Abstract: OPEN_EmoRec_II is an open multimodal corpus with
experimentally induced emotions. In the first half of the experiment,
emotions were induced with standardized picture material and in the
second half during a human-computer interaction (HCI), realized
with a wizard-of-oz design. The induced emotions are based on the
dimensional theory of emotions (valence, arousal and dominance).
These emotional sequences - recorded with multimodal data (facial
reactions, speech, audio and physiological reactions) during a
naturalistic-like HCI-environment one can improve classification
methods on a multimodal level.
This database is the result of an HCI-experiment, for which 30
subjects in total agreed to a publication of their data including the
video material for research purposes*. The now available open
corpus contains sensory signal of: video, audio, physiology (SCL,
respiration, BVP, EMG Corrugator supercilii, EMG Zygomaticus
Major) and facial reactions annotations.
Abstract: OPEN_EmoRec_II is an open multimodal corpus with
experimentally induced emotions. In the first half of the experiment,
emotions were induced with standardized picture material and in the
second half during a human-computer interaction (HCI), realized
with a wizard-of-oz design. The induced emotions are based on the
dimensional theory of emotions (valence, arousal and dominance).
These emotional sequences - recorded with multimodal data (facial
reactions, speech, audio and physiological reactions) during a
naturalistic-like HCI-environment one can improve classification
methods on a multimodal level.
This database is the result of an HCI-experiment, for which 30
subjects in total agreed to a publication of their data including the
video material for research purposes*. The now available open
corpus contains sensory signal of: video, audio, physiology (SCL,
respiration, BVP, EMG Corrugator supercilii, EMG Zygomaticus
Major) and facial reactions annotations.
Abstract: This paper presents data annotation models at
five levels of granularity (database, relation, column, tuple, and cell) of relational data to address the problem of unsuitability of most relational databases to express annotations. These models
do not require any structural and schematic changes to the
underlying database. These models are also flexible, extensible,
customizable, database-neutral, and platform-independent. This paper also presents an SQL-like query language, named Annotation Query Language (AnQL), to query annotation documents. AnQL is simple to understand and exploits the already-existent wide knowledge and skill set of SQL.
Abstract: This paper describes the NEAR (Navigating Exhibitions, Annotations and Resources) panel, a novel interactive visualization technique designed to help people navigate and interpret groups of resources, exhibitions and annotations by revealing hidden relations such as similarities and references. NEAR is implemented on A•VI•RE, an extended online information repository. A•VI•RE supports a semi-structured collection of exhibitions containing various resources and annotations. Users are encouraged to contribute, share, annotate and interpret resources in the system by building their own exhibitions and annotations. However, it is hard to navigate smoothly and efficiently in A•VI•RE because of its high capacity and complexity. We present a visual panel that implements new navigation and communication approaches that support discovery of implied relations. By quickly scanning and interacting with NEAR, users can see not only implied relations but also potential connections among different data elements. NEAR was tested by several users in the A•VI•RE system and shown to be a supportive navigation tool. In the paper, we further analyze the design, report the evaluation and consider its usage in other applications.
Abstract: Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.
Abstract: Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.
Abstract: Research papers are usually evaluated via peer
review. However, peer review has limitations in evaluating research
papers. In this paper, Scienstein and the new idea of 'collaborative
document evaluation' are presented. Scienstein is a project to
evaluate scientific papers collaboratively based on ratings, links,
annotations and classifications by the scientific community using the
internet. In this paper, critical success factors of collaborative
document evaluation are analyzed. That is the scientists- motivation
to participate as reviewers, the reviewers- competence and the
reviewers- trustworthiness. It is shown that if these factors are
ensured, collaborative document evaluation may prove to be a more
objective, faster and less resource intensive approach to scientific
document evaluation in comparison to the classical peer review
process. It is shown that additional advantages exist as collaborative
document evaluation supports interdisciplinary work, allows
continuous post-publishing quality assessments and enables the
implementation of academic recommendation engines. In the long
term, it seems possible that collaborative document evaluation will
successively substitute peer review and decrease the need for
journals.
Abstract: This paper presents data annotation models at five levels of granularity (database, relation, column, tuple, and cell) of relational data to address the problem of unsuitability of most relational databases to express annotations. These models do not require any structural and schematic changes to the underlying database. These models are also flexible, extensible, customizable, database-neutral, and platform-independent. This paper also presents an SQL-like query language, named Annotation Query Language (AnQL), to query annotation documents. AnQL is simple to understand and exploits the already-existent wide knowledge and skill set of SQL.
Abstract: Understanding the cell's large-scale organization is an
interesting task in computational biology. Thus, protein-protein
interactions can reveal important organization and function of the
cell. Here, we investigated the correspondence between protein
interactions and function for the yeast. We obtained the correlations
among the set of proteins. Then these correlations are clustered using
both the hierarchical and biclustering methods. The detailed analyses
of proteins in each cluster were carried out by making use of their
functional annotations. As a result, we found that some functional
classes appear together in almost all biclusters. On the other hand, in
hierarchical clustering, the dominancy of one functional class is
observed. In brief, from interaction data to function, some correlated
results are noticed about the relationship between interaction and
function which might give clues about the organization of the
proteins.
Abstract: We have developed a database for membrane protein functions, which has more than 3000 experimental data on functionally important amino acid residues in membrane proteins along with sequence, structure and literature information. Further, we have proposed different methods for identifying membrane proteins based on their functions: (i) discrimination of membrane transport proteins from other globular and membrane proteins and classifying them into channels/pores, electrochemical and active transporters, and (ii) β-signal for the insertion of mitochondrial β-barrel outer membrane proteins and potential targets. Our method showed an accuracy of 82% in discriminating transport proteins and 68% to classify them into three different transporters. In addition, we have identified a motif for targeting β-signal and potential candidates for mitochondrial β-barrel membrane proteins. Our methods can be used as effective tools for genome-wide annotations.
Abstract: With the advent of emerging personal computing paradigms such as ubiquitous and mobile computing, Web contents are becoming accessible from a wide range of mobile devices. Since these devices do not have the same rendering capabilities, Web contents need to be adapted for transparent access from a variety of client agents. Such content adaptation is exploited for either an individual element or a set of consecutive elements in a Web document and results in better rendering and faster delivery to the client device. Nevertheless, Web content adaptation sets new challenges for semantic markup. This paper presents an advanced components platform, called SMC, enabling the development of mobility applications and services according to a channel model based on the principles of Services Oriented Architecture (SOA). It then goes on to describe the potential for integration with the Semantic Web through a novel framework of external semantic annotation that prescribes a scheme for representing semantic markup files and a way of associating Web documents with these external annotations. The role of semantic annotation in this framework is to describe the contents of individual documents themselves, assuring the preservation of the semantics during the process of adapting content rendering. Semantic Web content adaptation is a way of adding value to Web contents and facilitates repurposing of Web contents (enhanced browsing, Web Services location and access, etc).