By Peter N. Robinson
Introduction to Bio-Ontologies explores the computational heritage of ontologies. Emphasizing computational and algorithmic concerns surrounding bio-ontologies, this self-contained textual content is helping readers comprehend ontological algorithms and their applications.
The first a part of the ebook defines ontology and bio-ontologies. It additionally explains the significance of mathematical good judgment for knowing strategies of inference in bio-ontologies, discusses the likelihood and facts themes useful for figuring out ontology algorithms, and describes ontology languages, together with OBO (the preeminent language for bio-ontologies), RDF, RDFS, and OWL.
The moment half covers major bio-ontologies and their purposes. The booklet offers the Gene Ontology; upper-level ontologies, similar to the elemental Formal Ontology and the Relation Ontology; and present bio-ontologies, together with a number of anatomy ontologies, Chemical Entities of organic curiosity, series Ontology, Mammalian Phenotype Ontology, and Human Phenotype Ontology.
The 3rd a part of the textual content introduces the most important graph-based algorithms for bio-ontologies. The authors speak about how those algorithms are utilized in overrepresentation research, model-based strategies, semantic similarity research, and Bayesian networks for molecular biology and biomedical applications.
With a spotlight on computational reasoning themes, the ultimate half describes the ontology languages of the Semantic internet and their purposes for inference. It covers the formal semantics of RDF and RDFS, OWL inference principles, a key inference set of rules, the SPARQL question language, and the state-of-the-art for querying OWL ontologies.
Software and information designed to enrich fabric within the textual content can be found at the book’s web site: http://bio-ontologies-book.org the location offers the R Robo package deal constructed for the ebook, besides a compressed archive of information and ontology records utilized in the various workouts. It additionally deals teaching/presentation slides and hyperlinks to different proper websites.
This booklet presents readers with the root to take advantage of ontologies as a place to begin for brand new bioinformatics study tasks or to help present molecular genetics learn initiatives. via delivering a self-contained advent to OBO ontologies and the Semantic net, it bridges the space among either fields and is helping readers see what each one can give a contribution to the research and knowing of biomedical data.
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Additional resources for Introduction to Bio-Ontologies
While statements of facts (propositions) were the basic building blocks of propositional logic, predicates are the building blocks of first-order logic. Predicates are a means of defining properties and relations among the things in a domain. FOL also uses function symbols, which are often written as lower case letters such as f or g. A function can be used for a relation which assigns to objects of the domain of the function exactly one object in the range. Thus, if we know that x is the mother of y and m is a function that represents the relation “is mother of,” then m(y) will return x.
6). 6: Interpretations and connectives in FOL. The left column is true if and only if the right column is true. ⊧: entails; ⊭: does not entail. 6 A formula is said to be satisfiable if it is true under at least one interpretation. Otherwise, it is said to be unsatisfiable (or inconsistent). Interpretations form the background of proof procedures in FOL, whereby certain formulas called axioms are assumed to be true, and a proof is generated by applying a series of formulas derived from axioms, definitions, or previous formulas by applying inference rules.
On the other hand, we write x ∈/ S to denote that S doesn’t contain x, that is, x is not a member of S. Note that x has been used a placeholder for an arbitrary element, which is commonly referred to as a variable. As we will see later, being (or not being) a member of a set S is a property of the element x that is assigned to a set. There are many ways of defining sets. The easiest way is to enumerate the elements of which the set consists. Another possibility is to name the properties of the elements.