User Experience document on VRC Design Guide - D6.1

This document is a comprehensive report on the first user experience (UX) workshop hosted to ensure a user centric design and usability of the PhenoMeNal Virtual Research Environment (VRE), aka. Virtual Research Community (VRC)

OntoQuery: easy-to-use web-based OWL querying

Summary: The Web Ontology Language (OWL) provides a sophisticated language for building complex domain ontologies and is widely used in bio-ontologies such as the Gene Ontology. The Protégé-OWL ontology editing tool provides a query facility that allows composition and execution of queries with the human-readable Manchester OWL syntax, with syntax checking and entity label lookup. No equivalent query facility such as the Protégé Description Logics (DL) query yet exists in web form. However, many users interact with bio-ontologies such as chemical entities of biological interest and the Gene Ontology using their online Web sites, within which DL-based querying functionality is not available. To address this gap, we introduce the OntoQuery web-based query utility. Availability and implementation: The source code for this implementation together with instructions for installation is available at http://github.com/IlincaTudose/OntoQuery. OntoQuery software is fully compatible with all OWL-based ontologies and is available for download (CC-0 license). The ChEBI installation, ChEBI OntoQuery, is available at http://www.ebi.ac.uk/chebi/tools/ontoquery. Contact: [email protected]

ChEBI in 2016: Improved services and an expanding collection of metabolites

ChEBI is a database and ontology containing infor-mation about chemical entities of biological inter-est. It currently includes over 46 000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, syn-onyms and literature citations. All content is freely available and can be accessed online a

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

BACKGROUND: The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. RESULTS: We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. CONCLUSIONS: The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl

Generalized ell for detecting and tracking through illumination model changes

In previous work, we developed the Illum-PF-MT, which is the PF-MT idea applied to the problem of tracking temporally and spatially varying illumination change. In many practical problems, the rate at which illumination changes varies over time. For e.g. when a car transitions from shadow to sunlight or vice-versa the rate of illumination change is much higher than when it is in shadow or in sunlight. One way to model illumination change in such problems is using a Gaussian random walk model with two values of the change covariance- a large covariance when a “transition ” is detected and a much smaller one when “no transition ” is detected. But to use such a model, one needs to first detect the transition. The transition is a natural one and so it happens gradually (unlike a sudden manual dimming of the light in the room) and thus existing change detection statistics which are designed only for sudden changes are unable to detect the transition. In this paper, we propose to use the recently proposed generalized ELL (gELL) idea which uses the tracked part of the change to detect it and hence detects such partially trackable changes very quickly. Since gELL detects much before loss of track occurs, one is able to transition to the “transition ” model and back without ever losing track. Also, for the first time, we demonstrate the use of gELL in combination with the PF-MT algorithm which is more stable to model change than the original PF. 1

Particle filter with mode tracker (PF-MT) for visual tracking across illumination change

In recent work, the authors introduced a multiplicative, low dimensional model of illumination that is computed as a linear combination of a set of simple-to-compute Legendre basis functions. The basis coefficients describing illumination change, are can be combined with the “shape ” vector to define a joint ‘shape”-illumination space for tracking. The increased dimensionality of the state vector necessitates an increase in the number of particles required to maintain tracking accuracy. In this paper, we utilize the recently proposed PF-MT algorithm to estimate the illumination vector. This is motivated by the fact that, except in case of occlusions, multimodality of the state posterior is usually due to multimodality in the “shape” vector (e.g. there may be multiple objects in the scene that roughly match the template). In other words, given the “shape ” vector at time t, the posterior of the illumination (probability distribution of illumination conditioned on the “shape ” and illumination at previous time) is unimodal. In addition, it is also true that this posterior is usually quite narrow since illumination changes over time are slow. The choice of the illumination model permits the illumination coefficients to be solved in closed form as a solution of a regularized least squares problem. We demonstrate the use of our method for the problem of face tracking under variable lighting conditions existing in the scene. 1

SMS FOR ANDROID APPLICATION BY USING 3D-AES, PGP AND STEGNOGRAPHY

Today the age of information technology has transformed the ways we communicate with each other. We send emails, send SMS, send message using social networking sites and many more. The uses of computers, smart phones and clouds have become an integral part of our life for sharing information with each other. Thus introduction of all these means have also given rise to misuse of information by third party which can steal our private information.Thus we are thinking of using cryptography for securing our information. Today there are many cryptographic algorithms available for securing data but those are common from AES to RSA. So we are thinking of enhancing the security by using an advanced version of AES called as 3D-AES which generates a symmetric key by shuffling the original key array three times and making the key better each time it is shuffled. Thus the final output key will be more strong then a normal AES key. It will help secure the data more accurately than the normal one. The studies should reflect a lower encryption time and more security then the normal one. The other technique is used PGP for encryption and Compress the encrypted message to reduce its length, using Shannon fano algorithm technique