GOmotif: A web server for investigating the biological role of protein sequence motifs

<p>Abstract</p> <p>Background</p> <p>Many proteins contain conserved sequence patterns (motifs) that contribute to their functionality. The process of experimentally identifying and validating novel protein motifs can be difficult, expensive, and time consuming. A means for helping to identify in advance the possible function of a novel motif is important to test hypotheses concerning the biological relevance of these motifs, thus reducing experimental trial-and-error.</p> <p>Results</p> <p>GOmotif accepts PROSITE and regular expression formatted motifs as input and searches a Gene Ontology annotated protein database using motif search tools. The search returns the set of proteins containing matching motifs and their associated Gene Ontology terms. These results are presented as: 1) a hierarchical, navigable tree separated into the three Gene Ontology biological domains - biological process, cellular component, and molecular function; 2) corresponding pie charts indicating raw and statistically adjusted distributions of the results, and 3) an interactive graphical network view depicting the location of the results in the Gene Ontology.</p> <p>Conclusions</p> <p>GOmotif is a web-based tool designed to assist researchers in investigating the biological role of novel protein motifs. GOmotif can be freely accessed at <url>http://www.gomotif.ca</url></p

Using ontology engineering for understanding needs and allocating resources in web-based industrial virtual collaboration systems

In many interactions in cross-industrial and inter-industrial collaboration, analysis and understanding of relative specialist and non-specialist language is one of the most pressing challenges when trying to build multi-party, multi-disciplinary collaboration system. Hence, identifying the scope of the language used and then understanding the relationships between the language entities are key problems. In computer science, ontologies are used to provide a common vocabulary for a domain of interest together with descriptions of the meaning of terms and relationships between them, like in an encyclopedia. These, however, often lack the fuzziness required for human orientated systems. This paper uses an engineering sector business collaboration system (www.wmccm.co.uk) as a case study to illustrate the issues. The purpose of this paper is to introduce a novel ontology engineering methodology, which generates structurally enriched cross domain ontologies economically, quickly and reliably. A semantic relationship analysis of the Google Search Engine Index was devised and evaluated. Using Semantic analysis seems to generate a viable list of subject terms. A social network analysis of the semantically derived terms was conducted to generate a decision support network with rich relationships between terms. The derived ontology was quicker to generate, provided richer internal relationships and relied far less on expert contribution. More importantly, it improved the collaboration matching capability of WMCCM

Semantic Jira - Semantic Expert Finder in the Bug Tracking Tool Jira

The semantic expert recommender extension for the Jira bug tracking system semantically searches for similar tickets in Jira and recommends experts and links to existing organizational (Wiki) knowledge for each ticket. This helps to avoid redundant work and supports the search and collaboration with experts in the project management and maintenance phase based on semantically enriched tickets in Jira.Comment: published in proceedings of the 9th International Workshop on Semantic Web Enabled Software Engineering (SWESE2013), Berlin, Germany, December 2-5, 201

A framework for automatic semantic video annotation

The rapidly increasing quantity of publicly available videos has driven research into developing automatic tools for indexing, rating, searching and retrieval. Textual semantic representations, such as tagging, labelling and annotation, are often important factors in the process of indexing any video, because of their user-friendly way of representing the semantics appropriate for search and retrieval. Ideally, this annotation should be inspired by the human cognitive way of perceiving and of describing videos. The difference between the low-level visual contents and the corresponding human perception is referred to as the ‘semantic gap’. Tackling this gap is even harder in the case of unconstrained videos, mainly due to the lack of any previous information about the analyzed video on the one hand, and the huge amount of generic knowledge required on the other. This paper introduces a framework for the Automatic Semantic Annotation of unconstrained videos. The proposed framework utilizes two non-domain-specific layers: low-level visual similarity matching, and an annotation analysis that employs commonsense knowledgebases. Commonsense ontology is created by incorporating multiple-structured semantic relationships. Experiments and black-box tests are carried out on standard video databases for action recognition and video information retrieval. White-box tests examine the performance of the individual intermediate layers of the framework, and the evaluation of the results and the statistical analysis show that integrating visual similarity matching with commonsense semantic relationships provides an effective approach to automated video annotation

Biomedical ontology alignment: An approach based on representation learning

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results

IMPROVING THE DEPENDABILITY OF DESTINATION RECOMMENDATIONS USING INFORMATION ON SOCIAL ASPECTS

Prior knowledge of the social aspects of prospective destinations can be very influential in making travel destination decisions, especially in instances where social concerns do exist about specific destinations. In this paper, we describe the implementation of an ontology-enabled Hybrid Destination Recommender System (HDRS) that leverages an ontological description of five specific social attributes of major Nigerian cities, and hybrid architecture of content-based and case-based filtering techniques to generate personalised top-n destination recommendations. An empirical usability test was conducted on the system, which revealed that the dependability of recommendations from Destination Recommender Systems (DRS) could be improved if the semantic representation of social attributes information of destinations is made a factor in the destination recommendation process

Global Network Alignment

Motivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment. Analogous to sequence alignment, efficient and reliable network alignment methods will improve our understanding of biological systems. Network alignment is computationally hard. Hence, devising efficient network alignment heuristics is currently one of the foremost challenges in computational biology. &#xd;&#xa;&#xd;&#xa;Results: We present a superior heuristic network alignment algorithm, called Matching-based GRAph ALigner (M-GRAAL), which can process and integrate any number and type of similarity measures between network nodes (e.g., proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity, and structural similarity. This is efficient in resolving ties in similarity measures and in finding a combination of similarity measures yielding the largest biologically sound alignments. When used to align protein-protein interaction (PPI) networks of various species, M-GRAAL exposes the largest known functional and contiguous regions of network similarity. Hence, we use M-GRAAL&#x2019;s alignments to predict functions of un-annotated proteins in yeast, human, and bacteria _C. jejuni_ and _E. coli_. Furthermore, using M-GRAAL to compare PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship and our phylogenetic tree is the same as sequenced-based one