Hierarchical Biological Pathway Data Integration and Mining

Biological pathway data integration trends, techniques, issues and challenges: A survey

2010 Second World Congress on Nature and Biologically Inspired Computing (NaBIC) ◽

10.1109/nabic.2010.5716330 ◽

2010 ◽

Cited By ~ 2

Author(s):

Shubhalaxmi Kher ◽

Julie Dickerson ◽

Neelam Rawat

Keyword(s):

Data Integration ◽

Biological Pathway ◽

Pathway Data

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Biological Pathway Data Formats and Standards

Encyclopedia of Bioinformatics and Computational Biology ◽

10.1016/b978-0-12-809633-8.20432-9 ◽

2019 ◽

pp. 1063-1066

Author(s):

Ramakanth C. Venkata ◽

Dario Ghersi

Keyword(s):

Biological Pathway ◽

Data Formats ◽

Pathway Data

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KEGGscape: a Cytoscape app for pathway data integration

F1000Research ◽

10.12688/f1000research.4524.1 ◽

2014 ◽

Vol 3 ◽

pp. 144 ◽

Cited By ~ 38

Author(s):

Kozo Nishida ◽

Keiichiro Ono ◽

Shigehiko Kanaya ◽

Koichi Takahashi

Keyword(s):

Experimental Data ◽

Data Integration ◽

Web Application ◽

Biological Database ◽

Data Sets ◽

E Coli ◽

Pathway Data ◽

Visual Style ◽

Interactive Visualizations ◽

Pathway Diagrams

In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape (http://apps.cytoscape.org/apps/keggscape). KEGG is a comprehensive public biological database that contains large collection of human curated pathways. KEGGscape utilizes the database to reproduce the corresponding hand-drawn pathway diagrams with as much detail as possible in Cytoscape. Further, it allows users to import pathway data sets to visualize biologist-friendly diagrams using the Cytoscape core visualization function (Visual Style) and the ability to perform pathway analysis with a variety of Cytoscape apps. From the analyzed data, users can create complex and interactive visualizations which cannot be done in the KEGG PATHWAY web application. Experimental data with Affymetrix E. coli chips are used as an example to demonstrate how users can integrate pathways, annotations, and experimental data sets to create complex visualizations that clarify biological systems using KEGGscape and other Cytoscape apps.

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Genetic analysis of biological pathway data through genomic randomization

Human Genetics ◽

10.1007/s00439-011-0956-2 ◽

2011 ◽

Vol 129 (5) ◽

pp. 563-571 ◽

Cited By ~ 35

Author(s):

Brian L. Yaspan ◽

William S. Bush ◽

Eric S. Torstenson ◽

Deqiong Ma ◽

Margaret A. Pericak-Vance ◽

...

Keyword(s):

Genetic Analysis ◽

Biological Pathway ◽

Pathway Data

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Pathway Commons, a web resource for biological pathway data

Nucleic Acids Research ◽

10.1093/nar/gkq1039 ◽

2010 ◽

Vol 39 (Database) ◽

pp. D685-D690 ◽

Cited By ~ 684

Author(s):

E. G. Cerami ◽

B. E. Gross ◽

E. Demir ◽

I. Rodchenkov ◽

O. Babur ◽

...

Keyword(s):

Biological Pathway ◽

Web Resource ◽

Pathway Data

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Pathway Resources at the Rat Genome Database

Handbook of Research on Computational and Systems Biology ◽

10.4018/978-1-60960-491-2.ch014 ◽

2011 ◽

pp. 316-336 ◽

Cited By ~ 1

Author(s):

Victoria Petri

Keyword(s):

Research Community ◽

Biological Pathway ◽

Genome Database ◽

Future Directions ◽

Pathway Information ◽

Pathway Data ◽

Pathway Diagrams ◽

Rat Genome ◽

Literature Curation

The set of interacting molecules representing a biological pathway or network is a central concept in biology. It is within the pathway context that the functioning of individual molecules acquires purpose and it is the integration of these molecular circuitries that underlies the functioning of biological systems. In order to provide the research community with a dynamic platform for accessing pathway information, the Rat Genome Database (RGD – http://rgd.mcw.edu) is using a multi-tiered approach. In this chapter, the pathway resources that RGD currently offers are presented. Issues covered include: the biological pathway, the concept and the ontology, pathway literature curation and annotation of genes, interactive pathway diagrams, and tools and resources to access and navigate between pathway data. A case study is presented; future directions are discussed.

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BioPAX - biological pathway data exchange format

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics ◽

10.1002/047001153x.g408117 ◽

2006 ◽

Cited By ~ 5

Author(s):

Gary D. Bader ◽

Michael P. Cary ◽

Chris Sander

Keyword(s):

Data Exchange ◽

Biological Pathway ◽

Data Exchange Format ◽

Exchange Format ◽

Pathway Data

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Multipath: An R Package to Generate Integrated Reproducible Pathway Models

Biology ◽

10.3390/biology9120483 ◽

2020 ◽

Vol 9 (12) ◽

pp. 483

Author(s):

Zaynab Hammoud ◽

Frank Kramer

Keyword(s):

Data Integration ◽

Wnt Pathway ◽

R Package ◽

The Past ◽

Pathway Data ◽

Multiple Pathway ◽

Pathway Models ◽

Numerous Data ◽

The Many ◽

Specific Pathway

Biological pathway data integration has become a topic of interest in the past years. This interest originates essentially from the continuously increasing size of existing prior knowledge as well as from the many challenges scientists face when studying biological pathways. Multipath is a framework that aims at helping re-trace the use of specific pathway knowledge in specific publications, and easing the data integration of multiple pathway types and further influencing knowledge sources. Multipath thus helps scientists to increase the reproducibility of their code and analysis by allowing the integration of numerous data sources and documentation of their integration steps while doing so. In this paper, we present the package Multipath, and we describe how it can be used for data integration and tracking pathway modifications. We present a multilayer model built from the Wnt Pathway as a demonstration.

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