• Corpus ID: 7197901

Representing, reasoning and answering questions about biological pathways - various applications

@article{Anwar2014RepresentingRA,
  title={Representing, reasoning and answering questions about biological pathways - various applications},
  author={Saadat Anwar},
  journal={ArXiv},
  year={2014},
  volume={abs/1403.0541}
}
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a primary task in biomedical research and a prerequisite for diagnosing diseases, and drug development. Scientists studying these processes have identified various pathways responsible for drug metabolism, and signal transduction, etc. Newer techniques and… 

References

SHOWING 1-10 OF 53 REFERENCES
A knowledge based approach for representing and reasoning about signaling networks
TLDR
This approach is different from most other qualitative systems biology approaches in that it is based on reasoning (or inferencing) rather than simulation, and can perform various kinds of reasoning such as planning, hypothetical reasoning and explaining observations.
Synthesis of Pharmacokinetic Pathways through Knowledge Acquisition and Automated Reasoning
TLDR
This paper proposes a novel approach for automated pathway synthesis that acquires facts from hand-curated knowledge bases that is capable of synthesizing these pathways but also uncovering information that is not available in the manually annotated pathways.
Querying Parse Tree Database of Medline Text to Synthesize User-Specific Biomolecular Networks
TLDR
This paper proposes a new paradigm in synthesizing biomolecular networks by allowing biologists to create their own networks through queries to a specialized database of Medline abstracts, and shows that this approach is capable of synthesizing these networks with high precision and even finds relations that have yet to be curated in public databases.
Discovering drug–drug interactions: a text-mining and reasoning approach based on properties of drug metabolism
TLDR
A novel approach that integrates text mining and automated reasoning to derive DDIs is proposed that can uncover potential DDIs with scientific evidences explaining the mechanism of the interactions.
Model validation of biological pathways using Petri nets
TLDR
The first steps of a new integrating methodology to develop and analyse models of biological pathways in a systematic manner using well established Petri net technologies using qualitative and quantitative analysis for behaviour prediction are demonstrated.
Molecular interaction maps of bioregulatory networks: a general rubric for systems biology.
TLDR
The molecular interaction map (MIM) notation is described formally and its merits relative to alternative proposals are discussed and it is shown by simple examples how to denote all of the molecular interactions commonly found in bioregulatory networks.
BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition
TLDR
BANNER is an open-source, executable survey of advances in biomedical named entity recognition, intended to serve as a benchmark for the field and is designed to maximize domain independence by not employing brittle semantic features or rule-based processing steps.
A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions
TLDR
This work automatically populate a repository of information on genetic variants, relations to drugs, occurrence in sub-populations, and associations with disease, focusing on SNPs that can be associated with variations in drug response.
DrugBank: a comprehensive resource for in silico drug discovery and exploration
TLDR
DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug data with comprehensive drug target information and is fully searchable supporting extensive text, sequence, chemical structure and relational query searches.
Pharmacogenomics and bioinformatics: PharmGKB.
TLDR
The challenges are to provide the tools and knowledge to plan and interpret genome-wide pharmacogenomics studies, predict gene-drug relationships based on shared mechanisms and support data-sharing consortia investigating clinical applications of pharmacogenetics.
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