AIMC Topic: Biological Ontologies

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

Artificial intelligence in medicine Apr 27, 2016
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...
Humans Biological Ontologies Anatomy Semantic Web Computational Biology Programming Languages
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Active learning for ontological event extraction incorporating named entity recognition and unknown word handling.

Journal of biomedical semantics Apr 27, 2016
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 ...
Data Mining Biological Ontologies Statistics as Topic Machine Learning Natural Language Processing
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An accurate and precise representation of drug ingredients.

Journal of biomedical semantics Apr 19, 2016
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. ...
Isoenzymes Pharmaceutical Preparations Excipients Cytochrome P-450 Enzyme System Cytochrome P-450 Enzyme Inhibitors Biological Ontologies
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Sortal anaphora resolution to enhance relation extraction from biomedical literature.

BMC bioinformatics Apr 14, 2016
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 ...
Linguistics Semantics Biological Ontologies Databases, Factual Natural Language Processing
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MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

Journal of biomedical semantics Apr 12, 2016
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...
Phenotype Biological Ontologies Archaea Bacteria Culture Media
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Simulated herbivory does not constrain phenotypic plasticity to shade through ontogeny in a relict tree.

Plant biology (Stuttgart, Germany) Apr 7, 2016
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...
Light Phenotype Ecology Stress, Physiological Plant Roots Plant Leaves Plant Shoots Biological Ontologies Trees Models, Biological Herbivory Seedlings
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Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.

Journal of biomedical semantics Apr 1, 2016
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...
Search Engine Internet Software Biological Ontologies User-Computer Interface
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Representing vision and blindness.

Journal of biomedical semantics Mar 30, 2016
BACKGROUND: There have been relatively few attempts to represent vision or blindness ontologically. This is unsurprising as the related phenomena of sight and blindness are difficult to represent ontologically for a variety of reasons. Blindness has ...
Humans Animals Biological Ontologies Color Vision Defects Vision, Ocular Blindness
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Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation.

Journal of biomedical semantics Mar 23, 2016
BACKGROUND: The Centre for Therapeutic Target Validation (CTTV - https://www.targetvalidation.org/) was established to generate therapeutic target evidence from genome-scale experiments and analyses. CTTV aims to support the validity of therapeutic t...
Rare Diseases Biological Ontologies Molecular Targeted Therapy Phenotype Databases, Factual Humans Reproducibility of Results Inflammatory Bowel Diseases Data Mining
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Transitive closure of subsumption and causal relations in a large ontology of radiological diagnosis.

Journal of biomedical informatics Mar 19, 2016
The Radiology Gamuts Ontology (RGO)-an ontology of diseases, interventions, and imaging findings-was developed to aid in decision support, education, and translational research in diagnostic radiology. The ontology defines a subsumption (is_a) relati...
Biological Ontologies Translational Research, Biomedical Semantics Decision Support Techniques Causality Radiography Radiology Humans
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