AIMC Topic: Biological Ontologies
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Development and Applications of Interoperable Biomedical Ontologies for Integrative Data and Knowledge Representation and Multiscale Modeling in Systems Medicine.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2022
The data FAIR Guiding Principles state that all data should be Findable, Accessible, Interoperable, and Reusable. Ontology is critical to data integration, sharing, and analysis. Given thousands of ontologies have been developed in the era of artific...
Developing a pneumonia diagnosis ontology from multiple knowledge sources.
Health informatics journal
Jan 1, 2022
Pneumonia is difficult to differentiate from other pulmonary diseases because it shares many symptoms with these diseases. Diagnosing pneumonia in clinical practice would benefit from having access to a codified representation of clinical knowledge....
Assessing Resolvability and Consistency in OBO Foundry Ontologies: Pilot Study.
Studies in health technology and informatics
Nov 18, 2021
Ontologies listed in the OBO Foundry are often regarded as reliable choices to be reused but ontology interoperability of them remains unknown. This study evaluated the resolvability of URIs and consistency of axioms in the OBO Foundry library, BFO o...
Understanding the Gap Between Information Models and Realism-Based Ontologies Using the Generic Component Model.
Studies in health technology and informatics
Oct 27, 2021
The wide-spread use of Common Data Models and information models in biomedical informatics encourages assumptions that those models could provide the entirety of what is needed for knowledge representation purposes. Based on the lack of computable se...
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.
Database : the journal of biological databases and curation
Oct 26, 2021
Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are deve...
Semantic similarity and machine learning with ontologies.
Briefings in bioinformatics
Jul 20, 2021
Ontologies have long been employed in the life sciences to formally represent and reason over domain knowledge and they are employed in almost every major biological database. Recently, ontologies are increasingly being used to provide background kno...
Standardization of assay representation in the Ontology for Biomedical Investigations.
Database : the journal of biological databases and curation
Jul 9, 2021
The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations, logic and hierarchy with a goal to improve and standardize these terms. As a result, inconsistencies in W3C Web Ontology Language (OWL) expressions...
Towards a Semantic Data Harmonization Federated Infrastructure.
Studies in health technology and informatics
May 27, 2021
Data integration is an increasing need in medical informatics projects like the EU Precise4Q project, in which multidisciplinary semantically and syntactically heterogeneous data across several institutions needs to be integrated. Besides, data shari...
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies.
Database : the journal of biological databases and curation
May 15, 2021
Crop phenotypic data underpin many pre-breeding efforts to characterize variation within germplasm collections. Although there has been an increase in the global capacity for accumulating and comparing such data, a lack of consistency in the systemat...
Predicting candidate genes from phenotypes, functions and anatomical site of expression.
Bioinformatics (Oxford, England)
May 5, 2021
MOTIVATION: Over the past years, many computational methods have been developed to incorporate information about phenotypes for disease-gene prioritization task. These methods generally compute the similarity between a patient's phenotypes and a data...
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