AIMC Topic: Biological Ontologies

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BIOINTMED: integrated biomedical knowledge base with ontologies and clinical trials.

Medical & biological engineering & computing
Biomedical data are complex and heterogeneous. An ample reliable quantity of data is important for understanding and exploring the domain. The work aims to integrate biomedical data from various heterogeneous sources like dictionaries or corpus and a...

BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint.

BMC bioinformatics
BACKGROUND: Managing and organizing biological knowledge remains a major challenge, due to the complexity of living systems. Recently, systemic representations have been promising in tackling such a challenge at the whole-cell scale. In such represen...

Developing a neurally informed ontology of creativity measurement.

NeuroImage
A central challenge for creativity research-as for all areas of experimental psychology and cognitive neuroscience-is to establish a mapping between constructs and measures (i.e., identifying a set of tasks that best captures a set of creative abilit...

UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization.

PloS one
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
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
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
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
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
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)
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...