Desiderata for domain reference ontologies in biomedicine

AbstractDomain reference ontologies represent knowledge about a particular part of the world in a way that is independent from specific objectives, through a theory of the domain. An example of reference ontology in biomedical informatics is the Foundational Model of Anatomy (FMA), an ontology of anatomy that covers the entire range of macroscopic, microscopic, and subcellular anatomy. The purpose of this paper is to explore how two domain reference ontologies—the FMA and the Chemical Entities of Biological Interest (ChEBI) ontology, can be used (i) to align existing terminologies, (ii) to infer new knowledge in ontologies of more complex entities, and (iii) to manage and help reasoning about individual data. We analyze those kinds of usages of these two domain reference ontologies and suggest desiderata for reference ontologies in biomedicine. While a number of groups and communities have investigated general requirements for ontology design and desiderata for controlled medical vocabularies, we are focusing on application purposes. We suggest five desirable characteristics for reference ontologies: good lexical coverage, good coverage in terms of relations, compatibility with standards, modularity, and ability to represent variation in reality

Conjunctive Queries: Unique Characterizations and Exact Learnability

We answer the question of which conjunctive queries are uniquely characterized by polynomially many positive and negative examples, and how to construct such examples efficiently. As a consequence, we obtain a new efficient exact learning algorithm for a class of conjunctive queries. At the core of our contributions lie two new polynomial-time algorithms for constructing frontiers in the homomorphism lattice of finite structures. We also discuss implications for the unique characterizability and learnability of schema mappings and of description logic concepts

Standard and Non-standard reasoning in Description Logics

The present work deals with Description Logics (DLs), a class of knowledge representation formalisms used to represent and reason about classes of individuals and relations between such classes in a formally well-defined way. We provide novel results in three main directions. (1) Tractable reasoning revisited: in the 1990s, DL research has largely answered the question for practically relevant yet tractable DL formalisms in the negative. Due to novel application domains, especially the Life Sciences, and a surprising tractability result by Baader, we have re-visited this question, this time looking in a new direction: general terminologies (TBoxes) and extensions thereof defined over the DL EL and extensions thereof. As main positive result, we devise EL++(D)-CBoxes as a tractable DL formalism with optimal expressivity in the sense that every additional standard DL constructor, every extension of the TBox formalism, or every more powerful concrete domain, makes reasoning intractable. (2) Non-standard inferences for knowledge maintenance: non-standard inferences, such as matching, can support domain experts in maintaining DL knowledge bases in a structured and well-defined way. In order to extend their availability and promote their use, the present work extends the state of the art of non-standard inferences both w.r.t. theory and implementation. Our main results are implementations and performance evaluations of known matching algorithms for the DLs ALE and ALN, optimal non-deterministic polynomial time algorithms for matching under acyclic side conditions in ALN and sublanguages, and optimal algorithms for matching w.r.t. cyclic (and hybrid) EL-TBoxes. (3) Non-standard inferences over general concept inclusion (GCI) axioms: the utility of GCIs in modern DL knowledge bases and the relevance of non-standard inferences to knowledge maintenance naturally motivate the question for tractable DL formalism in which both can be provided. As main result, we propose hybrid EL-TBoxes as a solution to this hitherto open question

Quantitative Variants of Language Equations and their Applications to Description Logics

Unification in description logics (DLs) has been introduced as a novel inference service that can be used to detect redundancies in ontologies, by finding different concepts that may potentially stand for the same intuitive notion. Together with the special case of matching, they were first investigated in detail for the DL FL0, where these problems can be reduced to solving certain language equations. In this thesis, we extend this service in two directions. In order to increase the recall of this method for finding redundancies, we introduce and investigate the notion of approximate unification, which basically finds pairs of concepts that “almost” unify, in order to account for potential small modelling errors. The meaning of “almost” is formalized using distance measures between concepts. We show that approximate unification in FL0 can be reduced to approximately solving language equations, and devise algorithms for solving the latter problem for particular distance measures. Furthermore, we make a first step towards integrating background knowledge, formulated in so-called TBoxes, by investigating the special case of matching in the presence of TBoxes of different forms. We acquire a tight complexity bound for the general case, while we prove that the problem becomes easier in a restricted setting. To achieve these bounds, we take advantage of an equivalence characterization of FL0 concepts that is based on formal languages. In addition, we incorporate TBoxes in computing concept distances. Even though our results on the approximate setting cannot deal with TBoxes yet, we prepare the framework that future research can build on. Before we journey to the technical details of the above investigations, we showcase our program in the simpler setting of the equational theory ACUI, where we are able to also combine the two extensions. In the course of studying the above problems, we make heavy use of automata theory, where we also derive novel results that could be of independent interest