AIMC Topic: Biological Ontologies

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Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies.

Journal of biomedical informatics
In previous research, we have demonstrated for a number of ontologies that structurally complex concepts (for different definitions of "complex") in an ontology are more likely to exhibit errors than other concepts. Thus, such complex concepts often ...

Querying archetype-based EHRs by search ontology-based XPath engineering.

Journal of biomedical semantics
BACKGROUND: Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of using free text searches, that le...

Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse.

Journal of biomedical semantics
BACKGROUND: Prompted by the frequency of concomitant use of prescription drugs with natural products, and the lack of knowledge regarding the impact of pharmacokinetic-based natural product-drug interactions (PK-NPDIs), the United States National Cen...

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...