AIMC Topic: Biological Ontologies

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The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Journal of biomedical semantics Jul 4, 2016
BACKGROUND: The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its ...
Biological Ontologies Cells Natural Language Processing Nervous System
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Normalizing acronyms and abbreviations to aid patient understanding of clinical texts: ShARe/CLEF eHealth Challenge 2013, Task 2.

Journal of biomedical semantics Jul 1, 2016
BACKGROUND: The ShARe/CLEF eHealth challenge lab aims to stimulate development of natural language processing and information retrieval technologies to aid patients in understanding their clinical reports. In clinical text, acronyms and abbreviations...
Natural Language Processing Telemedicine Biological Ontologies Humans
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A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.

Journal of biomedical informatics Jun 23, 2016
Software tools play a critical role in the development and maintenance of biomedical ontologies. One important task that is difficult without software tools is ontology quality assurance. In previous work, we have introduced different kinds of abstra...
Systematized Nomenclature of Medicine Biological Ontologies Software Quality Assurance, Health Care Statistics as Topic
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Knowledge Author: facilitating user-driven, domain content development to support clinical information extraction.

Journal of biomedical semantics Jun 23, 2016
BACKGROUND: Clinical Natural Language Processing (NLP) systems require a semantic schema comprised of domain-specific concepts, their lexical variants, and associated modifiers to accurately extract information from clinical texts. An NLP system leve...
Semantics Biological Ontologies Internet Data Mining Software User-Computer Interface Natural Language Processing
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Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

PLoS computational biology Jun 23, 2016
The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using s...
Biological Ontologies Computational Biology Information Storage and Retrieval Internet Semantics Humans Biomedical Research
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Large scale biomedical texts classification: a kNN and an ESA-based approaches.

Journal of biomedical semantics Jun 16, 2016
BACKGROUND: With the large and increasing volume of textual data, automated methods for identifying significant topics to classify textual documents have received a growing interest. While many efforts have been made in this direction, it still remai...
Machine Learning Semantics Natural Language Processing Humans Biomedical Research Biological Ontologies Data Mining
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An ontology-driven, case-based clinical decision support model for removable partial denture design.

Scientific reports Jun 14, 2016
We present the initial work toward developing a clinical decision support model for specific design of removable partial dentures (RPDs) in dentistry. We developed an ontological paradigm to represent knowledge of a patient's oral conditions and dent...
Denture, Partial, Removable Biological Ontologies Denture Retention Decision Support Techniques Reproducibility of Results Humans Natural Language Processing Algorithms Knowledge Bases Decision Support Systems, Clinical
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DermO; an ontology for the description of dermatologic disease.

Journal of biomedical semantics Jun 13, 2016
BACKGROUND: 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, formally structured terminologies, o...
Biological Ontologies Internet Publications Skin Diseases Data Mining Humans
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FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

Journal of biomedical semantics Jun 13, 2016
BACKGROUND: Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that descr...
Databases, Genetic Fuzzy Logic Humans Nucleotides Semantics Proteins Databases, Protein Reference Books Biological Ontologies Molecular Sequence Annotation
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Overlap in drug-disease associations between clinical practice guidelines and drug structured product label indications.

Journal of biomedical semantics Jun 8, 2016
BACKGROUND: Clinical practice guidelines (CPGs) recommend pharmacologic treatments for clinical conditions, and drug structured product labels (SPLs) summarize approved treatment indications. Both resources are intended to promote evidence-based medi...
Drug Labeling Pharmaceutical Preparations Data Mining Practice Guidelines as Topic Biological Ontologies Chronic Disease
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