OntoCAT - an integrated programming toolkit for common ontology application tasks

OntoCAT provides high level abstraction for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies

OntoCAT - a simpler way to access ontology resources

OntoCAT is an open source package developed to simplify the task of querying heterogeneous ontology resources. It supports local ontologies in OBO and OWL format as well as public repositories NCBO BioPortal and EBI Ontology Lookup Service (OLS). It is available from "http://ontocat.sourceforge.net":http://ontocat.sourceforge.ne

Desensitization protocol enabling pediatric crossmatch-positive renal transplantation: successful HLA-antibody-incompatible renal transplantation of two highly sensitized children

BACKGROUND: Renal transplantation improves quality of life (QoL) and survival in children requiring renal replacement therapy (RRT). Sensitization with development of a broad-spectrum of anti-HLA antibodies as a result of previous transplantation or after receiving blood products is an increasing problem. There are no published reports of desensitization protocols in children allowing renal transplantation from HLA-antibody-incompatible living donors. METHODS: We adopted our well-established adult desensitization protocol for this purpose and undertook HLA antibody-incompatible living donor renal transplants in two children: a 14-year-old girl and a 13-year-old boy. RESULTS: After 2 and 1.5 years of follow-up, respectively, both patients have stable renal allograft function despite a rise in donor-specific antibodies in one case. CONCLUSIONS: HLA-incompatible transplantation should be considered in selected cases for sensitized children

MageComet—web application for harmonizing existing large-scale experiment descriptions

Motivation: Meta-analysis of large gene expression datasets obtained from public repositories requires consistently annotated data. Curation of such experiments, however, is an expert activity which involves repetitive manipulation of text. Existing tools for automated curation are few, which bottleneck the analysis pipeline

Anatomy ontologies and potential users: bridging the gap.

MOTIVATION: To evaluate how well current anatomical ontologies fit the way real-world users apply anatomy terms in their data annotations. METHODS: Annotations from three diverse multi-species public-domain datasets provided a set of use cases for matching anatomical terms in two major anatomical ontologies (the Foundational Model of Anatomy and Uberon), using two lexical-matching applications (Zooma and Ontology Mapper). RESULTS: Approximately 1500 terms were identified; Uberon/Zooma mappings provided 286 matches, compared to the control and Ontology Mapper returned 319 matches. For the Foundational Model of Anatomy, Zooma returned 312 matches, and Ontology Mapper returned 397. CONCLUSIONS: Our results indicate that for our datasets the anatomical entities or concepts are embedded in user-generated complex terms, and while lexical mapping works, anatomy ontologies do not provide the majority of terms users supply when annotating data. Provision of searchable cross-products for compositional terms is a key requirement for using ontologies.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments

Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive and the European Nucleotide Archive. A simple interface allows the user to query for differential gene expression either by gene names or attributes or by biological conditions, e.g. diseases, organism parts or cell types. Since our previous report we made 20 monthly releases and, as of Release 11.08 (August 2011), the database supports 19 species, which contains expression data measured for 19 014 biological conditions in 136 551 assays from 5598 independent studies

Modeling sample variables with an Experimental Factor Ontology

Motivation: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions; however, for cross-domain investigations, multiple ontologies are needed to represent the data. These are subject to rapid change, are often not interoperable and present complexities that are a barrier to biological resource users

The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes

A codon consists of three nucleotides and functions during translation to dictate the insertion of a specific amino acid in a growing peptide or, in the case of stop codons, to specify the completion of protein synthesis. There are 64 possible single codons and there are 4096 double, 262 144 triple, 16 777 216 quadruple and 1 073 741 824 quintuple codon combinations available for use by specific genes and genomes. In order to evaluate the use of specific single, double, triple, quadruple and quintuple codon combinations in genes and gene networks, we have developed a codon counting tool and employed it to analyze 5780 Saccharomyces cerevisiae genes. We have also developed visualization approaches, including codon painting, combination and bar graphs, and have used them to identify distinct codon usage patterns in specific genes and groups of genes. Using our developed Gene-Specific Codon Counting Database, we have identified extreme codon runs in specific genes. We have also demonstrated that specific codon combinations or usage patterns are over-represented in genes whose corresponding proteins belong to ribosome or translation-associated biological processes. Our resulting database provides a mineable list of multi-codon data and can be used to identify unique sequence runs and codon usage patterns in individual and functionally linked groups of genes

ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments

The ArrayExpress Archive (http://www.ebi.ac.uk/arrayexpress) is one of the three international public repositories of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

<p>Abstract</p> <p>Background</p> <p>Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups.</p> <p>Results</p> <p>OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application.</p> <p>Conclusions</p> <p>OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases.</p> <p>Availability</p> <p><url>http://www.ontocat.org</url></p