OntoQuery: easy-to-use web-based OWL querying

Summary: The Web Ontology Language (OWL) provides a sophisticated language for building complex domain ontologies and is widely used in bio-ontologies such as the Gene Ontology. The Protégé-OWL ontology editing tool provides a query facility that allows composition and execution of queries with the human-readable Manchester OWL syntax, with syntax checking and entity label lookup. No equivalent query facility such as the Protégé Description Logics (DL) query yet exists in web form. However, many users interact with bio-ontologies such as chemical entities of biological interest and the Gene Ontology using their online Web sites, within which DL-based querying functionality is not available. To address this gap, we introduce the OntoQuery web-based query utility. Availability and implementation: The source code for this implementation together with instructions for installation is available at http://github.com/IlincaTudose/OntoQuery. OntoQuery software is fully compatible with all OWL-based ontologies and is available for download (CC-0 license). The ChEBI installation, ChEBI OntoQuery, is available at http://www.ebi.ac.uk/chebi/tools/ontoquery. Contact: [email protected]

ChEBI in 2016: Improved services and an expanding collection of metabolites

ChEBI is a database and ontology containing infor-mation about chemical entities of biological inter-est. It currently includes over 46 000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, syn-onyms and literature citations. All content is freely available and can be accessed online a

Identification of depressive disorder among older people in care homes – a feasibility study

Background: Depression is common among older people but more common among those living in care homes. Depression is not easily detected among older adults because of the presentation, and the tendency for older people not to complain of depression, particularly those living in care homes. In general, care home staff have limited training in recognising depression. Depression is undertreated and residents may not receive a therapeutic dose of antidepressant. The true prevalence of depression among care home residents is uncertain. Method: This feasibility study aimed to explore the level of depression among older people in care homes by comparing the outcome of an assessment by care home staff with the outcome of a diagnostic clinical interview, using ICD-10 criteria and the 30-item Geriatric Depression Scale (GDS), conducted by a psychiatrist. Results: In all, 47 older people from four care homes were interviewed by a psychiatrist. Of them, 39.1% (18/46) of residents were prescribed an antidepressant and were no longer depressed; 8.7% (4/46) were prescribed an antidepressant and remained depressed; and 6.5% (3/46) of residents assessed as being depressed, had not been prescribed an antidepressant. That is, 54% (25/46) of residents had been or were currently depressed. Using ICD-10 criteria, the sensitivity of the GDS at a threshold of 10 and 11 was 100%. In total, 89.4% of residents received a correct diagnosis (presence or absence of depression using the GDS at the 11 threshold. Summary: The prevalence of depression in these homes was 54%. Of the residents with depression, 72% (18/25) were managed with an antidepressant and 28% (7/25) were receiving ineffective or no treatment. The 30-item GDS can provide more useful information than a home care staff assessment for identifying depression. More research should explore the value of training home care staff to administer the 30-item GDS to optimise the management of depression in older people in care homes

Flexural Behaviour of Lightweight Reinforced Concrete Beams Internally Reinforced with Welded Wire Mesh

Lightweight clay aggregate (LECA) is manufactured by heating clay with no lime content in the kiln; as a result, the water evaporates and angular clay balls with pore structures are obtained. LECA possess internal curing properties as any other lightweight aggregate due to their pore structure and higher water absorption capacity. In this work, experimental and analytical behaviour using LECA as a 100% replacement for coarse aggregate to make lightweight concrete (LWC) beams was studied. The LWC beams were compared to the conventional concrete beams in load-deflection, energy absorption capacity, and ductility index. Internal mesh reinforcement using welded wire mesh (WWM) of (4 layers of 15 mm square spacing, 4 layers of 10 mm square spacing, and 4 layers of 15 mm and 10 mm mesh placed alternatively) was provided to enhance the load-carrying capacity of the LWC beam without increasing the dimensions and self-weight of the beams. The beam internally reinforced with WWM exhibited higher load carrying capacity and withstood more significant deflection without sudden failure. The internal reinforcement of WWM is provided to make steel rebars, and WWM works monolithically while loading; this will reduce the stress on tension bars and increase load-carrying capacity. Finally, the generated analytical findings agreed well with the experimental data, demonstrating that the analytical model could mimic the behaviour of LWC beams with WWM

libChEBI an API for accessing the ChEBI database

BACKGROUND: ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software. RESULTS: To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications. CONCLUSIONS: libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13321-016-0123-9) contains supplementary material, which is available to authorized users

Implementation of a Real-Time Database System

This paper reports on the design, development and performance evaluation of RT-Genesis, a real-time database management system resulting from modifying an existing commercial DBMS, Genesis. RT-Genesis is a relational database management system that accommodates SQL queries and transactions having time constraints. It features time-cognizant algorithms for scheduling, concurrency control and buffer management. The system has been tested and the performance of the different algorithms compared in isolation as well as in combination with different classes of SQL workloads. In addition, a two-phased approach to transaction execution has also been implemented with the goal of exploiting access invariance to improve predictability. This work demonstrates the feasibility of converting non-real-time DBMSs into real-time DBMSs for firm deadline transactions. Besides reporting on how this was achieved and on the performance of the incorporated algorithms, lessons learned from this experience are also discussed.

Building Bonds: Cancer Stem Cells Depend on Their Progeny to Drive Tumor Progression

Little is currently known about how cancer stem-like cells (CSCs) interact with their more restricted progeny. In this issue of Cell Stem Cell, Wang et al. (2018) demonstrate a novel bidirectional signaling axis between CSCs and their progeny that is mediated by brain-derived neurotrophic factor and VGF accelerating glioma progression