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The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish, Dan...
Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation t...
Systematic representation of information related to genetic and non-genetic variations is required to allow large scale studies, data mining and data integration, and to make it possible to reveal novel relati...
Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. With the currently existing wealth of formalised knowledge, the ability to ...
The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hier...
Terminologies that account for variation in language use by linking synonyms and abbreviations to their corresponding concept are important enablers of high-quality information extraction from medical texts. D...
The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHac...
Epidemiology is a data-intensive and multi-disciplinary subject, where data integration, curation and sharing are becoming increasingly relevant, given its global context and time constraints. The semantic ann...
Identifying phrases that refer to particular concept types is a critical step in extracting information from documents. Provided with annotated documents as training data, supervised machine learning can autom...
Natural human languages show a power law behaviour in which word frequency (in any large enough corpus) is inversely proportional to word rank - Zipf’s law. We have therefore asked whether similar power law be...
The diverse set of human brain structure and function analysis methods represents a difficult challenge for reconciling multiple views of neuroanatomical organization. While different views of organization are...
We built the Drug Ontology (DrOn) because we required correct and consistent drug information in a format for use in semantic web applications, and no existing resource met this requirement or could be altered...
As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growi...
We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representati...
In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based...
Licensed human vaccines can induce various adverse events (AE) in vaccinated patients. Due to the involvement of the whole immune system and complex immunological reactions after vaccination, it is difficult t...
Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipi...
Though the annotation of digital artifacts with metadata has a long history, the bulk of that work focuses on the association of single terms or concepts to single targets. As annotation efforts expand to capt...
Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple...
The Rat Genome Database (RGD) (http://rgd.mcw.edu/) is the premier site for comprehensive data on the different strains of the laboratory rat (Rattus n...
Large biomedical simulation initiatives, such as the Virtual Physiological Human (VPH), are substantially dependent on controlled vocabularies to facilitate the exchange of information, of data and of models. ...
A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, ...
Ontologies are useful in many branches of biomedical research. For instance, in the vaccine domain, the community-based Vaccine Ontology (VO) has been widely used to promote vaccine data standardization, integ...
Anatomy ontologies are query-able classifications of anatomical structures. They provide a widely-used means for standardising the annotation of phenotypes and expression in both human-readable and programmati...
The African clawed frogs Xenopus laevis and Xenopus tropicalis are prominent animal model organisms. Xenopus research contributes to the understanding of genetic, developmental and molecular mechanisms underlying...
Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to...
Large-scale mutagenesis projects are ongoing to improve our understanding about the pathology and subsequently the treatment of diseases. Such projects do not only record the genotype but also report phenotype...
The identification of protein and gene names (PGNs) from the scientific literature requires semantic resources: Terminological and lexical resources deliver the term candidates into PGN tagging solutions and t...
The increasing amount of textual information in biomedicine requires effective term recognition methods to identify textual representations of domain-specific concepts as the first step toward automating its s...
The Clinical Measurement Ontology (CMO), Measurement Method Ontology (MMO), and Experimental Condition Ontology (XCO) were originally developed at the Rat Genome Database (RGD) to standardize quantitative rat ...
Understanding, modelling and influencing the transition between different states of cells, be it reprogramming of somatic cells to pluripotency or trans-differentiation between cells, is a hot topic in current...
Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the ...
Biobanks are a critical resource for translational science. Recently, semantic web technologies such as ontologies have been found useful in retrieving research data from biobanks. However, recent research has...
Histology information management relies on complex knowledge derived from morphological tissue analyses. These approaches have not significantly facilitated the general integration of tissue- and molecular-lev...
Enrichment analysis is well established in the field of transcriptomics, where it is used to identify relevant biological features that characterize a set of genes obtained in an experiment.
The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingd...
Named entity recognition (NER) is an essential step in automatic text processing pipelines. A number of solutions have been presented and evaluated against gold standard corpora (GSC). The benchmarking against...
The capture and use of disease-related anatomic pathology data for both model organism phenotyping and human clinical practice requires a relatively simple nomenclature and coding system that can be integrated...
Clinical trials are important for patients, for researchers and for companies. One of the major bottlenecks is patient recruitment. This task requires the matching of a large volume of information about the pa...
With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on I...
The Edinburgh Mouse Atlas Project (EMAP) ontology of mouse developmental anatomy provides a standard nomenclature for describing normal and mutant mouse embryo anatomy. The ontology forms the core of the EMAP ...
A variety of informatics approaches have been developed that use information retrieval, NLP and text-mining techniques to identify biomedical concepts and relations within scientific publications or their sent...
The use of ontologies to standardize biological data and facilitate comparisons among datasets has steadily grown as the complexity and amount of available data have increased. Despite the numerous ontologies ...
Open metadata registries are a fundamental tool for researchers in the Life Sciences trying to locate resources. While most current registries assume that resources are annotated with well-structured metadata,...
The beta phase of the 11th revision of International Classification of Diseases (ICD-11) intends to accept public input through a distributed model of authoring. One of the core use cases is to create textual def...
As new biomedical technologies are developed, the amount of publically available biomedical data continues to increase. To help manage these vast and disparate data sources, researchers have turned to the Sema...
This article is part of a Supplement: Volume 4 Supplement 1
Ontologies categorize entities, express relationships between them, and provide standardized definitions. Thus, they can be used to present and enforce the specific relationships between database components. T...
This article is part of a Supplement: Volume 4 Supplement 1
The Gene Ontology and its associated annotations are critical tools for interpreting lists of genes. Here, we introduce a method for evaluating the Gene Ontology annotations and structure based on the impact t...
This article is part of a Supplement: Volume 4 Supplement 1
As the number and size of biological knowledge resources for physiology grows, researchers need improved tools for searching and integrating knowledge and physiological models. Unfortunately, current resources...
This article is part of a Supplement: Volume 4 Supplement 1
Over the 15 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 4 Supplement 1
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