AIMC Topic: Biological Ontologies

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Evaluation of an ontology-based system for computerized cognitive rehabilitation.

International journal of medical informatics
OBJECTIVES: This paper describes the results of a randomized clinical trial about the effectiveness of a computerized rehabilitation treatment on a sample of 31 patients affected by Parkinson disease.

Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs.

AMIA ... Annual Symposium proceedings. AMIA Symposium
A critical issue in the usage of cancer drugs is its association with various adverse events (AEs) in some, but not all, patients. The National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE) is a controlled terminology ...

ProvCaRe Semantic Provenance Knowledgebase: Evaluating Scientific Reproducibility of Research Studies.

AMIA ... Annual Symposium proceedings. AMIA Symposium
Scientific reproducibility is critical for biomedical research as it enables us to advance science by building on previous results, helps ensure the success of increasingly expensive drug trials, and allows funding agencies to make informed decisions...

Harnessing Biomedical Natural Language Processing Tools to Identify Medicinal Plant Knowledge from Historical Texts.

AMIA ... Annual Symposium proceedings. AMIA Symposium
The growing amount of data describing historical medicinal uses of plants from digitization efforts provides the opportunity to develop systematic approaches for identifying potential plant-based therapies. However, the task of cataloguing plant use ...

The Problems of Realism-Based Ontology Design: a Case Study in Creating Definitions for an Application Ontology for Diabetes Camps.

AMIA ... Annual Symposium proceedings. AMIA Symposium
A requirement of realism-based ontology design is that classes denote exclusively entities that exist objectively in reality and that their definitions adhere to strict criteria to ensure that the classes are re-usable in other ontologies while prese...

Evaluation of Semantic Web Technologies for Storing Computable Definitions of Electronic Health Records Phenotyping Algorithms.

AMIA ... Annual Symposium proceedings. AMIA Symposium
Electronic Health Records are electronic data generated during or as a byproduct of routine patient care. Structured, semi-structured and unstructured EHR offer researchers unprecedented phenotypic breadth and depth and have the potential to accelera...

Deep Learning Meets Biomedical Ontologies: Knowledge Embeddings for Epilepsy.

AMIA ... Annual Symposium proceedings. AMIA Symposium
While biomedical ontologies have traditionally been used to guide the identification of concepts or relations in biomedical data, recent advances in deep learning are able to capture high-quality knowledge from textual data and represent it in graphi...

Improving the 'Fitness for Purpose' of Common Data Models through Realism Based Ontology.

AMIA ... Annual Symposium proceedings. AMIA Symposium
Common data models are designed and built based on requirements that are aimed towards fitness for purpose. But when common data models are used as lenses through which reality is observed from the perspective according to which they are built, then ...

Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature.

Journal of biomedical semantics
BACKGROUND: 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 Cardiovascular Disease Ontology (CV...

An ontological approach to identifying cases of chronic kidney disease from routine primary care data: a cross-sectional study.

BMC nephrology
BACKGROUND: Accurately identifying cases of chronic kidney disease (CKD) from primary care data facilitates the management of patients, and is vital for surveillance and research purposes. Ontologies provide a systematic and transparent basis for cli...