library of known, previously-proposed, and newly-proposed ferroelectric materials. With our automated workflow, we screen over 67,000 candidate materials from the Materials Project database to generate a dataset of 255 ferroelectric candidates, and propose 126 new ferroelectric materials. We benchmark our results against experimental data and previous first-principles results. The data provided includes atomic structures, output files, and DFT values of band gaps, energies, and the spontaneous polarization for each ferroelectric candidate. We contribute our workflow and analysis code to the open-source python packages atomate and pymatgen so others can conduct analogous symmetry driven searches for ferroelectrics and related phenomena

Non-linear analysis of two-layer timber beams considering interlayer slip and uplift

A new mathematical model and its finite element formulation for the non-linear analysis of mechanical behaviour of a two-layer timber planar beam is presented. A modified principle of virtual work is employed in formulating the finite element method. The basic unknowns are strains. The following assumptions are adopted in the mathematical model: materials are taken to be non-linear and can differ from layer to layer; interacting shear and normal contact tractions between layers are derived from the non-linear shear contact traction-slip and the non-linear normal contact traction-uplift characteristics of the connectors; the geometrically linear and materially non-linear Bernoulli's beam theory is assumed for each layer. The formulation is found to be accurate, reliable and computationally effective. The suitability of the theory is validated by the comparison of the numerical solution and the experimental results of full-scale laboratory tests on a simply supported beam. An excellent agreement between measured and calculated results is observed for all load levels. The further objective of the paper is the analysis of the effect of different normal contact traction-uplift constitutive relationships on the kinematic and static quantities in a statically determined and undetermined structure. While the shear contact traction-slip constitutive relationship dictates the deformability of the composite beam and has a substantial influence on most of the static and kinematic quantities of the composite beam, a variable normal contact traction-uplift constitutive relationship is in most cases negligible

User Applications Driven by the Community Contribution Framework MPContribs in the Materials Project

This work discusses how the MPContribs framework in the Materials Project (MP) allows user-contributed data to be shown and analyzed alongside the core MP database. The Materials Project is a searchable database of electronic structure properties of over 65,000 bulk solid materials that is accessible through a web-based science-gateway. We describe the motivation for enabling user contributions to the materials data and present the framework's features and challenges in the context of two real applications. These use-cases illustrate how scientific collaborations can build applications with their own "user-contributed" data using MPContribs. The Nanoporous Materials Explorer application provides a unique search interface to a novel dataset of hundreds of thousands of materials, each with tables of user-contributed values related to material adsorption and density at varying temperature and pressure. The Unified Theoretical and Experimental x-ray Spectroscopy application discusses a full workflow for the association, dissemination and combined analyses of experimental data from the Advanced Light Source with MP's theoretical core data, using MPContribs tools for data formatting, management and exploration. The capabilities being developed for these collaborations are serving as the model for how new materials data can be incorporated into the Materials Project website with minimal staff overhead while giving powerful tools for data search and display to the user community.Comment: 12 pages, 5 figures, Proceedings of 10th Gateway Computing Environments Workshop (2015), to be published in "Concurrency in Computation: Practice and Experience

A mass spectrometry-guided genome mining approach for natural product peptidogenomics.

Peptide natural products show broad biological properties and are commonly produced by orthogonal ribosomal and nonribosomal pathways in prokaryotes and eukaryotes. To harvest this large and diverse resource of bioactive molecules, we introduce here natural product peptidogenomics (NPP), a new MS-guided genome-mining method that connects the chemotypes of peptide natural products to their biosynthetic gene clusters by iteratively matching de novo tandem MS (MS(n)) structures to genomics-based structures following biosynthetic logic. In this study, we show that NPP enabled the rapid characterization of over ten chemically diverse ribosomal and nonribosomal peptide natural products of previously unidentified composition from Streptomycete bacteria as a proof of concept to begin automating the genome-mining process. We show the identification of lantipeptides, lasso peptides, linardins, formylated peptides and lipopeptides, many of which are from well-characterized model Streptomycetes, highlighting the power of NPP in the discovery of new peptide natural products from even intensely studied organisms