AIMC Topic: Biological Ontologies
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Combining the Generic Entity-Attribute-Value Model and Terminological Models into a Common Ontology to Enable Data Integration and Decision Support.
Studies in health technology and informatics
Jan 1, 2018
The integration of clinical information models and termino-ontological models into a unique ontological framework is highly desirable for it facilitates data integration and management using the same formal mechanisms for both data concepts and infor...
XplOit: An Ontology-Based Data Integration Platform Supporting the Development of Predictive Models for Personalized Medicine.
Studies in health technology and informatics
Jan 1, 2018
Predictive models can support physicians to tailor interventions and treatments to their individual patients based on their predicted response and risk of disease and help in this way to put personalized medicine into practice. In allogeneic stem cel...
Improving precision in concept normalization.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Jan 1, 2018
Most natural language processing applications exhibit a trade-off between precision and recall. In some use cases for natural language processing, there are reasons to prefer to tilt that trade-off toward high precision. Relying on the Zipfian distri...
OWL-NETS: Transforming OWL Representations for Improved Network Inference.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Jan 1, 2018
Our knowledge of the biological mechanisms underlying complex human disease is largely incomplete. While Semantic Web technologies, such as the Web Ontology Language (OWL), provide powerful techniques for representing existing knowledge, well-establi...
Conceptual Challenges of the Systemic Approach in Understanding Cell Differentiation.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2018
The cells of a multicellular organism are derived from a single zygote and genetically identical. Yet, they are phenotypically very different. This difference is the result of a process commonly called cell differentiation. How the phenotypic diversi...
Conceptual Challenges in the Theoretical Foundations of Systems Biology.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2018
In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, w...
OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.
Proteomics
Oct 1, 2017
The availability of user-friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://ww...
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.
Bioinformatics (Oxford, England)
Sep 15, 2017
MOTIVATION: The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with ea...
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain.
Bioinformatics (Oxford, England)
Jul 15, 2017
MOTIVATION: The amount of information available in textual format is rapidly increasing in the biomedical domain. Therefore, natural language processing (NLP) applications are becoming increasingly important to facilitate the retrieval and analysis o...
Finding useful data across multiple biomedical data repositories using DataMed.
Nature genetics
May 26, 2017
The value of broadening searches for data across multiple repositories has been identified by the biomedical research community. As part of the US National Institutes of Health (NIH) Big Data to Knowledge initiative, we work with an international com...
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