Mapping Data to Ontologies with Exceptions Using Answer Set Programming

In ontology-based data access (OBDA), databases are connected to an ontology via mappings from queries over the database to queries over the ontology. In this paper, we define an ASP-based semantics for mappings from relational databases to first-order ontologies, augmented with queries over the ontology in the mapping rule bodies. The resulting formalism can be described as ”ASP modulo theories”, and can be used to express constraints and exceptions in OBDA systems, as well as being a powerful mechanism for succinctly representing OBDA mappings. Furthermore, we show that brave reasoning in this setting has either the same data complexity as ASP, or is at least as hard as the complexity of checking entailment for the ontology queries. Moreover, despite the interaction of ASP rules and the ontology, most properties of ASP are preserved. Finally, we show that for ontologies with UCQ-rewritable queries there exists a natural reduction from our framework to ASP with existential variables

Somatostatin receptors in GtoPdb v.2023.1

Somatostatin (somatotropin release inhibiting factor) is an abundant neuropeptide, which acts on five subtypes of somatostatin receptor (SST1-SST5; nomenclature as agreed by the NC-IUPHAR Subcommittee on Somatostatin Receptors [98]). Activation of these receptors produces a wide range of physiological effects throughout the body including the inhibition of secretion of many hormones. Endogenous ligands for these receptors are somatostatin-14 (SRIF-14) and somatostatin-28 (SRIF-28). cortistatin-14 has also been suggested to be an endogenous ligand for somatostatin receptors [61]

Somatostatin receptors (version 2019.4) in the IUPHAR/BPS Guide to Pharmacology Database

Somatostatin (somatotropin release inhibiting factor) is an abundant neuropeptide, which acts on five subtypes of somatostatin receptor (SST1-SST5; nomenclature as agreed by the NC-IUPHAR Subcommittee on Somatostatin Receptors [89]). Activation of these receptors produces a wide range of physiological effects throughout the body including the inhibition of secretion of many hormones. Endogenous ligands for these receptors are somatostatin-14 (SRIF-14) and somatostatin-28 (SRIF-28). cortistatin-14 has also been suggested to be an endogenous ligand for somatostatin receptors [56]

THE CONCISE GUIDE TO PHARMACOLOGY 2021/22: G protein-coupled receptors

The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes over 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/bph.15538. G protein-coupled receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2021, and supersedes data presented in the 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate

THE CONCISE GUIDE TO PHARMACOLOGY 2021/22: G protein-coupled receptors.

The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes over 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/bph.15538. G protein-coupled receptors are one of the six major pharmacological targets into which the Guide is divided, with the others being: ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2021, and supersedes data presented in the 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate

Template Libraries for Industrial Asset Maintenance: A Methodology for Scalable and Maintainable Ontologies

Data in engineering industries is highly standardized and information-dense, and usually distributed across many different sources with incompatible formats and implicit semantics. As such, it provides an ideal use case for application of semantic technologies for data integration and access. However, adoption of semantic technologies is hampered due to the complex set of competencies required to construct a scalable and maintainable ontology. We present a methodology for aiding domain experts and ontology engineers in constructing and maintaining industry-viable ontologies using a template-based approach for ontology modeling and instantiation. Using the OTTR framework, the structure of the input formats and the semantics of the target domain are modeled and maintained in separate modularized template libraries. Data provided by domain experts is mapped to these templates, allowing end-users to extend and amend the model without the need to directly interact with semantic technology languages and tools.Our approach is demonstrated on a real-world use case from the asset maintenance domain which has applicability to a wide range of industries

Generating Ontologies from Templates: A Rule-Based Approach for Capturing Regularity

We present a second-order language that can be used to succinctly specify ontologies in a consistent and transparent manner. This language is based on ontology templates (OTTR), a framework for capturing recurring patterns of axioms in ontological modelling. The language and our results are independent of any specific DL. We define the language and its semantics, including the case of negation-as-failure, investigate reasoning over ontologies specified using our language, and show results about the decidability of useful reasoning tasks about the language itself. We also state and discuss some open problems that we believe to be of interest.Comment: Technical report, extended version of paper accepted to DL Workshop 201

Practical Ontology Pattern Instantiation, Discovery, and Maintenance with Reasonable Ontology Templates

Reasonable Ontology Templates ( Open image in new window ) is a language for representing ontology modelling patterns in the form of parameterised ontologies. Ontology templates are simple and powerful abstractions useful for constructing, interacting with, and maintaining ontologies. With ontology templates, modelling patterns can be uniquely identified and encapsulated, broken down into convenient and manageable pieces, instantiated, and used as queries. Formal relations defined over templates support sophisticated maintenance tasks for sets of templates, such as revealing redundancies and suggesting new templates for representing implicit patterns. Ontology templates are designed for practical use; an Open image in new window vocabulary, convenient serialisation formats for the semantic web and for terse specification of template definitions and bulk instances are available, including an open source implementation for using templates. Our approach is successfully tested on a real-world large-scale ontology in the engineering domain