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Several query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stake...
Biological databases store data about laboratory experiments, together with semantic annotations, in order to support data aggregation and retrieval. The exact meaning of such annotations in the context of a d...
This article describes a high-recall, high-precision approach for the extraction of biomedical entities from scientific articles.
Although disease diagnosis has greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis purely based on sequencing technologies for many diseases with c...
This article is part of a Supplement: Volume 8 Supplement 1
Observational clinical studies play a pivotal role in advancing medical knowledge and patient healthcare. To lessen the prohibitive costs of conducting these studies and support evidence-based medicine, result...
The Environment Ontology (ENVO; http://www.environmentontology.org/), first described in 2013, is a resource and research target for the semantically c...
Biomedical ontologies are representations of classes of entities in the biomedical domain and how these classes are related in computer- and human-interpretable formats. Ontologies support data standardization...
The vigilant observation of medical devices during post-market surveillance (PMS) for identifying safety-relevant incidents is a non-trivial task. A wide range of sources has to be monitored in order to integr...
VerbNet, an extensive computational verb lexicon for English, has proved useful for supporting a wide range of Natural Language Processing tasks requiring information about the behaviour and meaning of verbs. ...
High-throughput technologies produce huge amounts of heterogeneous biological data ... as bio-ontologies to extract and share valuable information. In parallel, the development of recent...
With the emergence of high-throughput technologies, Big Data and eScience, the use of online data repositories and the establishment of new data standards that require data to be computer-parsable become incre...
In the clinical dentists and periodontal researchers’ community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. ...
Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of usin...
The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the ba...
The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important f...
Reasoning over biomedical ontologies using their OWL semantics has traditionally been a challenging task due to the high theoretical complexity of OWL-based automated reasoning. As a consequence, ontology repo...
Twitter updates now represent an enormous stream of information originating from a wide variety of formal and informal sources, much of which is relevant to real-world events. They can therefore be highly usef...
The ability to express the same meaning in different ways is a well-known property of natural language. This amazing property is the source of major difficulties in natural language processing. Given the const...
Automatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task. Ontologies, such as the Cardio...
Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to hete...
The motivation for the BioHub project is to create an Integrated Knowledge Management System (IKMS) that will enable chemists to source ingredients from bio-renewables, rather than from non-sustainable sources...
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
Genotype-phenotype studies aim to identify causative relationships between genes and phenotypes. The International Mouse Phenotyping Consortium is a high throughput phenotyping program whose goal is to collect...
Vaccine has been one of the most successful public health interventions to date. However, vaccines are pharmaceutical products that carry risks so that many adverse events (AEs) are reported after receiving va...
In recent years, numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network. These methods supposed that two proteins share the same function if they inter...
This article is part of a Supplement: Volume 8 Supplement 1
Inferring gene-to-phenotype and gene-to-human disease model relationships from annotated mouse phenotypes and disease associations is critical when researching gene function and identifying candidate disease g...
Research on medical vocabulary expansion from large corpora has primarily been conducted using text written in English or similar languages, due to a limited availability of large biomedical corpora in most la...
Discovering novel genes that are involved human diseases is a challenging task in biomedical research. In recent years, several computational approaches have been proposed to prioritize candidate disease genes...
This article is part of a Supplement: Volume 8 Supplement 1
There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formall...
The Genome Variant Format (GVF) uses the Sequence Ontology (SO) to enable detailed annotation of sequence variation. The annotation includes SO terms for the type of sequence alteration, the genomic features t...
Even though several high-quality clinical terminologies, such as SNOMED CT and LOINC, are readily available, uptake in clinical systems has been slow and many continue to capture information in plain text or u...
A standard task in pharmacogenomics research is identifying genes that may be involved in drug response variability, i.e., pharmacogenes. Because genomic experiments tended to generate many false positives, co...
Ontologies are widely used across biology and biomedicine for the annotation of databases. Ontology development is often a manual, time-consuming, and expensive process. Automatic or semi-automatic identificat...
Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomica...
Biomedical event extraction is one of the key tasks in biomedical text mining, supporting various applications such as database curation and hypothesis generation. Several systems, some of which have been appl...
Biological sequences, such as proteins, have been provided with annotations that assign functional information. These functional annotations are associations of proteins (or other biological sequences) with de...
In this paper, we describe a histological ontology of the human cardiovascular system developed in collaboration among histology experts and computer scientists.
Ectopic pregnancy is a frequent early complication of pregnancy associated with significant rates of morbidly and mortality. The positive diagnosis of this condition is established through transvaginal ultraso...
To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts ...
The increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the vali...
Identifying partial mappings between two terminologies is of special importance when one terminology is finer-grained than the other, as is the case for the Human Phenotype Ontology (HPO), mainly used for rese...
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