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Clinical phenotypes and disease-risk stratification are most often determined through the direct observations of clinicians in conjunction with published standards and guidelines, where the clinical expert is ...
Genome sequencing of many eukaryotic pathogens and the volume of data available on public resources have created a clear requirement for a consistent vocabulary to describe the range of developmental forms of ...
Transfusion and clinical laboratory services are high-volume activities involving complicated workflows across both ambulatory and inpatient environments. As a result, there are many opportunities for safety l...
The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), aims at providing a unified access to toxicity data, ...
This article is part of a Supplement: Volume 3 Supplement 1
A variety of topic-focused wikis are used in the biomedical sciences to enable the mass-collaborative synthesis and distribution of diverse bodies of knowledge. To address complex problems such as defining the...
This article is part of a Supplement: Volume 3 Supplement 1
The electronic surveillance for adverse drug events is largely based upon the analysis of coded data from reporting systems. Yet, the vast majority of electronic health data lies embedded within the free text ...
This article is part of a Supplement: Volume 3 Supplement 1
Identifying relationships between hitherto unrelated entities in different ontologies is the key task of ontology alignment. An alignment is either manually created by domain experts or automatically by an ali...
This article is part of a Supplement: Volume 3 Supplement 1
Ontologies such as the Gene Ontology (GO) and their use in annotations make cross species comparisons of genes possible, along with a wide range of other analytical activities. The bio-ontologies community, in...
This article is part of a Supplement: Volume 3 Supplement 1
The increasing number of scientific literature on the Web and the absence of efficient tools used for classifying and searching the documents are the two most important factors that influence the speed of the ...
This article is part of a Supplement: Volume 3 Supplement 1
Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model.
This article is part of a Supplement: Volume 3 Supplement 1
Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more gene...
This article is part of a Supplement: Volume 3 Supplement 1
The wide variety of morphological variants of domain-specific technical terms contributes to the complexity of performing natural language processing of the scientific literature related to molecular biology. ...
Rapid identification of subject experts for medical topics helps in improving the implementation of discoveries by speeding the time to market drugs and aiding in clinical trial recruitment, etc. Identifying s...
The International Classification of Functioning, Disability and Health (ICF) is a classification of health and health-related issues, aimed at describing and measuring health and disability at both individual ...
Caused by intracellular Gram-negative bacteria Brucella spp., brucellosis is the most common bacterial zoonotic disease. Extensive studies in brucellosis have yielded a large number of publications and data cover...
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past dec...
In this paper we describe our experience of adding globally unique identifiers to the Species 2000 and ITIS Catalogue of Life, an on-line index of organisms which is intended, ultimately, to cover all the worl...
Competitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consumin...
This article is part of a Supplement: Volume 2 Supplement 5
Online news reports are increasingly becoming a source for event-based early warning systems that detect natural disasters. Harnessing the massive volume of information available from multilingual newswire pre...
This article is part of a Supplement: Volume 2 Supplement 5
Micro-blogging services such as Twitter offer the potential to crowdsource epidemics in real-time. However, Twitter posts (‘tweets’) are often ambiguous and reactive to media trends. In order to ground user me...
This article is part of a Supplement: Volume 2 Supplement 5
The treatment of negation and hedging in natural language processing has received much interest recently, especially in the biomedical domain. However, open access corpora annotated for negation and/or specula...
This article is part of a Supplement: Volume 2 Supplement 5
This paper presents a novel approach to the problem of hedge detection, which involves identifying so-called hedge cues for labeling sentences as certain or uncertain. This is the classification problem for Task ...
This article is part of a Supplement: Volume 2 Supplement 5
This paper presents a new approach to exploit coreference information for extracting event-argument (E-A) relations from biomedical documents. This approach has two advantages: (1) it can extract a large numbe...
This article is part of a Supplement: Volume 2 Supplement 5
Event extraction following the GENIA Event corpus and BioNLP shared task models has been a considerable focus of recent work in biomedical information extraction. This work includes efforts applying event extr...
This article is part of a Supplement: Volume 2 Supplement 5
Information extraction is a complex task which is necessary to develop high-precision information retrieval tools. In this paper, we present the platform MeTAE (Medical Texts Annotation and Exploration). MeTAE...
This article is part of a Supplement: Volume 2 Supplement 5
The extraction of complex events from biomedical text is a challenging task and requires in-depth semantic analysis. Previous approaches associate lexical and syntactic resources with ontologies for the semant...
This article is part of a Supplement: Volume 2 Supplement 5
We consider the task of automatically extracting DNA methylation events from the biomedical domain literature. DNA methylation is a key mechanism of epigenetic control of gene expression and implicated in many...
This article is part of a Supplement: Volume 2 Supplement 5
Annotated reference corpora play an important role in biomedical information extraction. A semantic annotation of the natural language texts in these reference corpora using formal ontologies is challenging du...
This article is part of a Supplement: Volume 2 Supplement 5
This article is part of a Supplement: Volume 2 Supplement 5
Ontologies are increasingly used to structure and semantically describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a ...
The large-scale effort in developing, maintaining and making biomedical ontologies available motivates the application of similarity measures to compare ontology concepts or, by extension, the entities describ...
Dispositions and tendencies feature significantly in the biomedical domain and therefore in representations of knowledge of that domain. They are not only important for specific applications like an infectious...
This article is part of a Supplement: Volume 2 Supplement 4
To evaluate how well current anatomical ontologies fit the way real-world users apply anatomy terms in their data annotations.
This article is part of a Supplement: Volume 2 Supplement 4
In biomedical ontologies, mereological relations have always been subject to special interest due to their high relevance in structural descriptions of anatomical entities, cells, and biomolecules. This paper ...
This article is part of a Supplement: Volume 2 Supplement 4
This paper presents an ontologically founded basic architecture for information systems, which are intended to capture, represent, and maintain metadata for various domains of clinical and epidemiological rese...
This article is part of a Supplement: Volume 2 Supplement 4
The OBML 2010 workshop, held at the University of Mannheim on September 9-10, 2010, is the 2 nd in a series of meetings organized by the Working Group “Ontologies in Biomedicine...
This article is part of a Supplement: Volume 2 Supplement 4
The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively ...
Existing methods for calculating semantic similarity between gene products using the Gene Ontology (GO) often rely on external resources, which are not part of the ontology. Consequently, changes in these exte...
The HL7 Clinical Document Architecture (CDA) constrains the HL7 Reference Information model (RIM) to specify the format of HL7-compliant clinical documents, dubbed CDA documents. The use of clinical terminologies...
In this paper we present a detailed scheme for annotating medical web pages designed for health care consumers. The annotation is along two axes: first, by reliability (the extent to which the medical informat...
This article is part of a Supplement: Volume 2 Supplement 3
Test collections for information retrieval are scarce. Domain specific test collections even more so, and medical test collections in the Swedish language non-existent prior to the making of the MedEval test c...
This article is part of a Supplement: Volume 2 Supplement 3
Most methods for negation detection in clinical text have been developed for English text, and there is a need for evaluating the feasibility of adapting these methods to other languages. A Swedish adaption of...
This article is part of a Supplement: Volume 2 Supplement 3
Extracting medication information from clinical records has many potential applications, and recently published research, systems, and competitions reflect an interest therein. Much of the early extraction wor...
This article is part of a Supplement: Volume 2 Supplement 3
Free text is helpful for entering information into electronic health records, but reusing it is a challenge. The need for language technology for processing Finnish and Swedish healthcare text is therefore evi...
This article is part of a Supplement: Volume 2 Supplement 3
The papers presented in this supplement focus and reflect on computer use in every-day clinical work in hospitals and clinics such as electronic health record systems, pre-processing for computer aided summari...
This article is part of a Supplement: Volume 2 Supplement 3
Chronic renal disease is a global health problem. The identification of suitable biomarkers could facilitate early detection and diagnosis and allow better understanding of the underlying pathology. One of the...
This article is part of a Supplement: Volume 2 Supplement 2
Text definitions for entities within bio-ontologies are a cornerstone of the effort to gain a consensus in understanding and usage of those ontologies. Writing these definitions is, however, a considerable eff...
This article is part of a Supplement: Volume 2 Supplement 2
Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integr...
This article is part of a Supplement: Volume 2 Supplement 2
Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medici...
This article is part of a Supplement: Volume 2 Supplement 2
Over the years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organisation, presentation ...
This article is part of a Supplement: Volume 2 Supplement 2
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Journal of Biomedical Semantics