Biomedical subjects

Georgios V Gkoutos

Publications and source records attributed to Georgios V Gkoutos.

4 recordsLinked to original sources

PubMed2005

EMPReSS: European mouse phenotyping resource for standardized screens.

UNLABELLED: Standardized phenotyping protocols are essential for the characterization of phenotypes so that results are comparable between different laboratories and phenotypic data can be related to ontological descriptions in an automated manner. We describe a web-based resource for the visualization, searching and downloading of standard operating procedures and other documents, the European Mouse Phenotyping Resource for Standardized Screens-EMPReSS. AVAILABILITY: Direct access: http://www.empress.har.mrc.ac.uk CONTACT: e.green@har.mrc.ac.uk.

Animals↗

PubMed2004

Using ontologies to describe mouse phenotypes.

The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sources. This produces a framework with greater flexibility, power and economy than previous approaches. We discuss some of the issues this approach raises.

Animals↗

PubMed2004

CRAVE: a database, middleware and visualization system for phenotype ontologies.

MOTIVATION: A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. RESULTS: CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

Algorithms↗

PubMedDate not supplied

Chemical machine vision: automated extraction of chemical metadata from raster images.

We present a novel application of machine vision methods for the identification of chemical composition diagrams from two-dimensional digital raster images. The method is based on the use of Gabor wavelets and an energy function to derive feature vectors from digital images. These are used for training and classification purposes using a Kohonen network for classification with the Euclidean distance norm. We compare this method with previous approaches to transforming such images to a molecular connection table, which are designed to achieve complete atom connection table fidelity but at the expense of requiring human interaction. The present texture-based approach is complementary in attempting to recognize higher order features such as the presence of a chemical representation in the original raster image. This information can be used for providing chemical metadata descriptors of the original image as part of a robot-based Internet resource discovery tool.

Data Display↗