RegenBase: a knowledge base of spinal cord injury biology for translational research.

Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org

Data Model and Query Constructs for Versatile Web Query Languages

As the Semantic Web is gaining momentum, the need for truly versatile query languages becomes increasingly apparent. A Web query language is called versatile if it can access in the same query program data in different formats (e.g. XML and RDF). Most query languages are not versatile: they have not been specifically designed to cope with both worlds, providing a uniform language and common constructs to query and transform data in various formats. Moreover, most of them do not provide a flexible data model that is powerful enough to naturally convey both Semantic Web data formats (especially RDF and Topic Maps) and XML. This article highlights challenges related to the data model and language constructs for querying both standard Web and Semantic Web data with an emphasis on facilitating sophisticated reasoning. It is shown that Xcerpt’s data model and querying constructs are particularly well-suited for the Semantic Web, but that some adjustments of the Xcerpt syntax allow for even more effective and natural querying of RDF and Topic Maps

An infrastructure for building semantic web portals

In this paper, we present our KMi semantic web portal infrastructure, which supports two important tasks of semantic web portals, namely metadata extraction and data querying. Central to our infrastructure are three components: i) an automated metadata extraction tool, ASDI, which supports the extraction of high quality metadata from heterogeneous sources, ii) an ontology-driven question answering tool, AquaLog, which makes use of the domain specific ontology and the semantic metadata extracted by ASDI to answers questions in natural language format, and iii) a semantic search engine, which enhances traditional text-based searching by making use of the underlying ontologies and the extracted metadata. A semantic web portal application has been built, which illustrates the usage of this infrastructure

Identification of Design Principles

This report identifies those design principles for a (possibly new) query and transformation language for the Web supporting inference that are considered essential. Based upon these design principles an initial strawman is selected. Scenarios for querying the Semantic Web illustrate the design principles and their reflection in the initial strawman, i.e., a first draft of the query language to be designed and implemented by the REWERSE working group I4

Web and Semantic Web Query Languages

A number of techniques have been developed to facilitate powerful data retrieval on the Web and Semantic Web. Three categories of Web query languages can be distinguished, according to the format of the data they can retrieve: XML, RDF and Topic Maps. This article introduces the spectrum of languages falling into these categories and summarises their salient aspects. The languages are introduced using common sample data and query types. Key aspects of the query languages considered are stressed in a conclusion

Reasoning & Querying – State of the Art

Various query languages for Web and Semantic Web data, both for practical use and as an area of research in the scientific community, have emerged in recent years. At the same time, the broad adoption of the internet where keyword search is used in many applications, e.g. search engines, has familiarized casual users with using keyword queries to retrieve information on the internet. Unlike this easy-to-use querying, traditional query languages require knowledge of the language itself as well as of the data to be queried. Keyword-based query languages for XML and RDF bridge the gap between the two, aiming at enabling simple querying of semi-structured data, which is relevant e.g. in the context of the emerging Semantic Web. This article presents an overview of the field of keyword querying for XML and RDF

Survey over Existing Query and Transformation Languages

A widely acknowledged obstacle for realizing the vision of the Semantic Web is the inability of many current Semantic Web approaches to cope with data available in such diverging representation formalisms as XML, RDF, or Topic Maps. A common query language is the first step to allow transparent access to data in any of these formats. To further the understanding of the requirements and approaches proposed for query languages in the conventional as well as the Semantic Web, this report surveys a large number of query languages for accessing XML, RDF, or Topic Maps. This is the first systematic survey to consider query languages from all these areas. From the detailed survey of these query languages, a common classification scheme is derived that is useful for understanding and differentiating languages within and among all three areas

Querying a regulatory model for compliant building design audit

The ingredients for an effective automated audit of a building design include a BIM model containing the design information, an electronic regulatory knowledge model, and a practical method of processing these computerised representations. There have been numerous approaches to computer-aided compliance audit in the AEC/FM domain over the last four decades, but none has yet evolved into a practical solution. One reason is that they have all been isolated attempts that lack any form of standardisation. The current research project therefore focuses on using an open standard regulatory knowledge and BIM representations in conjunction with open standard executable compliant design workflows to automate the compliance audit process. This paper provides an overview of different approaches to access information from a regulatory model representation. The paper then describes the use of a purpose-built high-level domain specific query language to extract regulatory information as part of the effort to automate manual design procedures for compliance audit

Knowledge Rich Natural Language Queries over Structured Biological Databases

Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity are undeniable for obvious reasons, their engineering is far from simple. In most part, semantics and intent preserving mapping of a well understood natural language query expressed over a structured database schema to a structured query language is still a difficult task, and research to tame the complexity is intense. In this paper, we propose a multi-level knowledge-based middleware to facilitate such mappings that separate the conceptual level from the physical level. We augment these multi-level abstractions with a concept reasoner and a query strategy engine to dynamically link arbitrary natural language querying to well defined structured queries. We demonstrate the feasibility of our approach by presenting a Datalog based prototype system, called BioSmart, that can compute responses to arbitrary natural language queries over arbitrary databases once a syntactic classification of the natural language query is made