Commonsense knowledge in cognitive robotics: a systematic literature review.

One of the big challenges in robotics is the generalization necessary for performing unknown tasks in unknown environments on unknown objects. For us humans, this challenge is simplified by the commonsense knowledge we can access. For cognitive robotics, representing and acquiring commonsense knowledge is a relevant problem, so we perform a systematic literature review to investigate the current state of commonsense knowledge exploitation in cognitive robotics. For this review, we combine a keyword search on six search engines with a snowballing search on six related reviews, resulting in 2,048 distinct publications. After applying pre-defined inclusion and exclusion criteria, we analyse the remaining 52 publications. Our focus lies on the use cases and domains for which commonsense knowledge is employed, the commonsense aspects that are considered, the datasets/resources used as sources for commonsense knowledge and the methods for evaluating these approaches. Additionally, we discovered a divide in terminology between research from the knowledge representation and reasoning and the cognitive robotics community. This divide is investigated by looking at the extensive review performed by Zech et al. (The International Journal of Robotics Research, 2019, 38, 518-562), with whom we have no overlapping publications despite the similar goals.

Ontology design patterns to disambiguate relations between genes and gene products in GENIA.

MOTIVATION: Annotated reference corpora play an important role in biomedical information extraction. A semantic annotation of the natural language texts in these reference corpora using formal ontologies is challenging due to the inherent ambiguity of natural language. The provision of formal definitions and axioms for semantic annotations offers the means for ensuring consistency as well as enables the development of verifiable annotation guidelines. Consistent semantic annotations facilitate the automatic discovery of new information through deductive inferences. RESULTS: We provide a formal characterization of the relations used in the recent GENIA corpus annotations. For this purpose, we both select existing axiom systems based on the desired properties of the relations within the domain and develop new axioms for several relations. To apply this ontology of relations to the semantic annotation of text corpora, we implement two ontology design patterns. In addition, we provide a software application to convert annotated GENIA abstracts into OWL ontologies by combining both the ontology of relations and the design patterns. As a result, the GENIA abstracts become available as OWL ontologies and are amenable for automated verification, deductive inferences and other knowledge-based applications. AVAILABILITY: Documentation, implementation and examples are available from http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/.

Applying the functional abnormality ontology pattern to anatomical functions.

BACKGROUND: Several biomedical ontologies cover the domain of biological functions, including molecular and cellular functions. However, there is currently no publicly available ontology of anatomical functions.Consequently, no explicit relation between anatomical structures and their functions is expressed in the anatomy ontologies that are available for various species. Such an explicit relation between anatomical structures and their functions would be useful both for defining the classes of the anatomy and the phenotype ontologies accurately. RESULTS: We provide an ontological analysis of functions and functional abnormalities. From this analysis, we derive an approach to the automatic extraction of anatomical functions from existing ontologies which uses a combination of natural language processing, graph-based analysis of the ontologies and formal inferences. Additionally, we introduce a new relation to link material objects to processes that realize the function of these objects. This relation is introduced to avoid a needless duplication of processes already covered by the Gene Ontology in a new ontology of anatomical functions. CONCLUSIONS: Ontological considerations on the nature of functional abnormalities and their representation in current phenotype ontologies show that we can extract a skeleton for an ontology of anatomical functions by using a combination of process, phenotype and anatomy ontologies automatically. We identify several limitations of the current ontologies that still need to be addressed to ensure a consistent and complete representation of anatomical functions and their abnormalities. AVAILABILITY: The source code and results of our analysis are available at http://bioonto.de.

Statistical tests for associations between two directed acyclic graphs.

Biological data, and particularly annotation data, are increasingly being represented in directed acyclic graphs (DAGs). However, while relevant biological information is implicit in the links between multiple domains, annotations from these different domains are usually represented in distinct, unconnected DAGs, making links between the domains represented difficult to determine. We develop a novel family of general statistical tests for the discovery of strong associations between two directed acyclic graphs. Our method takes the topology of the input graphs and the specificity and relevance of associations between nodes into consideration. We apply our method to the extraction of associations between biomedical ontologies in an extensive use-case. Through a manual and an automatic evaluation, we show that our tests discover biologically relevant relations. The suite of statistical tests we develop for this purpose is implemented and freely available for download.