Clinical Bioinformatics: challenges and opportunities

Background: Network Tools and Applications in Biology (NETTAB) Workshops are a series of meetings focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. The NETTAB 2011 workshop, held in Pavia, Italy, in October 2011 was aimed at presenting some of the most relevant methods, tools and infrastructures that are nowadays available for Clinical Bioinformatics (CBI), the research field that deals with clinical applications of bioinformatics. Methods: In this editorial, the viewpoints and opinions of three world CBI leaders, who have been invited to participate in a panel discussion of the NETTAB workshop on the next challenges and future opportunities of this field, are reported. These include the development of data warehouses and ICT infrastructures for data sharing, the definition of standards for sharing phenotypic data and the implementation of novel tools to implement efficient search computing solutions. Results: Some of the most important design features of a CBI-ICT infrastructure are presented, including data warehousing, modularity and flexibility, open-source development, semantic interoperability, integrated search and retrieval of –omics information. Conclusions: Clinical Bioinformatics goals are ambitious. Many factors, including the availability of high-throughput “-omics” technologies and equipment, the widespread availability of clinical data warehouses and the noteworthy increase in data storage and computational power of the most recent ICT systems, justify research and efforts in this domain, which promises to be a crucial leveraging factor for biomedical research

Getting More out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics.

This software article describes the GATE family of open source text analysis tools and processes. GATE is one of the most widely used systems of its type with yearly download rates of tens of thousands and many active users in both academic and industrial contexts. In this paper we report three examples of GATE-based systems operating in the life sciences and in medicine. First, in genome-wide association studies which have contributed to discovery of a head and neck cancer mutation association. Second, medical records analysis which has significantly increased the statistical power of treatment/ outcome models in the UK’s largest psychiatric patient cohort. Third, richer constructs in drug-related searching. We also explore the ways in which the GATE family supports the various stages of the lifecycle present in our examples. We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies this process can be made defined and repeatable. The GATE research programme is now 20 years old and has grown from its roots as a specialist development tool for text processing to become a rather comprehensive ecosystem, bringing together software developers, language engineers and research staff from diverse fields. GATE now has a strong claim to cover a uniquely wide range of the lifecycle of text analysis systems. It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors’ own group) who work in text processing for biomedicine and other areas. GATE is available online ,1. under GNU open source licences and runs on all major operating systems. Support is available from an active user and developer community and also on a commercial basis

Distribution of immunodeficiency fact files with XML – from Web to WAP

BACKGROUND: Although biomedical information is growing rapidly, it is difficult to find and retrieve validated data especially for rare hereditary diseases. There is an increased need for services capable of integrating and validating information as well as proving it in a logically organized structure. A XML-based language enables creation of open source databases for storage, maintenance and delivery for different platforms. METHODS: Here we present a new data model called fact file and an XML-based specification Inherited Disease Markup Language (IDML), that were developed to facilitate disease information integration, storage and exchange. The data model was applied to primary immunodeficiencies, but it can be used for any hereditary disease. Fact files integrate biomedical, genetic and clinical information related to hereditary diseases. RESULTS: IDML and fact files were used to build a comprehensive Web and WAP accessible knowledge base ImmunoDeficiency Resource (IDR) available at . A fact file is a user oriented user interface, which serves as a starting point to explore information on hereditary diseases. CONCLUSION: The IDML enables the seamless integration and presentation of genetic and disease information resources in the Internet. IDML can be used to build information services for all kinds of inherited diseases. The open source specification and related programs are available at

Report on the 2015 NSF Workshop on Unified Annotation Tooling

On March 30 & 31, 2015, an international group of twenty-three researchers with expertise in linguistic annotation convened in Sunny Isles Beach, Florida to discuss problems with and potential solutions for the state of linguistic annotation tooling. The participants comprised 14 researchers from the U.S. and 9 from outside the U.S., with 7 countries and 4 continents represented, and hailed from fields and specialties including computational linguistics, artificial intelligence, speech processing, multi-modal data processing, clinical & medical natural language processing, linguistics, documentary linguistics, sign-language linguistics, corpus linguistics, and the digital humanities. The motivating problem of the workshop was the balkanization of annotation tooling, namely, that even though linguistic annotation requires sophisticated tool support to efficiently generate high-quality data, the landscape of tools for the field is fractured, incompatible, inconsistent, and lacks key capabilities. The overall goal of the workshop was to chart the way forward, centering on five key questions: (1) What are the problems with current tool landscape? (2) What are the possible benefits of solving some or all of these problems? (3) What capabilities are most needed? (4) How should we go about implementing these capabilities? And, (5) How should we ensure longevity and sustainability of the solution? I surveyed the participants before their arrival, which provided significant raw material for ideas, and the workshop discussion itself resulted in identification of ten specific classes of problems, five sets of most-needed capabilities. Importantly, we identified annotation project managers in computational linguistics as the key recipients and users of any solution, thereby succinctly addressing questions about the scope and audience of potential solutions. We discussed management and sustainability of potential solutions at length. The participants agreed on sixteen recommendations for future work. This technical report contains a detailed discussion of all these topics, a point-by-point review of the discussion in the workshop as it unfolded, detailed information on the participants and their expertise, and the summarized data from the surveys

KG-Hub-building and exchanging biological knowledge graphs.

MOTIVATION: Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking. RESULTS: Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract-transform-load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification. AVAILABILITY AND IMPLEMENTATION: https://kghub.org

Improving the Quality and Utility of Electronic Health Record Data through Ontologies

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs

Development of linguistic linked open data resources for collaborative data-intensive research in the language sciences

Making diverse data in linguistics and the language sciences open, distributed, and accessible: perspectives from language/language acquistiion researchers and technical LOD (linked open data) researchers. This volume examines the challenges inherent in making diverse data in linguistics and the language sciences open, distributed, integrated, and accessible, thus fostering wide data sharing and collaboration. It is unique in integrating the perspectives of language researchers and technical LOD (linked open data) researchers. Reporting on both active research needs in the field of language acquisition and technical advances in the development of data interoperability, the book demonstrates the advantages of an international infrastructure for scholarship in the field of language sciences. With contributions by researchers who produce complex data content and scholars involved in both the technology and the conceptual foundations of LLOD (linguistics linked open data), the book focuses on the area of language acquisition because it involves complex and diverse data sets, cross-linguistic analyses, and urgent collaborative research. The contributors discuss a variety of research methods, resources, and infrastructures. Contributors Isabelle Barrière, Nan Bernstein Ratner, Steven Bird, Maria Blume, Ted Caldwell, Christian Chiarcos, Cristina Dye, Suzanne Flynn, Claire Foley, Nancy Ide, Carissa Kang, D. Terence Langendoen, Barbara Lust, Brian MacWhinney, Jonathan Masci, Steven Moran, Antonio Pareja-Lora, Jim Reidy, Oya Y. Rieger, Gary F. Simons, Thorsten Trippel, Kara Warburton, Sue Ellen Wright, Claus Zin