Semantic Computing

Integrating Wiki Systems, Natural Language Processing, and Semantic Technologies for Cultural Heritage Data Management

Abstract

Modern documents can easily be structured and augmented to have the characteristics of a semantic knowledge base. Many older documents may also hold a trove of knowledge that would deserve to be organized as such a knowledge base. In this chapter, we show that modern semantic technologies offer the means to make these heritage documents accessible by transforming them into a semantic knowledge base. Using techniques from natural language processing and Semantic Computing, we automatically populate an ontology. Additionally, all content is made accessible in a user-friendly Wiki interface, combining original text with NLP-derived metadata and adding annotation capabilities for collaborative use. All these functions are combined into a single, cohesive system architecture that addresses the different requirements from end users, software engineering aspects, and knowledge discovery paradigms. The ideas were implemented and tested with a volume from the historic Encyclopedia of Architecture and a number of different user groups.

Algorithms and semantic infrastructure for mutation impact extraction and grounding

Abstract

Mutation Impact OntologyMutation Impact Ontology

Background

Mutation impact extraction is a hitherto unaccomplished task in state of the art mutation extraction systems. Protein mutations and their impacts on protein properties are hidden in scientific literature, making them poorly accessible for protein engineers and inaccessible for phenotype-prediction systems that currently depend on manually curated genomic variation databases.

Results

We present the first rule-based approach for the extraction of mutation impacts on protein properties, categorizing their directionality as positive, negative or neutral. Furthermore protein and mutation mentions are grounded to their respective UniProtKB IDs and selected protein properties, namely protein functions to concepts found in the Gene Ontology. The extracted entities are populated to an OWL-DL Mutation Impact ontology facilitating complex querying for mutation impacts using SPARQL. We illustrate retrieval of proteins and mutant sequences for a given direction of impact on specific protein properties. Moreover we provide programmatic access to the data through semantic web services using the SADI (Semantic Automated Discovery and Integration) framework.

Conclusion

We address the problem of access to legacy mutation data in unstructured form through the creation of novel mutation impact extraction methods which are evaluated on a corpus of full-text articles on haloalkane dehalogenases, tagged by domain experts. Our approaches show state of the art levels of precision and recall for Mutation Grounding and respectable level of precision but lower recall for the task of Mutant-Impact relation extraction. The system is deployed using text mining and semantic web technologies with the goal of publishing to a broad spectrum of consumers.

Ontology-Based Extraction and Summarization of Protein Mutation Impact Information

Introduction

Poster at BioNLP 2010: Ontology-Based Extraction and Summarization of Protein Mutation Impact InformationPoster at BioNLP 2010: Ontology-Based Extraction and Summarization of Protein Mutation Impact InformationNLP methods for extracting mutation information from the bibliome have become an important new research area within bio-NLP, as manually curated databases, like the Protein Mutant Database (PMD) (Kawabata et al., 1999), cannot keep up with the rapid pace of mutation research. However, while significant progress has been made with respect to mutation detection, the automated extraction of the impacts of these mutations has so far not been targeted. In this paper, we describe the first work to automatically summarize impact information from protein mutations. Our approach is based on populating an OWL-DL ontology with impact information, which can then be queried to provide structured information, including a summary.

Semantic Content Access using Domain-Independent NLP Ontologies

Abstract

We present a lightweight, user-centred approach for document navigation and analysis that is based on an ontology of text mining results. This allows us to bring the result of existing text mining pipelines directly to end users. Our approach is domain-independent and relies on existing NLP analysis tasks such as automatic multi-document summarization, clustering, question-answering, and opinion mining. Users can interactively trigger semantic processing services for tasks such as analyzing product reviews, daily news, or other document sets.

Leverage of OWL-DL axioms in a Contact Centre for Technical Product Support

Abstract

Real-time access to complex knowledge is a business driver in the contact centre environment. In this paper we outline for the domain of telecom technical product support a knowledge sharing paradigm in which a desktop client annotates named entities in technical documents with canonical names, class names or relevant class axioms, derived from an ontology by means of a web services framework. We described the system and its core components; OWL-DL telecom hardware ontology, ontological-natural language processing pipeline, an ontology axiom?extractor; and the Semantic Assistants framework.

Flexible Ontology Population from Text: The OwlExporter

Abstract

Ontology population from text is becoming increasingly important for NLP applications. Ontologies in OWL format provide for a standardized means of modeling, querying, and reasoning over large knowledge bases. Populated from natural language texts, they offer significant advantages over traditional export formats, such as plain XML. The development of text analysis systems has been greatly facilitated by modern NLP frameworks, such as the General Architecture for Text Engineering (GATE). However, ontology population is not currently supported by a standard component. We developed a GATE resource called the OwlExporter that allows to easily map existing NLP analysis pipelines to OWL ontologies, thereby allowing language engineers to create ontology population systems without requiring extensive knowledge of ontology APIs. A particular feature of our approach is the concurrent population and linking of a domain- and NLP-ontology, including NLP-specific features such as safe reasoning over coreference chains.

Converting a Historical Architecture Encyclopedia into a Semantic Knowledge Base

Abstract

Digitizing a historical document using ontologies and natural language processing techniques can transform it from arcane text to a useful knowledge base.

Semantic Assistants: SOA for Text Mining

With the rapidly growing amount of information available, employees spend an ever-increasing proportion of their time searching for the right information. Information overload has become a serious threat to productivity. We address this challenge with a service-oriented architecture that integrates semantic natural language processing services into desktop applications.

A Quality Perspective of Evolvability Using Semantic Analysis

Abstract

Software development and maintenance are highly distributed processes that involve a multitude of supporting tools and resources. Knowledge relevant to these resources is typically dispersed over a wide range of artifacts, representation formats, and abstraction levels. In order to stay competitive, organizations are often required to assess and provide evidence that their software meets the expected requirements. In our research, we focus on assessing non-functional quality requirements, specifically evolvability, through semantic modeling of relevant software artifacts. We introduce our SE-Advisor that supports the integration of knowledge resources typically found in software ecosystems by providing a unified ontological representation. We further illustrate how our SE-Advisor takes advantage of this unified representation to support the analysis and assessment of different types of quality attributes related to the evolvability of software ecosystems.

Semantic Assistants – User-Centric Natural Language Processing Services for Desktop Clients

Abstract

Semantic Assistants Workflow OverviewSemantic Assistants Workflow OverviewToday's knowledge workers have to spend a large amount of time and manual effort on creating, analyzing, and modifying textual content. While more advanced semantically-oriented analysis techniques have been developed in recent years, they have not yet found their way into commonly used desktop clients, be they generic (e.g., word processors, email clients) or domain-specific (e.g., software IDEs, biological tools). Instead of forcing the user to leave his current context and use an external application, we propose a ``Semantic Assistants'' approach, where semantic analysis services relevant for the user's current task are offered directly within a desktop application. Our approach relies on an OWL ontology model for context and service information and integrates external natural language processing (NLP) pipelines through W3C Web services.

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