Selected papers from the 15th Annual Bio-Ontologies special interest group meeting

© 2013 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Over the 15 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 and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes

Knowledge management, innovation and big data: Implications for sustainability, policy making and competitiveness

This Special Issue of Sustainability devoted to the topic of “Knowledge Management, Innovation and Big Data: Implications for Sustainability, Policy Making and Competitiveness” attracted exponential attention of scholars, practitioners, and policy-makers from all over the world. Locating themselves at the expanding cross-section of the uses of sophisticated information and communication technology (ICT) and insights from social science and engineering, all papers included in this Special Issue contribute to the opening of new avenues of research in the field of innovation, knowledge management, and big data. By triggering a lively debate on diverse challenges that companies are exposed to today, this Special Issue offers an in-depth, informative, well-structured, comparative insight into the most salient developments shaping the corresponding fields of research and policymaking

A generic operational simulation for early design civil unmanned aerial vehicles

Contemporary aerospace programmes often suffer from large cost overruns, delivery delays and inferior product quality. This is caused in part by poor predictive quality of the early design phase processes with regards to the operational environment of a product. This paper develops the idea of a generic operational simulation that can help designers to rigorously analyse and test their early product concepts. The simulation focusses on civil Unmanned Air Vehicle products and missions to keep the scope of work tractable. The research agenda is introduced along with ideas, initial results and future work. Designers specify details about their product, its environment and anticipated operational procedures. The simulation returns information that can help to estimate the value of the product using the value-driven design approach. Information will include recurring and non-recurring mission cost items. The research aim is to show that an operational simulation can improve early design concepts, thereby reducing delays and cost overruns. Moreover, a trade-off between mission fidelity and model generality is sought along with a generic ontology of civil Unmanned Air Vehicle missions and guidelines about capturing operational informatio

Ontology modelling methodology for temporal and interdependent applications

The increasing adoption of Semantic Web technology by several classes of applications in recent years, has made ontology engineering a crucial part of application development. Nowadays, the abundant accessibility of interdependent information from multiple resources and representing various fields such as health, transport, and banking etc., further evidence the growing need for utilising ontology for the development of Web applications. While there have been several advances in the adoption of the ontology for application development, less emphasis is being made on the modelling methodologies for representing modern-day application that are characterised by the temporal nature of the data they process, which is captured from multiple sources. Taking into account the benefits of a methodology in the system development, we propose a novel methodology for modelling ontologies representing Context-Aware Temporal and Interdependent Systems (CATIS). CATIS is an ontology development methodology for modelling temporal interdependent applications in order to achieve the desired results when modelling sophisticated applications with temporal and inter dependent attributes to suit today's application requirements

Natural Language Query in the Biochemistry and Molecular Biology Domains Based on Cognition Search™

Motivation: With the tremendous growth in scientific literature, it is necessary to improve upon the standard pattern matching style of the available search engines. Semantic NLP may be the solution to this problem. Cognition Search (CSIR) is a natural language technology. It is best used by asking a simple question that might be answered in textual data being queried, such as MEDLINE. CSIR has a large English dictionary and semantic database. Cognition’s semantic map enables the search process to be based on meaning rather than statistical word pattern matching and, therefore, returns more complete and relevant results. The Cognition Search engine uses downward reasoning and synonymy which also improves recall. It improves precision through phrase parsing and word sense disambiguation.
Result: Here we have carried out several projects to "teach" the CSIR lexicon medical, biochemical and molecular biological language and acronyms from curated web-based free sources. Vocabulary from the Alliance for Cell Signaling (AfCS), the Human Genome Nomenclature Consortium (HGNC), the United Medical Language System (UMLS) Meta-thesaurus, and The International Union of Pure and Applied Chemistry (IUPAC) was introduced into the CSIR dictionary and curated. The resulting system was used to interpret MEDLINE abstracts. Meaning-based search of MEDLINE abstracts yields high precision (estimated at >90%), and high recall (estimated at >90%), where synonym information has been encoded. The present implementation can be found at http://MEDLINE.cognition.com. 
&#xa

Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences

Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the European Commission press release are particularly notable. It has long been accepted that building research on the foundations laid by other scientists is both effective and efficient. Regrettably, some disciplines, chemistry being one, have been slow to recognise the value of sharing and have thus been reluctant to curate their data and information in preparation for exchanging it. The very significant increases in both the volume and the complexity of the datasets produced has encouraged the expansion of e-Research, and stimulated the development of methodologies for managing, organising, and analysing "big data". We review the evolution of cheminformatics, the amalgam of chemistry, computer science, and information technology, and assess the wider e-Science and e-Research perspective. Chemical information does matter, as do matters of communicating data and collaborating with data. For chemistry, unique identifiers, structure representations, and property descriptors are essential to the activities of sharing and exchange. Open science entails the sharing of more than mere facts: for example, the publication of negative outcomes can facilitate better understanding of which synthetic routes to choose, an aspiration of the Dial-a-Molecule Grand Challenge. The protagonists of open notebook science go even further and exchange their thoughts and plans. We consider the concepts of preservation, curation, provenance, discovery, and access in the context of the research lifecycle, and then focus on the role of metadata, particularly the ontologies on which the emerging chemical Semantic Web will depend. Among our conclusions, we present our choice of the "grand challenges" for the preservation and sharing of chemical information