AIMC Topic: Biological Ontologies

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The Infectious Disease Ontology in the age of COVID-19.

Journal of biomedical semantics Jul 18, 2021
BACKGROUND: Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool, and this holds especially f...
Humans COVID-19 Epidemics Communicable Disease Control Data Mining Information Dissemination Semantics Public Health Biological Ontologies Computational Biology Communicable Diseases SARS-CoV-2
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Visual comprehension and orientation into the COVID-19 CIDO ontology.

Journal of biomedical informatics Jul 2, 2021
The current intensive research on potential remedies and vaccinations for COVID-19 would greatly benefit from an ontology of standardized COVID terms. The Coronavirus Infectious Disease Ontology (CIDO) is the largest among several COVID ontologies, a...
Humans COVID-19 Biological Ontologies Comprehension Communicable Diseases SARS-CoV-2
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Development and application of the ocular immune-mediated inflammatory diseases ontology enhanced with synonyms from online patient support forum conversation.

Computers in biology and medicine Jun 8, 2021
BACKGROUND: Unstructured text created by patients represents a rich, but relatively inaccessible resource for advancing patient-centred care. This study aimed to develop an ontology for ocular immune-mediated inflammatory diseases (OcIMIDo), as a too...
Phenotype Databases, Factual Humans Language Biological Ontologies
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SPASOS 1.1: a program for the inference of ancestral shape ontogenies.

Cladistics : the international journal of the Willi Hennig Society May 28, 2021
We recently published a method to infer ancestral landmark-based shape ontogenies that takes into account the possible existence of changes in developmental timing. Here we describe SPASOS, a software to perform that analysis. SPASOS is an open-sourc...
Biological Evolution Algorithms Phylogeny Biological Ontologies Species Specificity Software
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IrGO: Iranian traditional medicine General Ontology and knowledge base.

Journal of biomedical semantics Apr 16, 2021
BACKGROUND: Iranian traditional medicine, also known as Persian Medicine, is a holistic school of medicine with a long prolific history. It describes numerous concepts and the relationships between them. However, no unified language system has been p...
Language Biological Ontologies Medicine, Traditional Iran Data Mining
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Improved characterisation of clinical text through ontology-based vocabulary expansion.

Journal of biomedical semantics Apr 12, 2021
BACKGROUND: Biomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining. For several reasons, redundancies exist in the ontology ecosystem, which lead to the same entities being described...
Vocabulary Vocabulary, Controlled Humans Data Mining Ecosystem Biological Ontologies
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SIENA: Semi-automatic semantic enhancement of datasets using concept recognition.

Journal of biomedical semantics Mar 24, 2021
BACKGROUND: The amount of available data, which can facilitate answering scientific research questions, is growing. However, the different formats of published data are expanding as well, creating a serious challenge when multiple datasets need to be...
Biological Ontologies Semantics Machine Learning
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1, 2, 3, GO! Venture beyond gene ontologies in plant evolutionary research.

American journal of botany Mar 8, 2021
Biological Ontologies Gene Ontology Biological Evolution Plants
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RDmap: a map for exploring rare diseases.

Orphanet journal of rare diseases Feb 25, 2021
BACKGROUND: The complexity of the phenotypic characteristics and molecular bases of many rare human genetic diseases makes the diagnosis of such diseases a challenge for clinicians. A map for visualizing, locating and navigating rare diseases based o...
Humans Rare Diseases Phenotype Biological Ontologies Gene Ontology
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Comparative study using inverse ontology cogency and alternatives for concept recognition in the annotated National Library of Medicine database.

Neural networks : the official journal of the International Neural Network Society Feb 11, 2021
This paper introduces inverse ontology cogency, a concept recognition process and distance function that is biologically-inspired and competitive with alternative methods. The paper introduces inverse ontology cogency as a new alternative method. It ...
United States Cerebral Cortex Nerve Net Natural Language Processing Biological Ontologies National Library of Medicine (U.S.) Neural Networks, Computer Databases, Factual Humans
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