Image annotation with Photocopain

Photo annotation is a resource-intensive task, yet is increasingly essential as image archives and personal photo collections grow in size. There is an inherent con?ict in the process of describing and archiving personal experiences, because casual users are generally unwilling to expend large amounts of e?ort on creating the annotations which are required to organise their collections so that they can make best use of them. This paper describes the Photocopain system, a semi-automatic image annotation system which combines information about the context in which a photograph was captured with information from other readily available sources in order to generate outline annotations for that photograph that the user may further extend or amend.

Task-based annotation and retrieval for image information management

Continuing advances in digital image capture and storage are resulting in a proliferation of imagery and associated problems of information overload in image domains. In this work we present a framework that supports image management using an interactive approach that captures and reuses task-based contextual information. Our framework models the relationship between images and domain tasks they support by monitoring the interactive manipulation and annotation of task-relevant imagery. During image analysis, interactions are captured and a task context is dynamically constructed so that human expertise, proficiency and knowledge can be leveraged to support other users in carrying out similar domain tasks using case-based reasoning techniques. In this article we present our framework for capturing task context and describe how we have implemented the framework as two image retrieval applications in the geo-spatial and medical domains. We present an evaluation that tests the efficiency of our algorithms for retrieving image context information and the effectiveness of the framework for carrying out goal-directed image tasks. © 2010 Springer Science+Business Media, LLC.

Semantic annotation for knowledge management:requirements and a survey of the state of the art

While much of a company's knowledge can be found in text repositories, current content management systems have limited capabilities for structuring and interpreting documents. In the emerging Semantic Web, search, interpretation and aggregation can be addressed by ontology-based semantic mark-up. In this paper, we examine semantic annotation, identify a number of requirements, and review the current generation of semantic annotation systems. This analysis shows that, while there is still some way to go before semantic annotation tools will be able to address fully all the knowledge management needs, research in the area is active and making good progress.

Semantic annotation support in the absence of consensus

We are interested in the annotation of knowledge which does not necessarily require a consensus. Scholarly debate is an example of such a category of knowledge where disagreement and contest are widespread and desirable, and unlike many Semantic Web approaches, we are interested in the capture and the compilation of these conflicting viewpoints and perspectives. The Scholarly Ontologies project provides the underlying formalism to represent this meta-knowledge, and we will look at ways to lighten the burden of its creation. After having described some particularities of this kind of knowledge, we introduce ClaimSpotter, our approach to support its ‘capture’, based on the elicitation of a number of recommendations which are presented for consideration to our annotators (or analysts), and give some elements of evaluation.

Task-based image annotation and retrieval

In order to address problems of information overload in digital imagery task domains we have developed an interactive approach to the capture and reuse of image context information. Our framework models different aspects of the relationship between images and domain tasks they support by monitoring the interactive manipulation and annotation of task-relevant imagery. The approach allows us to gauge a measure of a user's intentions as they complete goal-directed image tasks. As users analyze retrieved imagery their interactions are captured and an expert task context is dynamically constructed. This human expertise, proficiency, and knowledge can then be leveraged to support other users in carrying out similar domain tasks. We have applied our techniques to two multimedia retrieval applications for two different image domains, namely the geo-spatial and medical imagery domains. © Springer-Verlag Berlin Heidelberg 2007.

Integrative bioinformatics for functional genorne annotation:trawling for G protein-coupled receptors

G protein-coupled receptors (GPCR) are amongst the best studied and most functionally diverse types of cell-surface protein. The importance of GPCRs as mediates or cell function and organismal developmental underlies their involvement in key physiological roles and their prominence as targets for pharmacological therapeutics. In this review, we highlight the requirement for integrated protocols which underline the different perspectives offered by different sequence analysis methods. BLAST and FastA offer broad brush strokes. Motif-based search methods add the fine detail. Structural modelling offers another perspective which allows us to elucidate the physicochemical properties that underlie ligand binding. Together, these different views provide a more informative and a more detailed picture of GPCR structure and function. Many GPCRs remain orphan receptors with no identified ligand, yet as computer-driven functional genomics starts to elaborate their functions, a new understanding of their roles in cell and developmental biology will follow.

Expression and purification of tau protein and its frontotemporal dementia variants using a cleavable histidine tag

Recombinant tau protein is widely used to study the biochemical, cellular and pathological aspects of tauopathies, including Alzheimer's disease and frontotemporal dementia with Parkinsonism linked to chromosome 17 (FTPD-17). Pure tau in high yield is a requirement for in vitro evaluation of the protein's physiological and toxic functions. However, the preparation of recombinant tau is complicated by the protein's propensity to aggregate and form truncation products, necessitating the use of multiple, time-consuming purification methods. In this study, we investigated parameters that influence the expression of wild type and FTPD-17 pathogenic tau, in an attempt to identify ways to maximise expression yield. Here, we report on the influence of the choice of host strain, induction temperature, duration of induction, and media supplementation with glucose on tau expression in Escherichia coli. We also describe a straightforward process to purify the expressed tau proteins using immobilised metal affinity chromatography, with favourable yields over previous reports. An advantage of the described method is that it enables high yield production of functional oligomeric and monomeric tau, both of which can be used to study the biochemical, physiological and toxic properties of the protein.