Semantic integration

Abstract: Preface 1. What is the Philosophy of Information? 2. Open Problems in the Philosophy of Information 3. The Method of Levels of Abstraction 4. Semantic Information and the Veridicality Thesis 5. Outline of a Theory of Strongly Semantic Information 6. The Symbol Grounding Problem 7. Action-Based Semantics 8. Semantic Information and the Correctness Theory of Truth 9. The Logical Unsolvability of the Gettier Problem 10. The Logic of Being Informed 11. Understanding Epistemic Relevance 12. Semantic Information and the Network Theory of Account 13. Consciousness, Agents and the Knowledge Game 14. Against Digital Ontology 15. A Defence of Informational Structural Realism References

Abstract: Ontologies play a prominent role on the Semantic Web. They make possible the widespread publication of machine understandable data, opening myriad opportunities for automated information processing. However, because of the Semantic Web's distributed nature, data on it will inevitably come from many different ontologies. Information processing across ontologies is not possible without knowing the semantic mappings between their elements. Manually finding such mappings is tedious, error-prone, and clearly not possible at the Web scale. Hence, the development of tools to assist in the ontology mapping process is crucial to the success of the Semantic Web.We describe glue, a system that employs machine learning techniques to find such mappings. Given two ontologies, for each concept in one ontology glue finds the most similar concept in the other ontology. We give well-founded probabilistic definitions to several practical similarity measures, and show that glue can work with all of them. This is in contrast to most existing approaches, which deal with a single similarity measure. Another key feature of glue is that it uses multiple learning strategies, each of which exploits a different type of information either in the data instances or in the taxonomic structure of the ontologies. To further improve matching accuracy, we extend glue to incorporate commonsense knowledge and domain constraints into the matching process. For this purpose, we show that relaxation labeling, a well-known constraint optimization technique used in computer vision and other fields, can be adapted to work efficiently in our context. Our approach is thus distinguished in that it works with a variety of well-defined similarity notions and that it efficiently incorporates multiple types of knowledge. We describe a set of experiments on several real-world domains, and show that glue proposes highly accurate semantic mappings.

Abstract: The Disease Ontology (DO) database (http://disease-ontology.org) represents a comprehensive knowledge base of 8043 inherited, developmental and acquired human diseases (DO version 3, revision 2510). The DO web browser has been designed for speed, efficiency and robustness through the use of a graph database. Full-text contextual searching functionality using Lucene allows the querying of name, synonym, definition, DOID and cross-reference (xrefs) with complex Boolean search strings. The DO semantically integrates disease and medical vocabularies through extensive cross mapping and integration of MeSH, ICD, NCI's thesaurus, SNOMED CT and OMIM disease-specific terms and identifiers. The DO is utilized for disease annotation by major biomedical databases (e.g. Array Express, NIF, IEDB), as a standard representation of human disease in biomedical ontologies (e.g. IDO, Cell line ontology, NIFSTD ontology, Experimental Factor Ontology, Influenza Ontology), and as an ontological cross mappings resource between DO, MeSH and OMIM (e.g. GeneWiki). The DO project (http://diseaseontology.sf.net) has been incorporated into open source tools (e.g. Gene Answers, FunDO) to connect gene and disease biomedical data through the lens of human disease. The next iteration of the DO web browser will integrate DO's extended relations and logical definition representation along with these biomedical resource cross-mappings.

Abstract: In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies have been published in the last few years describing and evaluating diverse approaches. Semantic similarity has become a valuable tool for validating the results drawn from biomedical studies such as gene clustering, gene expression data analysis, prediction and validation of molecular interactions, and disease gene prioritization. We review semantic similarity measures applied to biomedical ontologies and propose their classification according to the strategies they employ: node-based versus edge-based and pairwise versus groupwise. We also present comparative assessment studies and discuss the implications of their results. We survey the existing implementations of semantic similarity measures, and we describe examples of applications to biomedical research. This will clarify how biomedical researchers can benefit from semantic similarity measures and help them choose the approach most suitable for their studies. Biomedical ontologies are evolving toward increased coverage, formality, and integration, and their use for annotation is increasingly becoming a focus of both effort by biomedical experts and application of automated annotation procedures to create corpora of higher quality and completeness than are currently available. Given that semantic similarity measures are directly dependent on these evolutions, we can expect to see them gaining more relevance and even becoming as essential as sequence similarity is today in biomedical research.