AIMC Topic: Biological Ontologies

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YummyData: providing high-quality open life science data.

Database : the journal of biological databases and curation
Many life science datasets are now available via Linked Data technologies, meaning that they are represented in a common format (the Resource Description Framework), and are accessible via standard APIs (SPARQL endpoints). While this is an important ...

Identification of errors in the IEDB using ontologies.

Database : the journal of biological databases and curation
The Immune Epitope Database (IEDB) is a free online resource that has manually curated over 18 500 references from the scientific literature. Our database presents experimental data relating to the recognition of immune epitopes by the adaptive immun...

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

Database : the journal of biological databases and curation
The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we...

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
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
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
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
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.)
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.)
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
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...