A nanopublication framework for biological networks using cytoscape.Js

James P. McCusker; Rui Yan; Kusum Solanki; John Erickson; Cynthia Chang; Michel Dumontier; Jonathan S. Dordick; Deborah L. McGuinness

A nanopublication framework for biological networks using cytoscape.Js

James P. McCusker
, Rui Yan
, Kusum Solanki
, John Erickson
, Cynthia Chang
, Michel Dumontier
, Jonathan S. Dordick
, Deborah L. McGuinness

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

1 Scopus citations

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
State	Published - 2014
Externally published	Yes
Event	5th International Conference on Biomedical Ontology, ICBO 2014 - Houston, United States Duration: 8 Oct 2014 → 9 Oct 2014

Cite this

@article{47c689aa1b69402c90d6ea1add16cb24,

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 Rui Yan and Kusum Solanki and John Erickson and Cynthia Chang and Michel 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",

note = "5th International Conference on Biomedical Ontology, ICBO 2014 ; Conference date: 08-10-2014 Through 09-10-2014",

}

TY - JOUR

T1 - A nanopublication framework for biological networks using cytoscape.Js

AU - McCusker, James P.

AU - Yan, Rui

AU - Solanki, Kusum

AU - Erickson, John

AU - Chang, Cynthia

AU - Dumontier, Michel

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.

UR - https://www.scopus.com/pages/publications/84926333652

M3 - Conference article

AN - SCOPUS:84926333652

SN - 1613-0073

VL - 1327

SP - 90

EP - 92

JO - CEUR Workshop Proceedings

JF - CEUR Workshop Proceedings

T2 - 5th International Conference on Biomedical Ontology, ICBO 2014

Y2 - 8 October 2014 through 9 October 2014

ER -

A nanopublication framework for biological networks using cytoscape.Js

Abstract

Fingerprint

Cite this