ADO: A disease ontology representing the domain knowledge specific to Alzheimer's disease

Malhotra, Ashutosh; Younesi, Erfan; Gündel, Michaela; Müller, Burkhard; Heneka, Michael T.; Hofmann‐Apitius, Martin

doi:10.1016/j.jalz.2013.02.009

Cited by 97 publications

(68 citation statements)

References 8 publications

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“…Ontologies are semantic frameworks that provide a reference for standardization and harmonization of diverse datasets. For instance, AD ontology (ADO) has been developed to provide such a reference for AD knowledge domain [593]. ADO was used by Kodamullil and colleagues (2015) to represent scientific findings in a computable, cause-and-effect model of AD pathology, which was designed and coded in Open Biological Expression Language (available at http://openbel.org/) [594].…”

Section: The Emerging Field Of Systems Pharmacology In Alzheimer’s DImentioning

confidence: 99%

Revolution of Alzheimer Precision Neurology. Passageway of Systems Biology and Neurophysiology

Hampel

Toschi

Babiloni

et al. 2018

JAD

Self Cite

131

113

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The Precision Neurology development process implements systems theory with system biology and neurophysiology in a parallel, bidirectional research path: a combined hypothesis-driven investigation of systems dysfunction within distinct molecular, cellular and large-scale neural network systems in both animal models as well as through tests for the usefulness of these candidate dynamic systems biomarkers in different diseases and subgroups at different stages of pathophysiological progression. This translational research path is paralleled by an “omics”-based, hypothesis-free, exploratory research pathway, which will collect multimodal data from progressing asymptomatic, preclinical and clinical neurodegenerative disease (ND) populations, within the wide continuous biological and clinical spectrum of ND, applying high-throughput and high-content technologies combined with powerful computational and statistical modeling tools, aimed at identifying novel dysfunctional systems and predictive marker signatures associated with ND. The goals are to identify common biological denominators or differentiating classifiers across the continuum of ND during detectable stages of pathophysiological progression, characterize systems-based intermediate endophenotypes, validate multi-modal novel diagnostic systems biomarkers, and advance clinical intervention trial designs by utilizing systems-based intermediate endophenotypes and candidate surrogate markers. Achieving these goals is key to the ultimate development of early and effective individualized treatment of ND, such as Alzheimer’s disease (AD). The Alzheimer Precision Medicine Initiative (APMI) and cohort program (APMI-CP), as well as the Paris based core of the Sorbonne University Clinical Research Group “Alzheimer Precision Medicine” (GRC-APM) were recently launched to facilitate the passageway from conventional clinical diagnostic and drug development towards breakthrough innovation based on the investigation of the comprehensive biological nature of aging individuals. The APMI movement is gaining momentum to systematically apply both systems neurophysiology and systems biology in exploratory translational neuroscience research on ND.

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Section: The Emerging Field Of Systems Pharmacology In Alzheimer’s DImentioning

confidence: 99%

Revolution of Alzheimer Precision Neurology. Passageway of Systems Biology and Neurophysiology

Hampel

Toschi

Babiloni

et al. 2018

JAD

Self Cite

131

113

View full text Add to dashboard Cite

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“…To enhance interoperability, consistency, sharing, portability, and reusability, our ontology must be extracted from existing standard ontologies and terminologies (Malhotra et al 2014). An ontology alignment technique can be employed.…”

Section: Methodsmentioning

confidence: 99%

“…All of the existing studies are insufficient. On the other hand, when we searched for other diseases, such as Alzheimer's, we were able to find self-contained ontologies that can be utilized in diverse CDSS applications (Malhotra et al 2014).…”

mentioning

confidence: 99%

DDO: a diabetes mellitus diagnosis ontology

El–Sappagh

Ali

2016

Appl Inform

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“…Speculative statements related to human proteins, which define the progression of AD from 'Mild' to 'Severe' stage, were retrieved from Medline abstracts by using the 'human gene/protein dictionary', 'HypothesisFinder' [8], and ' Alzheimer's disease ontology' (ADO) [11] terminologies within SCAIView [12], a scalable indexing and retrieval platform that has exhibited successful information retrieval scenarios from Medline [13], patents [14], and e-health records [15]. SCAIView supports named entity recognition (NER), information retrieval and information extraction.…”

Section: Domain-specific Information Retrieval and Knowledge Extractionmentioning

confidence: 99%

Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer's disease

Malhotra¹,

Younesi²,

Bagewadi³

et al. 2014

Genome Medicine

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Background: A number of compelling candidate Alzheimer's biomarkers remain buried within the literature. Indeed, there should be a systematic effort towards gathering this information through approaches that mine publicly available data and substantiate supporting evidence through disease modeling methods. In the presented work, we demonstrate that an integrative gray zone mining approach can be used as a way to tackle this challenge successfully. Methods: The methodology presented in this work combines semantic information retrieval and experimental data through context-specific modeling of molecular interactions underlying stages in Alzheimer's disease (AD). Information about putative, highly speculative AD biomarkers was harvested from the literature using a semantic framework and was put into a functional context through disease-and stage-specific models. Staging models of AD were further validated for their functional relevance and novel biomarker candidates were predicted at the mechanistic level.

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ADO: A disease ontology representing the domain knowledge specific to Alzheimer's disease

Abstract: Development of ADO as an open ADO is a first attempt to organize information related to Alzheimer's disease in a formalized, structured manner. We demonstrate that ADO is able to capture both established and scattered knowledge existing in scientific text.

Cited by 97 publications

References 8 publications

Revolution of Alzheimer Precision Neurology. Passageway of Systems Biology and Neurophysiology

Revolution of Alzheimer Precision Neurology. Passageway of Systems Biology and Neurophysiology

DDO: a diabetes mellitus diagnosis ontology

Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer's disease

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