Representation of research hypotheses

BACKGROUND: Hypotheses are now being automatically produced on an industrial scale by computers in biology, e.g. the annotation of a genome is essentially a large set of hypotheses generated by sequence similarity programs; and robot scientists enable the full automation of a scientific investigation, including generation and testing of research hypotheses. RESULTS: This paper proposes a logically defined way for recording automatically generated hypotheses in machine amenable way. The proposed formalism allows the description of complete hypotheses sets as specified input and output for scientific investigations. The formalism supports the decomposition of research hypotheses into more specialised hypotheses if that is required by an application. Hypotheses are represented in an operational way – it is possible to design an experiment to test them. The explicit formal description of research hypotheses promotes the explicit formal description of the results and conclusions of an investigation. The paper also proposes a framework for automated hypotheses generation. We demonstrate how the key components of the proposed framework are implemented in the Robot Scientist “Adam”. CONCLUSIONS: A formal representation of automatically generated research hypotheses can help to improve the way humans produce, record, and validate research hypotheses. AVAILABILITY: http://www.aber.ac.uk/en/cs/research/cb/projects/robotscientist/results

Comprehensive contextual visualization of a news archive for aiding story planning

Writing is a complex mental process of generating ideas and organizing the flow of information to convey the intended message to the appropriate audience for educating, enriching or entertaining. Strategic story planning in the pre-writing phase can enrich the quality of writing. The facts of news are encapsulated in five basic questions "Who", "Where", "What", "When" and "Why" which are fundamental for any readers’ understanding. Focusing on these 5Ws, this paper demonstrates visualizations designed to provide cognitive guidance for planning editorial news stories that require comprehensive analysis using a news archive. The visualizations are contextual: global (considering the whole archive), relative (considering topic-based news collection) and local (considering single news). Global context visualizations are designed to aid the identification of a historically important or a decaying topic of interest that can be beneficial to review/compare against raising new topic s in the current time. On selecting a topic, a relative context Terms Board is produced to aid brainstorming in the pre-writing phase. During reviewing related documents presented via Terms Board, Local Context visualization is presented to aid in recalling strategic terms' emphasis in the selected news

Comprehensive Terms Board Visualization for News Analysis and Editorial Story Planning

Knowledge providers, such as authors, teachers, researchers and journalists rely on researching facts to convey evidence-driven information about a selected topic and story planning in the pre-writing phase enhances engagement and understanding of the audience through a better content organization. Typical search engines support finding relevant facts, but they do not aid an individual’s metacognition process of a topic. In this demo, we introduce the concept of the Terms Board, a topic-driven comprehensive visualization for presenting terms to provide a cognitive guide for news analysis and formulating their plans for storytelling in editorial writing. Terms Board is composed of six cards reflecting the major storytelling aspects: what the story is about, who are the characters of the story, where the story is located, why there are challenges, what has been done to address the challenges and why the actions were effective. Each card shows three top terms based on three factual timeline aspects: historical, consistent and latest. For this demo, we extracted emphasised terms from a collection of documents in a news archive and produced a Terms Board for the most frequent topics which were then presented to a group of study participants. Participants’ performances on several tasks have been measured and analysed. The study results are encouraging. The major contribution of this research is presenting a Terms Board visualisation approach as a cognitive guide for news analysis and editorial story planning and presenting an experimental evaluation of this approach via cognitive reading and writing user experiment tasks

A Cognitive Theoretical Approach of Rhetorical News Analysis

The storytelling narrative is the key to conveying an author's opinion and argument about a specific topic to intended readers. A good narrative not only conveys the underlying message but also leads readers to a better conceptual understanding of the discussed topic. Stories play a vital role in understanding through their chronological style of reporting. Similarly, to gain readers’ attention from beginning to end, news agencies generally adopt an inverted pyramid structure where a story starts with stating the most important material. The facts of news are encapsulated in fve basic questions Who, Where, What, When and Why which are fundamental for any news readers' understanding. Distributions of the categorical facts of the news correlate to the answers to What, When, Where and Who questions and the answer to Why is correlated to the authors' argumentation and evidence. In this paper, we presented a theory of mapping 5Ws and Aristotle's Rhetoric into the format of Joseph Campbell's The Hero's Journey as a structural story template to assist in automatic understanding of the structure of news and evaluated the approach via cognitive reading and writing user experiment tasks

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data

Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting

Over the years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The ten papers selected for this supplement are extended versions of the original papers presented at the 2010 SIG. The papers span a wide range of topics including practical solutions for data and knowledge integration for translational medicine, hypothesis based querying , understanding kidney and urinary pathways, mining the pharmacogenomics literature; theoretical research into the orthogonality of biomedical ontologies, the representation of diseases, the representation of research hypotheses, the combination of ontologies and natural language processing for an annotation framework, the generation of textual definitions, and the discovery of gene interaction networks

ART: An ontology based tool for the translation of papers into Semantic Web format

The paper describes initial work on an ontology based tool, ART, for the semantic annotation of papers stored in digital repositories. ART is intended for the annotation not only of data and metadata about a paper, but also the main elements of the described scientific investigation, such as goals, hypotheses, and observations. ART will also be able to aid in the expression of research results directly in a semantic format, through the composition of text using ontology-based templates and stored typical key phrases for the description of basic elements of the research. ART's system design, its functionality, and related projects are discussed. An example annotated paper is presented in order to demonstrate the expected output of the tool.

Local communities as а tool for urban conflict resolution

A modern city is a concentration of a whole range of diverse processes and activities, residents with different needs, traditions and beliefs. The city is also an arena of clashing economic, political and social interests. Urban development trends are expressed both in the need for centralized determination of the direction of urban environment, and public demand for greater civic engagement. Accordingly, conflicts cannot be avoided, but it is important not to accept this obvious truth, but to create a tradition of constant thoughtful analysis of ongoing processes, identifying causes and searching for solutions. As awareness of the importance of collective efforts in creating a comfortable urban environment grows, knowledge about the approaches and public technologies used to resolve urban conflicts becomes more in demand. One of the effective tools for resolving urban conflicts are local communities created on sub-municipal territories within the city boundaries. However, the effectiveness of this tool depends on the proper organization of intra-urban communities and provision of legal guarantees for their functioning. This study is carried out using a comprehensive interdisciplinary approach, implying the analysis of urban development and urban environment through the prism of law. The study of Russian and foreign doctrinal sources, along with normative legal acts and materials of judicial and law enforcement practice, allows to form a sufficient picture of the state of urban conflictology and substantiate the role of local communities in their resolution