Developing a kidney and urinary pathway knowledge base

<p>Abstract</p> <p>Background</p> <p>Chronic renal disease is a global health problem. The identification of suitable biomarkers could facilitate early detection and diagnosis and allow better understanding of the underlying pathology. One of the challenges in meeting this goal is the necessary integration of experimental results from multiple biological levels for further analysis by data mining. Data integration in the life science is still a struggle, and many groups are looking to the benefits promised by the Semantic Web for data integration.</p> <p>Results</p> <p>We present a Semantic Web approach to developing a knowledge base that integrates data from high-throughput experiments on kidney and urine. A specialised KUP ontology is used to tie the various layers together, whilst background knowledge from external databases is incorporated by conversion into RDF. Using SPARQL as a query mechanism, we are able to query for proteins expressed in urine and place these back into the context of genes expressed in regions of the kidney.</p> <p>Conclusions</p> <p>The KUPKB gives KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. The Semantic Web technologies we use, together with the background knowledge from the domain’s ontologies, allows both rapid conversion and integration of this knowledge base. The KUPKB is still relatively small, but questions remain about scalability, maintenance and availability of the knowledge itself.</p> <p>Availability</p> <p>The KUPKB may be accessed via <url>http://www.e-lico.eu/kupkb</url>.</p

PeptiCKDdb-peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease

The peptiCKDdb is a publicly available database platform dedicated to support research in the field of chronic kidney disease (CKD) through identification of novel biomarkers and molecular features of this complex pathology. PeptiCKDdb collects peptidomics and proteomics datasets manually extracted from published studies related to CKD. Datasets from peptidomics or proteomics, human case/control studies on CKD and kidney or urine profiling were included. Data from 114 publications (studies of body fluids and kidney tissue: 26 peptidomics and 76 proteomics manuscripts on human CKD, and 12 focusing on healthy proteome profiling) are currently deposited and the content is quarterly updated. Extracted datasets include information about the experimental setup, clinical study design, discovery-validation sample sizes and list of differentially expressed proteins (P-value &lt; 0.05). A dedicated interactive web interface, equipped with multiparametric search engine, data export and visualization tools, enables easy browsing of the data and comprehensive analysis. In conclusion, this repository might serve as a source of data for integrative analysis or a knowledgebase for scientists seeking confirmation of their findings and as such, is expected to facilitate the modeling of molecular mechanisms underlying CKD and identification of biologically relevant biomarkers.Database URL: www.peptickddb.com

Populous: A tool for populating ontology templates

We present Populous, a tool for gathering content with which to populate an ontology. Domain experts need to add content, that is often repetitive in its form, but without having to tackle the underlying ontological representation. Populous presents users with a table based form in which columns are constrained to take values from particular ontologies; the user can select a concept from an ontology via its meaningful label to give a value for a given entity attribute. Populated tables are mapped to patterns that can then be used to automatically generate the ontology's content. Populous's contribution is in the knowledge gathering stage of ontology development. It separates knowledge gathering from the conceptualisation and also separates the user from the standard ontology authoring environments. As a result, Populous can allow knowledge to be gathered in a straight-forward manner that can then be used to do mass production of ontology content.Comment: in Adrian Paschke, Albert Burger begin_of_the_skype_highlighting end_of_the_skype_highlighting, Andrea Splendiani, M. Scott Marshall, Paolo Romano: Proceedings of the 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences, Berlin,Germany, December 8-10, 201

Influence of nutrition on feline calcium oxalate urolithiasis with emphasis on endogenous oxalate synthesis

The prevalence of calcium oxalate (CaOx) uroliths detected in cats with lower urinary tract disease has shown a sharp increase over the last decades with a concomitant reciprocal decrease in the occurrence of struvite (magnesium ammonium phosphate) uroliths. CaOx stone-preventative diets are available nowadays, but seem to be marginally effective, as CaOx urolith recurrence occurs in patients fed these diets. In order to improve the preventative measures against CaOx urolithiasis, it is important to understand its aetiopathogenesis. The main research focus in CaOx formation in cats has been on the role of Ca, whereas little research effort has been directed towards the role and origin of urinary oxalates. As in man, the exogenous origin of urinary oxalates in cats is thought to be of minor importance, although the precise contribution of dietary oxalates remains unclear. The generally accepted dietary risk factors for CaOx urolithiasis in cats are discussed and a model for the biosynthetic pathways of oxalate in feline liver is provided. Alanine:glyoxylate aminotransferase 1 (AGT1) in endogenous oxalate metabolism is a liver-specific enzyme targeted in the mitochondria in cats, and allows for efficient conversion of glyoxylate to glycine when fed a carnivorous diet. The low peroxisomal activity of AGT1 in cat liver is compatible with the view that felids utilised a low-carbohydrate diet throughout evolution. Future research should focus on understanding de novo biosynthesis of oxalate in cats and their adaptation(s) in oxalate metabolism, and on dietary oxalate intake and absorption by cats

Claudins in the Renal Collecting Duct

The renal collecting duct fine-tunes urinary composition, and thereby, coordinates key physiological processes, such as volume/blood pressure regulation, electrolyte-free water reabsorption, and acid-base homeostasis. The collecting duct epithelium is comprised of a tight epithelial barrier resulting in a strict separation of intraluminal urine and the interstitium. Tight junctions are key players in enforcing this barrier and in regulating paracellular transport of solutes across the epithelium. The features of tight junctions across different epithelia are strongly determined by their molecular composition. Claudins are particularly important structural components of tight junctions because they confer barrier and transport properties. In the collecting duct, a specific set of claudins (Cldn-3, Cldn-4, Cldn-7, Cldn-8) is expressed, and each of these claudins has been implicated in mediating aspects of the specific properties of its tight junction. The functional disruption of individual claudins or of the overall barrier function results in defects of blood pressure and water homeostasis. In this concise review, we provide an overview of the current knowledge on the role of the collecting duct epithelial barrier and of claudins in collecting duct function and pathophysiology

Current Perspective on the Location and Function of Gamma- Aminobutyric Acid (GABA) and its Metabolic Partners in the Kidney.

Gamma-aminobutyric acid (GABA) is an inhibitory neurotransmitter located in the mammalian central nervous system, which binds to GABAA and GABAB receptors to mediate its neurological effects. In addition to its role in the CNS, an increasing number of publications have suggested that GABA might also play a role in the regulation of renal function. All three enzymes associated with GABA metabolism; glutamic acid decarboxylase, GABA ?-oxoglutarate transaminase (GABA-T) and succinic semialdehyde dehydrogenase (SSADH) have been localised to the kidney providing the necessary machinery for localised GABA synthesis and metabolism. Moreover GABA receptors have been localised to both tubular and vascular structures in the kidney, and GABA is excreted in urine (~3 ?M) in humans. Despite the collective evidence describing the presence of a GABA system in the kidney, the precise function of such a system requires further clarification. Here we provide an overview of the current renal GABA literature and provide novel data that indicates GABA can act at contractile pericyte cells located along vasa recta capillaries in the renal medulla to potentially regulate medullary blood flow

Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting

Over the years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The ten papers selected for this supplement are extended versions of the original papers presented at the 2010 SIG. The papers span a wide range of topics including practical solutions for data and knowledge integration for translational medicine, hypothesis based querying , understanding kidney and urinary pathways, mining the pharmacogenomics literature; theoretical research into the orthogonality of biomedical ontologies, the representation of diseases, the representation of research hypotheses, the combination of ontologies and natural language processing for an annotation framework, the generation of textual definitions, and the discovery of gene interaction networks

Stop adding insult to injury—identifying and managing risk factors for the progression of acute kidney injury in children

Acute kidney injury (AKI) is common in children admitted to hospital. Whilst some recover normal kidney function following an acute kidney insult, a significant proportion experience long-term sequelae. The aim of this review is to summarize current understanding of the processes that can lead to sequelae following AKI. Kidney injury, repair, recovery and progression are described. Risk factors for progression are outlined, and potential strategies to stratify the risk of progression in children with AKI are discussed. Clinical management priorities to minimize sequelae are suggested. Looking ahead, novel therapeutic targets are discussed with the potential to accelerate adaptive repair and ameliorate the progression and sequelae of AKI in the future