AIMC Topic: Biological Ontologies

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Collective intelligence in medical diagnosis systems: A case study.

Computers in biology and medicine
Diagnosing a patient's condition is one of the most important and challenging tasks in medicine. We present a study of the application of collective intelligence in medical diagnosis by applying consensus methods. We compared the accuracy obtained wi...

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.

Journal of biomedical semantics
BACKGROUND: MicroRNAs are increasingly being appreciated as critical players in human diseases, and questions concerning the role of microRNAs arise in many areas of biomedical research. There are several manually curated databases of microRNA-diseas...

The Ontology for Biomedical Investigations.

PloS one
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide...

From frames to OWL2: Converting the Foundational Model of Anatomy.

Artificial intelligence in medicine
OBJECTIVE: The Foundational Model of Anatomy (FMA) [Rosse C, Mejino JLV. A reference ontology for bioinformatics: the Foundational Model of Anatomy. J. Biomed. Inform. 2003;36:478-500] is an ontology that represents canonical anatomy at levels rangin...

Active learning for ontological event extraction incorporating named entity recognition and unknown word handling.

Journal of biomedical semantics
BACKGROUND: Biomedical text mining may target various kinds of valuable information embedded in the literature, but a critical obstacle to the extension of the mining targets is the cost of manual construction of labeled data, which are required for ...

An accurate and precise representation of drug ingredients.

Journal of biomedical semantics
BACKGROUND: In previous work, we built the Drug Ontology (DrOn) to support comparative effectiveness research use cases. Here, we have updated our representation of ingredients to include both active ingredients (and their strengths) and excipients. ...

Sortal anaphora resolution to enhance relation extraction from biomedical literature.

BMC bioinformatics
BACKGROUND: Entity coreference is common in biomedical literature and it can affect text understanding systems that rely on accurate identification of named entities, such as relation extraction and automatic summarization. Coreference resolution is ...

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

Journal of biomedical semantics
BACKGROUND: MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The o...

Simulated herbivory does not constrain phenotypic plasticity to shade through ontogeny in a relict tree.

Plant biology (Stuttgart, Germany)
Ecological limits to phenotypic plasticity (PP), induced by simultaneous biotic and abiotic factors, can prevent organisms from exhibiting optimal plasticity, and in turn lead to decreased fitness. Herbivory is an important biotic stressor and may li...

Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.

Journal of biomedical semantics
BACKGROUND: Authoring bio-ontologies is a task that has traditionally been undertaken by skilled experts trained in understanding complex languages such as the Web Ontology Language (OWL), in tools designed for such experts. As requests for new terms...