AIMC Topic: Biological Ontologies
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UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization.
PloS one
Jul 9, 2020
BACKGROUND: Biomedical ontologies have been growing quickly and proven to be useful in many biomedical applications. Important applications of those data include estimating the functional similarity between ontology terms and between annotated biomed...
The African wildlife ontology tutorial ontologies.
Journal of biomedical semantics
Jun 23, 2020
BACKGROUND: Most tutorial ontologies focus on illustrating one aspect of ontology development, notably language features and automated reasoners, but ignore ontology development factors, such as emergent modelling guidelines and ontological principle...
CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis.
Scientific data
Jun 12, 2020
The Coronavirus Infectious Disease Ontology (CIDO) is a community-based ontology that supports coronavirus disease knowledge and data standardization, integration, sharing, and analysis.
Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive.
F1000Research
May 19, 2020
The Sequence Read Archive (SRA) is a large public repository that stores raw next-generation sequencing data from thousands of diverse scientific investigations. Despite its promise, reuse and re-analysis of SRA data has been challenged by the heter...
Development and Evaluation of Ontologies in Traditional Medicine: A Review Study.
Methods of information in medicine
Apr 29, 2020
BACKGROUND: Development of ontologies in traditional medicine can be a foundation for other applications of informatics in this field. Despite the importance of the development of ontologies in traditional medicine, there are few review studies in t...
Ontologically simple theories do not indicate the true nature of complex biological systems: three test cases.
History and philosophy of the life sciences
Apr 28, 2020
A longstanding philosophical premise perceives simplicity as a desirable attribute of scientific theories. One of several raised justifications for this notion is that simple theories are more likely to indicate the true makeup of natural systems. Qu...
Ontologies in radiation oncology.
Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB)
Apr 2, 2020
Ontologies are a formal, computer-compatible method for representing scientific knowledge about a given domain. They provide a standardized vocabulary, taxonomy and set of relations between concepts. When formatted in a standard way, they can be read...
A Neuro-ontology for the neurological examination.
BMC medical informatics and decision making
Mar 4, 2020
BACKGROUND: The use of clinical data in electronic health records for machine-learning or data analytics depends on the conversion of free text into machine-readable codes. We have examined the feasibility of capturing the neurological examination as...
Training a Convolutional Neural Network with Terminology Summarization Data Improves SNOMED CT Enrichment.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Mar 4, 2020
As a step toward learning to automatically insert new concepts into a large biomedical ontology, we are studying the easier problem of automatically verifying that an IS-A link should exist between a new child concept and an existing parent concept. ...
FHIR OWL: Transforming OWL ontologies into FHIR terminology resources.
AMIA ... Annual Symposium proceedings. AMIA Symposium
Mar 4, 2020
The FHIR specification provides a mechanism to access clinical terminologies using a standard API, and many existing terminologies, such as SNOMED CT, are well supported. However, in areas such as genomics, terminologies from other domains are starti...
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