OpenPVSignal: Advancing Information Search, Sharing and Reuse on Pharmacovigilance Signals via FAIR Principles and Semantic Web Technologies

@article{Natsiavas2018OpenPVSignalAI,
  title={OpenPVSignal: Advancing Information Search, Sharing and Reuse on Pharmacovigilance Signals via FAIR Principles and Semantic Web Technologies},
  author={Pantelis Natsiavas and Richard David Boyce and Marie-Christine Jaulent and Vassilis Koutkias},
  journal={Frontiers in Pharmacology},
  year={2018},
  volume={9}
}
Signal detection and management is a key activity in pharmacovigilance (PV). When a new PV signal is identified, the respective information is publicly communicated in the form of periodic newsletters or reports by organizations that monitor and investigate PV-related information (such as the World Health Organization and national PV centers). However, this type of communication does not allow for systematic access, discovery and explicit data interlinking and, therefore, does not facilitate… 

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References

SHOWING 1-10 OF 49 REFERENCES
Evaluation of Linked, Open Data Sources for Mining Adverse Drug Reaction Signals
TLDR
This paper presents the design, the challenges and an evaluation of a Linked Data model to be used in the context of a platform exploiting social media and bibliographic data sources, focusing on the application of Adverse Drug Reaction (ADR) signal identification.
Computational Approaches for Pharmacovigilance Signal Detection: Toward Integrated and Semantically-Enriched Frameworks
TLDR
It is argued that semantic technologies provide the means to address some of the challenges of the concurrent analysis setting and can facilitate seamless access and use of different data sources and computational methods in an integrated fashion, bringing a new perspective for large-scale, knowledge-intensive signal detection.
BioKB - Text mining and semantic technologies for the biomedical content discovery
TLDR
A pipeline which, by exploiting text mining and semantic technologies, helps researchers easily access semantic content of thousands of abstracts and full text articles and standardized using unique resource identifiers and a custom ontology based on Genia ontology is implemented.
Bridging Islands of Information to Establish an Integrated Knowledge Base of Drugs and Health Outcomes of Interest
TLDR
A workgroup within the Observational Health Data Sciences and Informatics (OHDSI) collaborative is established to develop an open-source standardized knowledge base for the effects of medical products and an efficient procedure for maintaining and expanding it.
Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data
TLDR
The architecture and functionality of a system called Large-scale Adverse Effects Related to Treatment Evidence Standardization (LAERTES) that aims to address shortcomings of existing frameworks are discussed, providing useful functionality while creating opportunities for further research.
Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data
TLDR
The architecture and functionality of a system called Large-scale Adverse Effects Related to Treatment Evidence Standardization (LAERTES) that aims to address shortcomings of existing frameworks are discussed, providing useful functionality while creating opportunities for further research.
Extending the “Web of Drug Identity” with Knowledge Extracted from United States Product Labels
TLDR
This paper describes the mapping that LinkedSPLs provides between SPL active ingredients and DrugBank chemical entities, created using three approaches: InChI chemical structure descriptors comparison, exact string matching based on the chemical name, and automatic (unsupervised) linkage identification.
...
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