Ontologies tend to be found everywhere. They are viewed as the silver bullet for many applications, such as database integration, peer-to-peer systems, e-commerce, semantic web services, or social networks. However, in open or evolving systems, such as the semantic web, different parties would, in general, adopt different ontologies. Thus, merely using ontologies, like using XML, does not reduce heterogeneity: it just raises heterogeneity problems to a higher level. Euzenat and Shvaikos book is devoted to ontology matching as a solution to the semantic heterogeneity problem faced by computer systems. Ontology matching aims at finding correspondences between semantically related entities of different ontologies. These correspondences may stand for equivalence as well as other relations, such as consequence, subsumption, or disjointness, between ontology entities. Many different matching solutions have been proposed so far from various viewpoints, e.g., databases, information systems, and artificial intelligence. The second edition of Ontology Matching has been thoroughly revised and updated to reflect the most recent advances in this quickly developing area, which resulted in more than 150 pages of new content. In particular, the book includes a new chapter dedicated to the methodology for performing ontology matching. It also covers emerging topics, such as data interlinking, ontology partitioning and pruning, context-based matching, matcher tuning, alignment debugging, and user involvement in matching, to mention a few. More than 100 state-of-the-art matching systems and frameworks were reviewed. With Ontology Matching, researchers and practitioners will find a reference book that presents currently available work in a uniform framework. In particular, the work and the techniques presented in this book can be equally applied to database schema matching, catalog integration, XML schema matching and other related problems. The objectives of the book include presenting (i) the state of the art and (ii) the latest research results in ontology matching by providing a systematic and detailed account of matching techniques and matching systems from theoretical, practical and application perspectives.

Ontology Matching

https://bura.brunel.ac.uk/bitstream/2438/13152/4/Fulltext.pdf

Critical analysis of Big Data challenges and analytical methods

After years of research on ontology matching, it is reasonable to consider several questions: is the field of ontology matching still making progress? Is this progress significant enough to pursue further research? If so, what are the particularly promising directions? To answer these questions, we review the state of the art of ontology matching and analyze the results of recent ontology matching evaluations. These results show a measurable improvement in the field, the speed of which is albeit slowing down. We conjecture that significant improvements can be obtained only by addressing important challenges for ontology matching. We present such challenges with insights on how to approach them, thereby aiming to direct research into the most promising tracks and to facilitate the progress of the field.

/pdf/ontology-matching-state-of-the-art-and-future-challenges-486jer3je8.pdf

Ontology Matching: State of the Art and Future Challenges

A survey of context modelling and reasoning techniques

https://re.public.polimi.it/bitstream/11311/1049863/2/Negri%20et%20al%202017%20FAIM.pdf

A Review of the Roles of Digital Twin in CPS-based Production Systems

The OWL 2 Web Ontology Language, informally OWL 2, is an ontology language for the Semantic Web with formally defined meaning. OWL 2 ontologies provide classes, properties, individuals, and data values and are stored as Semantic Web documents. OWL 2 ontologies can be used along with information written in RDF, and OWL 2 ontologies themselves are primarily exchanged as RDF documents. The OWL 2 Document Overview describes the overall state of OWL 2, and should be read before other OWL 2 documents. The meaningful constructs provided by OWL 2 are defined in terms of their structure. As well, a functional-style syntax is defined for these constructs, with examples and informal descriptions. One can reason with OWL 2 ontologies under either the RDF-Based Semantics [OWL 2 RDF-Based Semantics] or the Direct Semantics [OWL 2 Direct Semantics]. If certain restrictions on OWL 2 ontologies are satisfied and the ontology is in OWL 2 DL, reasoning under the Direct Semantics can be implemented using techniques well known in the literature.

/pdf/owl-2-web-ontology-language-structural-specification-and-16ue9glrem.pdf

OWL 2 Web Ontology Language: structural specification and functional-style syntax

The identification of drug-target interactions (DTIs) is a key task in drug discovery, where drugs are chemical compounds and targets are proteins.  Traditional DTI prediction methods are either time consuming (simulation-based methods) or heavily dependent on domain expertise (similarity-based and feature-based methods). In this work, we propose an end-to-end neural network model that predicts DTIs directly from low level representations.  In addition to making predictions, our model provides biological interpretation using two-way attention mechanism. Instead of using simplified settings where a dataset is evaluated as a whole, we designed an evaluation dataset from BindingDB following more realistic settings where predictions of unobserved examples (proteins and drugs) have to be made.  We experimentally compared our model with matrix factorization, similarity-based methods, and a previous deep learning approach.  Overall, the results show that our model outperforms other approaches without requiring domain knowledge and feature engineering.  In a case study, we illustrated the ability of our approach to provide biological insights to interpret the predictions.

/pdf/interpretable-drug-target-prediction-using-deep-neural-25csjhhsto.pdf

Interpretable Drug Target Prediction Using Deep Neural Representation

As collaborative, or network science spreads into more science, engineering and medical fields, both the participants and their funders have expressed a very strong desire for highly functional data and information capabilities that are a) easy to use, b) integrated in a variety of ways, c) leverage prior investments and keep pace with rapid technical change, and d) are not expensive or timeconsuming to build or maintain. In response, and based on our accummulated experience over the last decade and a maturing of several key semantic web approaches, we have adapted, extended, and integrated several open source applications and frameworks that handle major portions of functionality for these platforms. At minimum, these functions include: an object-type repository, collaboration tools, an ability to identify and manage all key entities in the platform, and an integrated portal to manage diverse content and applications, with varied access levels and privacy options. At the same time, there is increasing attention to how researchers present and explain results based on interpretation of increasingly diverse and heterogeneous data and information sources. With the renewed emphasis on good data practices, informatics practitioners have responded to this challenge with maturing informatics-based approaches. These approaches include, but are not limited to, use case development; information modeling and architectures; elaborating vocabularies; mediating interfaces to data and related services on the Web; and traceable provenance. The current era of data-intensive research presents numerous challenges to both individuals and research teams. In environmental science especially, sub-fields that were data-poor are becoming data-rich (volume, type and mode), while some that were largely model/ simulation driven are now dramatically shifting to data-driven or least to data-model assimilation approaches. These paradigm shifts make it very hard for researchers used to one mode to shift to another, let alone produce products of their work that are usable or understandable by non-specialists. However, it is exactly at these frontiers where much of the exciting environmental science needs to be performed and appreciated.

The Semantic Web - ISWC 2013

This paper describes a large case study that explores the applicability of ontology reasoning to problems in the medical domain. We investigate whether it is possible to use such reasoning to automate common clinical tasks that are currently labor intensive and error prone, and focus our case study on improving cohort selection for clinical trials. An obstacle to automating such clinical tasks is the need to bridge the semantic gulf between raw patient data, such as laboratory tests or specific medications, and the way a clinician interprets this data. Our key insight is that matching patients to clinical trials can be formulated as a problem of semantic retrieval. We describe the technical challenges to building a realistic case study, which include problems related to scalability, the integration of large ontologies, and dealing with noisy, inconsistent data. Our solution is based on the SNOMED CT ® ontology, and scales to one year of patient records (approx. 240, 000 patients).

/pdf/matching-patient-records-to-clinical-trials-using-ontologies-1osps467hm.pdf

Matching patient records to clinical trials using ontologies

We show that existing mature, relational optimizers can be exploited with a novel schema to give better performance for property graph storage and retrieval than popular noSQL graph stores. The schema combines relational storage for adjacency information with JSON storage for vertex and edge attributes. We demonstrate that this particular schema design has benefits compared to a purely relational or purely JSON solution. The query translation mechanism translates Gremlin queries with no side effects into SQL queries so that one can leverage relational query optimizers. We also conduct an empirical evaluation of our schema design and query translation mechanism with two existing popular property graph stores. We show that our system is 2-8 times better on query performance, and 10-30 times better in throughput on 4.3 billion edge graphs compared to existing stores.

https://static.googleusercontent.com/media/research.google.com/en//pubs/archive/43287.pdf

Achille Fokoue

Papers

OWL 2 Web Ontology Language: structural specification and functional-style syntax

Interpretable Drug Target Prediction Using Deep Neural Representation

The Semantic Web - ISWC 2013

Matching patient records to clinical trials using ontologies

SQLGraph: An Efficient Relational-Based Property Graph Store