AIMC Topic: Biological Ontologies
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A numerical similarity approach for using retired Current Procedural Terminology (CPT) codes for electronic phenotyping in the Scalable Collaborative Infrastructure for a Learning Health System (SCILHS).
BMC medical informatics and decision making
Dec 11, 2015
BACKGROUND: Interoperable phenotyping algorithms, needed to identify patient cohorts meeting eligibility criteria for observational studies or clinical trials, require medical data in a consistent structured, coded format. Data heterogeneity limits s...
Biological Model Development as an Opportunity to Provide Content Auditing for the Foundational Model of Anatomy Ontology.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Nov 5, 2015
Constructing a biological model using an established ontology provides a unique opportunity to perform content auditing on the ontology. We built a Markov chain model to study tumor metastasis in the regional lymphatics of patients with head and neck...
A Data Quality Ontology for the Secondary Use of EHR Data.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Nov 5, 2015
The secondary use of EHR data for research is expected to improve health outcomes for patients, but the benefits will only be realized if the data in the EHR is of sufficient quality to support these uses. A data quality (DQ) ontology was developed t...
POETenceph - Automatic identification of clinical notes indicating encephalopathy using a realist ontology.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Nov 5, 2015
Identifying inpatients with encephalopathy is important. The disorder is prevalent, often missed, and puts patients at risk. We describe POETenceph, natural language processing pipeline, which ranks clinical notes on the extent to which they indicate...
COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Nov 5, 2015
Biomedical ontologies play a vital role in healthcare information management, data integration, and decision support. Ontology quality assurance (OQA) is an indispensable part of the ontology engineering cycle. Most existing OQA methods are based on ...
Characterization of the Context of Drug Concepts in Research Protocols: An Empiric Study to Guide Ontology Development.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Nov 5, 2015
We examined a large body of research study documents (protocols) to identify mentions of drug concepts and established base concepts and roles needed to characterize the semantics of these instances. We found these concepts in three general situation...
Building integrated ontological knowledge structures with efficient approximation algorithms.
BioMed research international
Oct 13, 2015
The integration of ontologies builds knowledge structures which brings new understanding on existing terminologies and their associations. With the steady increase in the number of ontologies, automatic integration of ontologies is preferable over ma...
Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.
SAR and QSAR in environmental research
Sep 21, 2015
Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales t...
SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data.
Database : the journal of biological databases and curation
Sep 18, 2015
There is an urgent need to standardize the semantics of biomedical data values, such as phenotypes, to enable comparative and integrative analyses. However, it is unlikely that all studies will use the same data collection protocols. As a result, ret...
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.
Journal of integrative bioinformatics
Sep 4, 2015
The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the stru...
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