SWAT4LS

The genome-wide association study (GWAS) database - GWAS Central (http://www.gwascentral.org) - allows the sophisticated interrogation and comparison of summary-level GWAS data. Here we present the application of ontologies within GWAS Central for the ...

A major challenge of linked data is resolving the many different identifiers representing the same object Interconnecting the data requires mappings between the vocabularies and identifiers used in different data sets. To help with this issue, we have ...

Advances in DNA synthesis technology have enabled the design of novel genomes. Semantic web will improve the capability of genome design tools for integrating experimental data to guide the DNA design process. Here we review software tools, suggest ...

Sharing and describing experimental results unambiguously with sufficient detail to enable replication of results is a fundamental tenet of scientific research. In today's cluttered world of "-omics" sciences, data standards and standardized use of ...

Ontologies, structured vocabularies and terminologies are used as knowledge organization system (KOS) for building knowledge-based applications. KOS are used for facilitating sharing data and the Linked Open Data initiative has opened new perspectives ...

In biomedical sciences new and increasingly complex technologies are constantly being introduced, and to facilitate new scientific discoveries they need to be able to adapt to current demands and provide seamless functionality. However, the ...

Biomedical ontologies are key to the success of Semantic Web technologies in Life Sciences; therefore, it is important to provide appropriate tools for their development and further exploitation. The Ontology Pre Processor Language (OPPL) can be used ...

In this paper, we introduce the approach we are taking to generate a knowledge model for biomedical literature with the ultimate goal of improving information retrieval over our digital library and facilitating the discovery of hidden relationships ...

We have reviewed different approaches on community-based annotation on protein and gene sequences, mainly relying on the wiki paradigms. Currently such approaches are not fully exploiting the social component that naturally emerges within communities. ...

Life Sciences have emerged as a key domain in the Linked Data community because of the diversity of data semantics and formats available by means of a great variety of databases and web technologies. Thus, it has been used as the perfect domain for ...

The valuable Internet web of information is not sufficient to help computers leverage hidden meanings and assets just by using the HTML that renders data understandable to people. Institutions of the Linking Open Data movement have applied LOD ...

We describe a method for automating the detection and correction of spelling errors in the Foundational Model of Anatomy (FMA). The FMA was tokenized into 4893 distinct words; misspellings were identified and corrected using the National Library of ...

One of the main challenges for biomedical research lies in the integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms, for instance to explain the onset and progression of human diseases. ...

The beta phase of the 11^th revision of International Classification of Diseases (ICD-11) intends to accept public input through a distributed model of crowdsourcing. One of the core use cases is to create textual definitions for the ICD categories. The ...

In this paper we present a much improved version of LogMap, a highly scalable ontology matching system with 'built-in' reasoning and diagnosis capabilities. LogMap 2.0 is not only more scalable and robust than its predecessor, but it also provides the ...

Building an efficient SPAQRL query over the great variety of copious bio-medical Linked Open Data (LOD) requires users to understand the data schema, and makes it difficult for biologists to handle such data. To address this problem, we challenge to ...

In this paper, we address the issue of automatically adding U-Compare workflows to BioCatalogue by exploring the compatibility of UIMA to a REST-like web service. We aim to make workflows consisting of state-of-the-art text mining components available ...

With the proliferation of ontologies and their use in semantically-enabled applications, the issue of finding and repairing defects in ontologies has become increasingly important. In this paper we address the problem of defects in the is-a structure of ...

As the "omics" revolution unfolds, the growth in data quantity and diversity is pushing forward the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, ...

OWL 2 is commonly used to represent objects with complex structure, such as complex assemblies in engineering applications, human anatomy or the structure of chemical molecules [2]. Towards that direction, the European Bioinformatics Institute (EBI) has ...

Detecting planned and unplanned deviations from guidelines that give rise to patterns in ontologies can be difficult, even simply in terms of detecting regularities in a complex artefact. In this paper we demonstrate the usage of RIO; a framework for ...

The increasing amount of biomedical scientific literature published on the Web is demanding new tools and methods to automatically process and extract relevant information. Traditional information extraction has focused on recognizing well-defined ...

The vast amount of various life sciences data at RIKEN and other institutes including genome, transcriptome, proteome, metabolome, and phenome data are ontologically integrated into a common system. The challenge is to facilitate data retrieval, ...

Systematic study of clinical phenotypes is important to better understand the genetic basis of human diseases and more effective gene-based disease management. The Linked Clinical Data (LCD) project at Mayo Clinic aims to develop a semantics-driven ...

Two notable trends currently impacting biology curation are 1) the use of wikis to input, store, and disseminate research data and 2) the development of semantic technologies to facilitate higher-order data description and exploration. These separate ...

Open metadata registries are a fundamental tool for researchers in the Life Sciences trying to locate resources such as web services or databases. While sophisticated standards have been produced for annotating these resources with rich, well-structured ...

Clinical Intelligence, as a research and engineering discipline, is dedicated to the development of tools for data analysis for the purposes of clinical research, surveillance and rational health care management. Ad hoc querying of clinical data is one ...

We introduce CLI-mate, a framework to facilitate development of user-friendly interfaces for command line programs.

In the agile development environment of bioinformatics, many command line programs are created quickly to fill the gaps between complex ...

Integrating, visualizing and exploring Semantic Web data is the primary focus of the Sentient Knowledge Explorer (KE). To date, export of displayed data to arbitrary analytical tools has not been possible through the KE interface. Here we describe a ...

In the biomedical domain, Protégé and OBO-Edit are the main ontology editors supporting the manual construction of ontologies. Since manual creation is a laborious and hence costly process, there have been efforts to automate parts of this process. Here,...