A platform for semantic web studies

The Semantic Web can be seen as a large, heterogeneous network of ontologies and semantic documents. Characterizing these ontologies, the way they relate and the way they are organized can help in better understanding how knowledge is produced and published online. It also provides new ways to explore and exploit this large collection of ontologies. In this paper, we present the foundation of a research platform for characterizing the Semantic Web, relying on the collection of ontologies and the functionalities provided by the Watson Semantic Web search engine. We more specifically focus on formalizing and monitoring relationships between ontologies online, considering a variety of different relations (similarity, versioning, agreement, modularity) and how they can help us obtaining meaningful overviews of the current state of the Semantic Web

LogMap family participation in the OAEI2018

We present the participation of LogMap and its variants in the OAEI 2018 campaign. The LogMap project started in January 2011 with the objective of developing a scalable and logic-based ontology matching system. This is our eight participation in the OAEI and the experience has so far been very positive. LogMap is one of the few systems that participates in (almost) all OAEI tracks

How orthogonal are the OBO Foundry ontologies?

<p>Abstract</p> <p>Background</p> <p>Ontologies in biomedicine facilitate information integration, data exchange, search and query of biomedical data, and other critical knowledge-intensive tasks. The OBO Foundry is a collaborative effort to establish a set of principles for ontology development with the eventual goal of creating a set of interoperable reference ontologies in the domain of biomedicine. One of the key requirements to achieve this goal is to ensure that ontology developers reuse term definitions that others have already created rather than create their own definitions, thereby making the ontologies orthogonal.</p> <p>Methods</p> <p>We used a simple lexical algorithm to analyze the extent to which the set of OBO Foundry candidate ontologies identified from September 2009 to September 2010 conforms to this vision. Specifically, we analyzed (1) the level of explicit term reuse in this set of ontologies, (2) the level of overlap, where two ontologies define similar terms independently, and (3) how the levels of reuse and overlap changed during the course of this year.</p> <p>Results</p> <p>We found that 30% of the ontologies reuse terms from other Foundry candidates and 96% of the candidate ontologies contain terms that overlap with terms from the other ontologies. We found that while term reuse increased among the ontologies between September 2009 and September 2010, the level of overlap among the ontologies remained relatively constant. Additionally, we analyzed the six ontologies announced as OBO Foundry members on March 5, 2010, and identified that the level of overlap was extremely low, but, notably, so was the level of term reuse.</p> <p>Conclusions</p> <p>We have created a prototype web application that allows OBO Foundry ontology developers to see which classes from their ontologies overlap with classes from other ontologies in the OBO Foundry (<url>http://obomap.bioontology.org</url>). From our analysis, we conclude that while the OBO Foundry has made significant progress toward orthogonality during the period of this study through increased adoption of explicit term reuse, a large amount of overlap remains among these ontologies. Furthermore, the characteristics of the identified overlap, such as the terms it comprises and its distribution among the ontologies, indicate that the achieving orthogonality will be exceptionally difficult, if not impossible.</p

PowerAqua: Open Question Answering on the Semantic Web

With the rapid growth of semantic information in the Web, the processes of searching and querying these very large amounts of heterogeneous content have become increasingly challenging. This research tackles the problem of supporting users in querying and exploring information across multiple and heterogeneous Semantic Web (SW) sources. A review of literature on ontology-based Question Answering reveals the limitations of existing technology. Our approach is based on providing a natural language Question Answering interface for the SW, PowerAqua. The realization of PowerAqua represents a considerable advance with respect to other systems, which restrict their scope to an ontology-specific or homogeneous fraction of the publicly available SW content. To our knowledge, PowerAqua is the only system that is able to take advantage of the semantic data available on the Web to interpret and answer user queries posed in natural language. In particular, PowerAqua is uniquely able to answer queries by combining and aggregating information, which can be distributed across heterogeneous semantic resources. Here, we provide a complete overview of our work on PowerAqua, including: the research challenges it addresses; its architecture; the techniques we have realised to map queries to semantic data, to integrate partial answers drawn from different semantic resources and to rank alternative answers; and the evaluation studies we have performed, to assess the performance of PowerAqua. We believe our experiences can be extrapolated to a variety of end-user applications that wish to open up to large scale and heterogeneous structured datasets, to be able to exploit effectively what possibly is the greatest wealth of data in the history of Artificial Intelligence

Building a biomedical ontology recommender web service

<p>Abstract</p> <p>Background</p> <p>Researchers in biomedical informatics use ontologies and terminologies to annotate their data in order to facilitate data integration and translational discoveries. As the use of ontologies for annotation of biomedical datasets has risen, a common challenge is to identify ontologies that are best suited to annotating specific datasets. The number and variety of biomedical ontologies is large, and it is cumbersome for a researcher to figure out which ontology to use.</p> <p>Methods</p> <p>We present the <it>Biomedical Ontology Recommender web service</it>. The system uses textual metadata or a set of keywords describing a domain of interest and suggests appropriate ontologies for annotating or representing the data. The service makes a decision based on three criteria. The first one is <it>coverage</it>, or the ontologies that provide most terms covering the input text. The second is <it>connectivity</it>, or the ontologies that are most often mapped to by other ontologies. The final criterion is <it>size</it>, or the number of concepts in the ontologies. The service scores the ontologies as a function of scores of the annotations created using the National Center for Biomedical Ontology (NCBO) <it>Annotator web service</it>. We used all the ontologies from the UMLS Metathesaurus and the NCBO BioPortal.</p> <p>Results</p> <p>We compare and contrast our Recommender by an exhaustive functional comparison to previously published efforts. We evaluate and discuss the results of several recommendation heuristics in the context of three real world use cases. The best recommendations heuristics, rated ‘very relevant’ by expert evaluators, are the ones based on coverage and connectivity criteria. The Recommender service (alpha version) is available to the community and is embedded into BioPortal.</p

LogMap family participation in the OAEI 2020

We present the participation of LogMap and its variants in the OAEI 2020 campaign. The LogMap project started in January 2011 with the objective of developing a scalable and logic-based ontology matching system. This is the ninth participation in the OAEI and the experience has so far been very positive. LogMap is one of the few systems that participates in (almost) all OAEI tracks

Visual analysis of anatomy ontologies and related genomic information

Challenges in scientific research include the difficulty in obtaining overviews of the large amount of data required for analysis, and in resolving the differences in terminology used to store and interpret information in multiple, independently created data sets. Ontologies provide one solution for analysis involving multiple data sources, improving cross-referencing and data integration. This thesis looks at harnessing advanced human perception to reduce the cognitive load in the analysis of the multiple, complex data sets the bioinformatics user group studied use in research, taking advantage also of users’ domain knowledge, to build mental models of data that map to its underlying structure. Guided by a user-centred approach, prototypes were developed to provide a visual method for exploring users’ information requirements and to identify solutions for these requirements. 2D and 3D node-link graphs were built to visualise the hierarchically structured ontology data, to improve analysis of individual and comparison of multiple data sets, by providing overviews of the data, followed by techniques for detailed analysis of regions of interest. Iterative, heuristic and structured user evaluations were used to assess and refine the options developed for the presentation and analysis of the ontology data. The evaluation results confirmed the advantages that visualisation provides over text-based analysis, and also highlighted the advantages of each of 2D and 3D for visual data analysis.Overseas Research Students Awards SchemeJames Watt Scholarshi

Is question answering fit for the Semantic Web? A survey

With the recent rapid growth of the Semantic Web (SW), the processes of searching and querying content that is both massive in scale and heterogeneous have become increasingly challenging. User-friendly interfaces, which can support end users in querying and exploring this novel and diverse, structured information space, are needed to make the vision of the SW a reality. We present a survey on ontology-based Question Answering (QA), which has emerged in recent years to exploit the opportunities offered by structured semantic information on the Web. First, we provide a comprehensive perspective by analyzing the general background and history of the QA research field, from influential works from the artificial intelligence and database communities developed in the 70s and later decades, through open domain QA stimulated by the QA track in TREC since 1999, to the latest commercial semantic QA solutions, before tacking the current state of the art in open userfriendly interfaces for the SW. Second, we examine the potential of this technology to go beyond the current state of the art to support end-users in reusing and querying the SW content. We conclude our review with an outlook for this novel research area, focusing in particular on the R&D directions that need to be pursued to realize the goal of efficient and competent retrieval and integration of answers from large scale, heterogeneous, and continuously evolving semantic sources