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NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

Kevin R. Brown, David Otasek, Muhammad Ali, Michael J. McGuffin, Wing Xie, Baiju Devani, Ian Lawson van Toch, Igor Jurisica
2009 Computer applications in the biosciences : CABIOS  
NAViGaTOR supports community-developed data formats (PSI-XML, BioPax and GML), is platform-independent and is extensible through a plug-in architecture.  ...  NAViGaTOR includes a rich suite of visual mark-up tools for manual and automated annotation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large  ...  the GRIP layout, and Uzma Khan for helping with updating and improving the NAViGaTOR web site (http://ophid.utoronto.ca/navigator/).  ... 
doi:10.1093/bioinformatics/btp595 pmid:19837718 pmcid:PMC2788933 fatcat:nzwexmnclzaalbu4hi54pnswba

An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence

Satya S. Sahoo, Olivier Bodenreider, Joni L. Rutter, Karen J. Skinner, Amit P. Sheth
2008 Journal of Biomedical Informatics  
The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created.  ...  We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources.  ...  The authors want to thank Lee Peters who created the RDF store in Oracle and helped craft and run the SPARQL queries and Jonathan Pollock for valuable input on model organism databases.  ... 
doi:10.1016/j.jbi.2008.02.006 pmid:18395495 pmcid:PMC2766186 fatcat:2pyc76cacvfl5npklwhksksb7a

PathCase: pathways database system

B. Elliott, M. Kirac, A. Cakmak, G. Yavas, S. Mayes, E. Cheng, Y. Wang, C. Gupta, G. Ozsoyoglu, Z. Meral Ozsoyoglu
2008 Bioinformatics  
PathCase is now available for three different datasets, namely, KEGG pathways data, sample pathways from the literature and BioCyc pathways for humans.  ...  , (ii) an interactive client-side visualization tool for metabolic pathways, with powerful visualization capabilities, and with integrated gene and organism viewers, (iii) two distinct querying capabilities  ...  Wang Foundation to the Center for  ... 
doi:10.1093/bioinformatics/btn459 pmid:18728044 fatcat:25jn4wwelzahlp235bygmz2hha

PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways

N. Maltsev
2006 Nucleic Acids Research  
Genomic data is annotated with information integrated from .20 sequence, structural and metabolic databases and ontologies.  ...  PUMA2 allows users to submit batch sequence data for automated functional analysis and construction of metabolic models.  ...  ACKNOWLEDGEMENTS The PUMA2 development team is grateful for the help, advice and invaluable contributions from the ANL Globus group, especially Mike Wilde, Veronika Nefedova and Ian Foster; former members  ... 
doi:10.1093/nar/gkj095 pmid:16381888 pmcid:PMC1347457 fatcat:mgv7alb7cfapnl55exjkgs2ru4

Reactome pathway analysis to enrich biological discovery in proteomics data sets

Robin Haw, Henning Hermjakob, Peter D'Eustachio, Lincoln Stein
2011 Proteomics  
Reactome's diverse pathway knowledge and suite of data analysis tools provide a platform for data mining, modeling and the analysis of large-scale proteomics datasets.  ...  PSI Common Query Interface (PSIQUIC) web services to overlay pathways with molecular interaction data from the Reactome Functional Interaction (FI) Network and interaction databases such as IntAct, ChEMBL  ...  We are also grateful to the many scientists who collaborated with us to build the Reactome pathway content.  ... 
doi:10.1002/pmic.201100066 pmid:21751369 pmcid:PMC4617659 fatcat:vbijvdmnuvbdrc4xicxpnq2zoy

Navigating the disease landscape: knowledge representations for contextualizing molecular signatures

2018 Briefings in Bioinformatics  
The contextualization of these patterns is important for obtaining mechanistic insight into the aberrant processes associated with a disease, and this typically involves the integration of multiple heterogeneous  ...  types of data.  ...  The work was also partially supported by Core Research for Evolutional Science and Technology (CREST) Grant from the Japan Science and Technology Agency (Grant Number: JPMJCR1412), and Japan Society for  ... 
doi:10.1093/bib/bby025 pmid:29684165 pmcid:PMC6556902 fatcat:iyfard4tdzgnnmhhiqibld756a

PharmGKB: The Pharmacogenomics Knowledge Base [chapter]

Caroline F. Thorn, Teri E. Klein, Russ B. Altman
2013 Msphere  
The PharmGKB Web site, http:// www.pharmgkb.org, displays genotype, molecular, and clinical knowledge integrated into pathway representations and Very Important Pharmacogene (VIP) summaries with links  ...  Registered users can access and download data to aid in the design of future pharmacogenetics and pharmacogenomics studies.  ...  PharmGKB exchanges data with Drugbank, dbSNP, the CYP alleles database, and HuGE Navigator. Data is imported from HGNC, Entrez, and UCSC Golden Path.  ... 
doi:10.1007/978-1-62703-435-7_20 pmid:23824865 pmcid:PMC4084821 fatcat:gd3vn7hncjeyjku4lixwpncubi

BiNA: A Visual Analytics Tool for Biological Network Data

Andreas Gerasch, Daniel Faber, Jan Küntzer, Peter Niermann, Oliver Kohlbacher, Hans-Peter Lenhof, Michael Kaufmann, Alexey Porollo
2014 PLoS ONE  
Highly configurable visualization styles for regulatory and metabolic network data offer sophisticated drawings and intuitive navigation and exploration techniques using hierarchical graph concepts.  ...  Concise and easily readable graphical representation of data and interactive navigation of large data sets are essential in this context.  ...  Acknowledgments Our thanks go to Mark Rurik, Johannes Veit, and Matthias Walzer for persistent and intensive software testing.  ... 
doi:10.1371/journal.pone.0087397 pmid:24551056 pmcid:PMC3923765 fatcat:m6mtpy5cr5f75ezss43tf466li

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

Anwesha Bohler, Lars M. T. Eijssen, Martijn P. van Iersel, Christ Leemans, Egon L. Willighagen, Martina Kutmon, Magali Jaillard, Chris T. Evelo
2015 BMC Bioinformatics  
Subsequently, we analyse a publicly available NCBI GEO gene expression dataset studying tumour bearing mice treated with cyclophosphamide in R.  ...  for functional analysis of processed genomics data.  ...  Acknowledgements We thank Sacha Bohler for his help with the manuscript and figures, Susan Coort for helpful discussions, and Nuno Nunes for technical support.  ... 
doi:10.1186/s12859-015-0708-8 pmid:26298294 pmcid:PMC4546821 fatcat:cutzestcqrbwxe5bz5gosj5qce

An Overview of Computational Life Science Databases & Exchange Formats of Relevance to Chemical Biology Research

Aaron Smalter Hall, Yunfeng Shan, Gerald Lushington, Mahesh Visvanathan
2013 Combinatorial chemistry & high throughput screening  
This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations.  ...  Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences.  ...  BIOPAX-Biological pathway data exchange) [32] format was designed to support metabolic pathway data and is implemented according to OWL standards which are the most important for biological pathways  ... 
doi:10.2174/1386207311316030004 pmid:22934944 pmcid:PMC4782780 fatcat:ysdou5m3nvdg5gzhkzyczo6jyq

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

Yves Sucaet, Eve Wurtele
2010 BMC Research Notes  
Convenient programmatic access to different biological databases allows automated integration of scientific knowledge.  ...  Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates).  ...  Special thanks go to John L Van Hemert and Xiaoyong Sun, as well as Martijn Van Iersel for off-site interface testing.  ... 
doi:10.1186/1756-0500-3-312 pmid:21083943 pmcid:PMC2998519 fatcat:4ik6yrcp5vdjhkv5l42wjpncpu

Visual Data Mining of Biological Networks: One Size Does Not Fit All

Chiara Pastrello, David Otasek, Kristen Fortney, Giuseppe Agapito, Mario Cannataro, Elize Shirdel, Igor Jurisica, Fran Lewitter
2013 PLoS Computational Biology  
It is often useful to integrate these datasets using pathways and protein interaction networks to get a broader view of the experiment.  ...  The integration of such diverse data is necessary for the qualitative analysis of information relevant to hypotheses or discoveries.  ...  At this point, the network comprised 219 nodes and 1,195 edges (data available as a NAViGaTOR XML file in Dataset S1); the default visualization for this network is the infamous ''hairball''.  ... 
doi:10.1371/journal.pcbi.1002833 pmid:23341759 pmcid:PMC3547662 fatcat:6n5zpe6s6zbepdwybfdo3heqd4

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Mikaela Koutrouli, Foteini Thanati, Kleanthi Voutsadaki, Maria Gkonta, Joana Hotova, Ioannis Kasionis, Pantelis Hatzis, Georgios A. Pavlopoulos
2021 Biomolecules  
To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability  ...  Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions.  ...  For example, the Systems Biology Markup Language (SBML) is mainly used for biochemical networks and biological processes, the Biological Pathway Exchange format (BioPAX) for biological pathways, the PSI-MI  ... 
doi:10.3390/biom11081245 pmid:34439912 pmcid:PMC8391349 fatcat:32aums2jtbc5vdcdknzfczajsy

Resources for integrative systems biology: from data through databases to networks and dynamic system models

Aylwin Ng, Borisas Bursteinas, Qiong Gao, Ewan Mollison, Marketa Zvelebil
2006 Briefings in Bioinformatics  
He is a scientific officer at the Ludwig Institute and is currently involved in data curation and integration.  ...  In systems biology, biologically relevant quantitative modelling of physiological processes requires the integration of experimental data from diverse sources.  ...  Acknowledgements The authors thank Anne Ridley and Buzz Baum for very helpful discussions, David Sims and Konstantinos Lykostratis for suggesting several useful websites for inclusion into the list of  ... 
doi:10.1093/bib/bbl036 pmid:17040977 fatcat:lfu4hga62zegdalxxvex3ugfju

Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer

Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Zinovyev, Inna Kuperstein
2019 BMC Bioinformatics  
The integrated networks were applied for comparison of immunoreactive and proliferative ovarian cancer subtypes using transcriptomic, copy number and mutation multiomics data.  ...  We aim at filling in this gap by integrating of both signalling and metabolic pathways allowing a visual exploration of multi-level omics data and study of cross-regulatory circuits between these processes  ...  This article did not receive sponsorship for publication. Availability of data and materials The open sources of multi-omics data used in this article are indicated.  ... 
doi:10.1186/s12859-019-2682-z fatcat:p25o3csfmnd73klsslbn537xvu
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