Background: Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery. Results: We developed the Translational Medicine Ontology (TMO) as a unifying ontology to integrate chemical, genomic and proteomic data with disease, treatment, and electronic health records. We demonstrate the use of Semantic Web technologies in the integration of patient and biomedical data, and reveal how such a knowledge base can aid physicians in providing tailored patient care and facilitate the recruitment of patients into active clinical trials. Thus, patients, physicians and researchers may explore the knowledge base to better understand therapeutic options, efficacy, and mechanisms of action. Conclusions: This work takes an important step in using Semantic Web technologies to facilitate integration of relevant, distributed, external sources and progress towards a computational platform to support personalized medicine. Availability: TMO can be downloaded from http://code.google.com/p/translationalmedicineontology and TMKB can be accessed at http://tm.semanticscience.org/sparql.

People can affect change in their eating patterns by substituting ingredients in recipes. Such substitutions may be motivated by specific goals, like modifying the intake of a specific nutrient or avoiding a particular category of ingredients. Determining how to modify a recipe can be difficult because people need to 1) identify which ingredients can act as valid replacements for the original and 2) figure out whether the substitution is “good” for their particular context, which may consider factors such as allergies, nutritional contents of individual ingredients, and other dietary restrictions. We propose an approach to leverage both explicit semantic information about ingredients, encapsulated in a knowledge graph of food, and implicit semantics, captured through word embeddings, to develop a substitutability heuristic to rank plausible substitute options automatically. Our proposed system also helps determine which ingredient substitution options are “healthy” using nutritional information and food classification constraints. We evaluate our substitutability heuristic, diet-improvement ingredient substitutability heuristic (DIISH), using a dataset of ground-truth substitutions scraped from ingredient substitution guides and user reviews of recipes, demonstrating that our approach can help reduce the human effort required to make recipes more suitable for specific dietary needs.

Data analysis used for biomedical research, particularly analysis involving metabolic or signaling pathways, is often based upon univariate statistical analysis. One common approach is to compute means and standard deviations individually for each variable or to determine where each variable falls between upper and lower bounds. Additionally, p-values are often computed to determine if there are differences between data taken from two groups. However, these approaches ignore that the collected data are often correlated in some form, which may be due to these measurements describing quantities that are connected by biological networks. Multivariate analysis approaches are more appropriate in these scenarios, as they can detect differences in datasets that the traditional univariate approaches may miss. This work presents three case studies that involve data from clinical studies of autism spectrum disorder that illustrate the need for and demonstrate the potential impact of multivariate analysis.