Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks.

BackgroundUsing knowledge representation for biomedical projects is now commonplace. In previous work, we represented the knowledge found in a college-level biology textbook in a fashion useful for answering questions. We showed that embedding the knowledge representation and question-answering abilities in an electronic textbook helped to engage student interest and improve learning. A natural question that arises from this success, and this paper's primary focus, is whether a similar approach is applicable across a range of life science textbooks. To answer that question, we considered four different textbooks, ranging from a below-introductory college biology text to an advanced, graduate-level neuroscience textbook. For these textbooks, we investigated the following questions: (1) To what extent is knowledge shared between the different textbooks? (2) To what extent can the same upper ontology be used to represent the knowledge found in different textbooks? (3) To what extent can the questions of interest for a range of textbooks be answered by using the same reasoning mechanisms?ResultsOur existing modeling and reasoning methods apply especially well both to a textbook that is comparable in level to the text studied in our previous work (i.e., an introductory-level text) and to a textbook at a lower level, suggesting potential for a high degree of portability. Even for the overlapping knowledge found across the textbooks, the level of detail covered in each textbook was different, which requires that the representations must be customized for each textbook. We also found that for advanced textbooks, representing models and scientific reasoning processes was particularly important.ConclusionsWith some additional work, our representation methodology would be applicable to a range of textbooks. The requirements for knowledge representation are common across textbooks, suggesting that a shared semantic infrastructure for the life sciences is feasible. Because our representation overlaps heavily with those already being used for biomedical ontologies, this work suggests a natural pathway to include such representations as part of the life sciences curriculum at different grade levels

Methionine Adenosyltransferase 1a (MAT1A) Enhances Cell Survival During Chemotherapy Treatment and is Associated with Drug Resistance in Bladder Cancer PDX Mice.

Bladder cancer is among the top ten most common cancers, with about ~380,000 new cases and ~150,000 deaths per year worldwide. Tumor relapse following chemotherapy treatment has long been a significant challenge towards completely curing cancer. We have utilized a patient-derived bladder cancer xenograft (PDX) platform to characterize molecular mechanisms that contribute to relapse following drug treatment in advanced bladder cancer. Transcriptomic profiling of bladder cancer xenograft tumors by RNA-sequencing analysis, before and after relapse, following a 21-day cisplatin/gemcitabine drug treatment regimen identified methionine adenosyltransferase 1a (MAT1A) as one of the significantly upregulated genes following drug treatment. Survey of patient tumor sections confirmed elevated levels of MAT1A in individuals who received chemotherapy. Overexpression of MAT1A in 5637 bladder cancer cells increased tolerance to gemcitabine and stalled cell proliferation rates, suggesting MAT1A upregulation as a potential mechanism by which bladder cancer cells persist in a quiescent state to evade chemotherapy

A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

New Frontiers of Quantified Self: Finding New Ways for Engaging Users in Collecting and Using Personal Data

In spite of the fast growth in the market of devices and applications that allow people to collect personal information, Quantified Self (QS) tools still present a variety of issues when they are used in everyday lives of common people. In this workshop we aim at exploring new ways for designing QS systems, by gathering different researchers in a unique place for imagining how the tracking, management, interpretation and visualization of personal data could be addressed in the future

A Process for Engineer Domain Ontology: An Experience in Developing Business Analysis Ontology

During the last years several works have been aimed to improve ontology technological as-pects, like representation language and inference mechanisms. This paper presents a discussion on the process and product of an experience in developing ontology for the public sector whose organization requires a strong knowledge management. This process is applied to engineer and develop ontology for Business analysis domain.Ontology, Ontology Engineering, Methodology, Protégé, Business Analysis

About the nature of Kansei information, from abstract to concrete

Designer’s expertise refers to the scientific fields of emotional design and kansei information. This paper aims to answer to a scientific major issue which is, how to formalize designer’s knowledge, rules, skills into kansei information systems. Kansei can be considered as a psycho-physiologic, perceptive, cognitive and affective process through a particular experience. Kansei oriented methods include various approaches which deal with semantics and emotions, and show the correlation with some design properties. Kansei words may include semantic, sensory, emotional descriptors, and also objects names and product attributes. Kansei levels of information can be seen on an axis going from abstract to concrete dimensions. Sociological value is the most abstract information positioned on this axis. Previous studies demonstrate the values the people aspire to drive their emotional reactions in front of particular semantics. This means that the value dimension should be considered in kansei studies. Through a chain of value-function-product attributes it is possible to enrich design generation and design evaluation processes. This paper describes some knowledge structures and formalisms we established according to this chain, which can be further used for implementing computer aided design tools dedicated to early design. These structures open to new formalisms which enable to integrate design information in a non-hierarchical way. The foreseen algorithmic implementation may be based on the association of ontologies and bag-of-words.AN

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