A nanopublication framework for biological networks using Cytoscape.js

James P. McCusker; R. Yan; K. Solanki; J. Erickson; C. Chang; M. Dumontier; Jonathan S. Dordick; Deborah L. McGuinness

A nanopublication framework for biological networks using Cytoscape.js

James P. McCusker, R. Yan, K. Solanki, J. Erickson, C. Chang, M. Dumontier, Jonathan S. Dordick, Deborah L. McGuinness

Research output: Contribution to journal › Conference article in journal › Academic › peer-review

Abstract

We leverage semantic technologies and Cytoscape.js to create a provenance-aware, probabilistic analysis platform for systems biology and evaluate its usefulness in discovering links between drugs and diseases. In our efforts to create a systematic approach to discovering new uses for existing drugs, we have developed Repurposing Drugs with Semantics (ReDrugS). ReDrugS is a data curation and publication framework that accepts data from nearly any database containing biological or chemical entity interactions and produces visualizations using Cytoscape.js. A semantic web service API is provided that enables search, traversal, and provides composite probabilities for the resulting graph of biological entities using the SADI web service framework and Nanopublications. We show how associations between a postive control, topiramate, allows us to independently reconstruct a positive control of epilepsy and migraine, and potential consequences on bone health.

Original language	English
Pages (from-to)	90-92
Number of pages	3
Journal	CEUR Workshop Proceedings
Volume	1327
Publication status	Published - 2014
Externally published	Yes

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title = "A nanopublication framework for biological networks using Cytoscape.js",

abstract = "We leverage semantic technologies and Cytoscape.js to create a provenance-aware, probabilistic analysis platform for systems biology and evaluate its usefulness in discovering links between drugs and diseases. In our efforts to create a systematic approach to discovering new uses for existing drugs, we have developed Repurposing Drugs with Semantics (ReDrugS). ReDrugS is a data curation and publication framework that accepts data from nearly any database containing biological or chemical entity interactions and produces visualizations using Cytoscape.js. A semantic web service API is provided that enables search, traversal, and provides composite probabilities for the resulting graph of biological entities using the SADI web service framework and Nanopublications. We show how associations between a postive control, topiramate, allows us to independently reconstruct a positive control of epilepsy and migraine, and potential consequences on bone health.",

author = "McCusker, {James P.} and R. Yan and K. Solanki and J. Erickson and C. Chang and M. Dumontier and Dordick, {Jonathan S.} and McGuinness, {Deborah L.}",

year = "2014",

language = "English",

volume = "1327",

pages = "90--92",

journal = "CEUR Workshop Proceedings",

issn = "1613-0073",

publisher = "CEUR-WS",

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TY - JOUR

T1 - A nanopublication framework for biological networks using Cytoscape.js

AU - McCusker, James P.

AU - Yan, R.

AU - Solanki, K.

AU - Erickson, J.

AU - Chang, C.

AU - Dumontier, M.

AU - Dordick, Jonathan S.

AU - McGuinness, Deborah L.

PY - 2014

Y1 - 2014

N2 - We leverage semantic technologies and Cytoscape.js to create a provenance-aware, probabilistic analysis platform for systems biology and evaluate its usefulness in discovering links between drugs and diseases. In our efforts to create a systematic approach to discovering new uses for existing drugs, we have developed Repurposing Drugs with Semantics (ReDrugS). ReDrugS is a data curation and publication framework that accepts data from nearly any database containing biological or chemical entity interactions and produces visualizations using Cytoscape.js. A semantic web service API is provided that enables search, traversal, and provides composite probabilities for the resulting graph of biological entities using the SADI web service framework and Nanopublications. We show how associations between a postive control, topiramate, allows us to independently reconstruct a positive control of epilepsy and migraine, and potential consequences on bone health.

AB - We leverage semantic technologies and Cytoscape.js to create a provenance-aware, probabilistic analysis platform for systems biology and evaluate its usefulness in discovering links between drugs and diseases. In our efforts to create a systematic approach to discovering new uses for existing drugs, we have developed Repurposing Drugs with Semantics (ReDrugS). ReDrugS is a data curation and publication framework that accepts data from nearly any database containing biological or chemical entity interactions and produces visualizations using Cytoscape.js. A semantic web service API is provided that enables search, traversal, and provides composite probabilities for the resulting graph of biological entities using the SADI web service framework and Nanopublications. We show how associations between a postive control, topiramate, allows us to independently reconstruct a positive control of epilepsy and migraine, and potential consequences on bone health.

M3 - Conference article in journal

SN - 1613-0073

VL - 1327

SP - 90

EP - 92

JO - CEUR Workshop Proceedings

JF - CEUR Workshop Proceedings

ER -

A nanopublication framework for biological networks using Cytoscape.js

Abstract

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