Towards ontology-driven navigation of the lipid bibliosphere

10.1186/1471-2105-9-S1-S5BMC Bioinformatics9SUPPL. 1BBMI

Knowledge representation and ontologies for lipids and lipidomics

Master'sMASTER OF SCIENC

Lipoprotein ontology as a functional knowledge base

The advances of high throughput research in the biomedical domain have resulted in an onslaught of data being generated at an exponential rate. As a result, researchers face challenges in navigating through overwhelming amounts of information in order to derive relevant scientific insights. Ontologies address these issues by providing explicit description of biomedical entities and a platform for the integration of data, thereby enabling a more efficient retrieval of information. There have been major efforts in the development of biomedical ontologies in the recent years; however no such ontology exists for lipoproteins, which play a crucial role in various biological and cellular functions. Dysregulation in lipoprotein metabolism is significantly associated with an increased risk to cardiovascular disease, the leading cause of mortality in the world today. The aim of this paper is to propose a preliminary framework for Lipoprotein Ontology, with particular focus on the etiology and treatment of lipoprotein dysregulation. This may provide a novel and effective strategy for managing at risk individuals

Linguistic Processing and Classification of Semi Structured Bibliographic Data on Complementary Medicine

Complementary and alternative therapies and medicines (CAM) such as acupuncture or mistletoe treatment are much asked for by cancer patients. With a growing interest in such therapies, physicians need a simple tool with which to get an overview of the scientific publications on CAM, particularly those that are not listed in common bibliographic databases like MEDLINE. CAMbase is an XML-based bibliographical database on CAM which serves to address this need. A custom front end search engine performs semantic analysis of textual input enabling users to quickly find information relevant to the search queries. This article describes the technical background and the architecture behind CAMbase, a free online database on CAM (www.cambase.de). We give examples on its use, describe the underlying algorithms and present recent statistics for search terms related to complementary therapies in oncology

Prototype semantic infrastructure for automated small molecule classification and annotation in lipidomics

<p>Abstract</p> <p>Background</p> <p>The development of high-throughput experimentation has led to astronomical growth in biologically relevant lipids and lipid derivatives identified, screened, and deposited in numerous online databases. Unfortunately, efforts to annotate, classify, and analyze these chemical entities have largely remained in the hands of human curators using manual or semi-automated protocols, leaving many novel entities unclassified. Since chemical function is often closely linked to structure, accurate structure-based classification and annotation of chemical entities is imperative to understanding their functionality.</p> <p>Results</p> <p>As part of an exploratory study, we have investigated the utility of semantic web technologies in automated chemical classification and annotation of lipids. Our prototype framework consists of two components: an ontology and a set of federated web services that operate upon it. The formal lipid ontology we use here extends a part of the LiPrO ontology and draws on the lipid hierarchy in the LIPID MAPS database, as well as literature-derived knowledge. The federated semantic web services that operate upon this ontology are deployed within the Semantic Annotation, Discovery, and Integration (SADI) framework. Structure-based lipid classification is enacted by two core services. Firstly, a structural annotation service detects and enumerates relevant functional groups for a specified chemical structure. A second service reasons over lipid ontology class descriptions using the attributes obtained from the annotation service and identifies the appropriate lipid classification. We extend the utility of these core services by combining them with additional SADI services that retrieve associations between lipids and proteins and identify publications related to specified lipid types. We analyze the performance of SADI-enabled eicosanoid classification relative to the LIPID MAPS classification and reflect on the contribution of our integrative methodology in the context of high-throughput lipidomics.</p> <p>Conclusions</p> <p>Our prototype framework is capable of accurate automated classification of lipids and facile integration of lipid class information with additional data obtained with SADI web services. The potential of programming-free integration of external web services through the SADI framework offers an opportunity for development of powerful novel applications in lipidomics. We conclude that semantic web technologies can provide an accurate and versatile means of classification and annotation of lipids.</p

ПРОТОТИП ПРОГРАММНОЙ ПЛАТФОРМЫ ДЛЯ ПУБЛИКАЦИИ СЕМАНТИЧЕСКИХ ДАННЫХ ИЗ МАТЕМАТИЧЕСКИХ НАУЧНЫХ КОЛЛЕКЦИЙ // Ученые записки КФУ. Физико-математические науки 2012 том154 N3

В статье представлен прототип программной платформы для извлечения связанных открытых данных (Linked Open Data) из заданной коллекции математических научных статей. Задача получения семантического представления из коллекций выбранной предметной области является актуальной, так как в настоящий момент в облаке связанных открытых данных отсутствуют новейшие данные по профессиональной математике. По нашему мнению, одной из основных причин этого является отсутствие специализированных инструментов, способных анализировать семантику, лежащую в основе статей по математике, и эффективно строить их консолидированное представление. В статье описан комплексный подход к анализу математических документов для представления содержимого статей и их метаданных в формате RDF. Рассмотрены методы и технологии извлечения семантических данных из математических статей на основе специальных онтологий, а также описаны эксперименты по интеграции построенного математического RDF-набора с существующими наборами данных в Интернете

Lipoprotein ontology: a formal representation of Lipoproteins

Lipoproteins serve as a mode of transport for the uptake, storage and metabolism of lipids. Dysregulation in lipoprotein metabolism, known as dyslipidaemia, is strongly correlated to various diseases such as cardiovascular disease. Lipoprotein Ontology provides a formal representation of lipoprotein concepts and relationships that can be used to support the intelligent retrieval of information, faciliate collaboration between research groups, and provide the basis for the development of tools for the diagnosis and treatment of dyslipidaemia

Novel lipidomic approaches to analyse glycerophospholipids and sphingolipids in complex mixtures using mass spectrometry

Ph.DDOCTOR OF PHILOSOPH