Biomedical semantics: the hub for biomedical research 2.0

The potential use of social media and other internet-related data and communications for child maltreatment surveillance and epidemiological research: Scoping review and recommendations

Collecting child maltreatment data is a complicated undertaking for many reasons. As a result, there is an interest by child maltreatment researchers to develop methodologies that allow for the triangulation of data sources. To better understand how social media and internet-based technologies could contribute to these approaches, we conducted a scoping review to provide an overview of social media and internet-based methodologies for health research, to report results of evaluation and validation research on these methods, and to highlight studies with potential relevance to child maltreatment research and surveillance. Many approaches were identified in the broad health literature; however, there has been limited application of these approaches to child maltreatment. The most common use was recruiting participants or engaging existing participants using online methods. From the broad health literature, social media and internet-based approaches to surveillance and epidemiologic research appear promising. Many of the approaches are relatively low cost and easy to implement without extensive infrastructure, but there are also a range of limitations for each method. Several methods have a mixed record of validation and sources of error in estimation are not yet understood or predictable. In addition to the problems relevant to other health outcomes, child maltreatment researchers face additional challenges, including the complex ethical issues associated with both internet-based and child maltreatment research. If these issues are adequately addressed, social media and internet-based technologies may be a promising approach to reducing some of the limitations in existing child maltreatment data.

Linked data and online classifications to organise mined patterns in patient data

In this paper, we investigate the use of web data resources in medicine, especially through medical classifications made available using the principles of Linked Data, to support the interpretation of patterns mined from patient care trajectories. Interpreting such patterns is naturally a challenge for an analyst, as it requires going through large amounts of results and access to sufficient background knowledge. We employ linked data, especially as exposed through the BioPortal system, to create a navigation structure within the patterns obtained form sequential pattern mining. We show how this approach provides a flexible way to explore data about trajectories of diagnoses and treatments according to different medical classifications.

A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources

In the Semantic Enrichment of the Scientific Literature (SESL) project, researchers from academia and from life science and publishing companies collaborated in a pre-competitive way to integrate and share information for type 2 diabetes mellitus (T2DM) in adults. This case study exposes benefits from semantic interoperability after integrating the scientific literature with biomedical data resources, such as UniProt Knowledgebase (UniProtKB) and the Gene Expression Atlas (GXA). We annotated scientific documents in a standardized way, by applying public terminological resources for diseases and proteins, and other text-mining approaches. Eventually, we compared the genetic causes of T2DM across the data resources to demonstrate the benefits from the SESL triple store. Our solution enables publishers to distribute their content with little overhead into remote data infrastructures, such as into any Virtual Knowledge Broker.

Using rule-based natural language processing to improve disease normalization in biomedical text

BACKGROUND AND OBJECTIVE

In order for computers to extract useful information from unstructured text, a concept normalization system is needed to link relevant concepts in a text to sources that contain further information about the concept. Popular concept normalization tools in the biomedical field are dictionary-based. In this study we investigate the usefulness of natural language processing (NLP) as an adjunct to dictionary-based concept normalization.

METHODS

We compared the performance of two biomedical concept normalization systems, MetaMap and Peregrine, on the Arizona Disease Corpus, with and without the use of a rule-based NLP module. Performance was assessed for exact and inexact boundary matching of the system annotations with those of the gold standard and for concept identifier matching.

RESULTS

Without the NLP module, MetaMap and Peregrine attained F-scores of 61.0% and 63.9%, respectively, for exact boundary matching, and 55.1% and 56.9% for concept identifier matching. With the aid of the NLP module, the F-scores of MetaMap and Peregrine improved to 73.3% and 78.0% for boundary matching, and to 66.2% and 69.8% for concept identifier matching. For inexact boundary matching, performances further increased to 85.5% and 85.4%, and to 73.6% and 73.3% for concept identifier matching.

CONCLUSIONS

We have shown the added value of NLP for the recognition and normalization of diseases with MetaMap and Peregrine. The NLP module is general and can be applied in combination with any concept normalization system. Whether its use for concept types other than disease is equally advantageous remains to be investigated.

Knowledge sharing and collaboration in translational research, and the DC-THERA Directory

Biomedical research relies increasingly on large collections of data sets and knowledge whose generation, representation and analysis often require large collaborative and interdisciplinary efforts. This dimension of ‘big data’ research calls for the development of computational tools to manage such a vast amount of data, as well as tools that can improve communication and access to information from collaborating researchers and from the wider community. Whenever research projects have a defined temporal scope, an additional issue of data management arises, namely how the knowledge generated within the project can be made available beyond its boundaries and life-time. DC-THERA is a European ‘Network of Excellence’ (NoE) that spawned a very large collaborative and interdisciplinary research community, focusing on the development of novel immunotherapies derived from fundamental research in dendritic cell immunobiology. In this article we introduce the DC-THERA Directory, which is an information system designed to support knowledge management for this research community and beyond. We present how the use of metadata and Semantic Web technologies can effectively help to organize the knowledge generated by modern collaborative research, how these technologies can enable effective data management solutions during and beyond the project lifecycle, and how resources such as the DC-THERA Directory fit into the larger context of e-science.

Biomedical semantics in the Semantic Web

The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intensive areas such as systems biology and translational medicine. As for any new paradigm, the adoption of the Semantic Web offers opportunities and poses questions and challenges to the life sciences scientific community: which technologies in the Semantic Web stack will be more beneficial for the life sciences? Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation? What are the incentives for the adoption of the Semantic Web, and who are the facilitators? Is there going to be a Semantic Web revolution in the life sciences?

We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics special issue presents selected papers from the 2009 edition, held in Amsterdam on November 20^th.