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Graph-based analysis and visualization of experimental results with ONDEX

J. Kohler, J. Baumbach, J. Taubert, M. Specht, A. Skusa, A. Ruegg, C. Rawlings, P. Verrier, S. Philippi
2006 Bioinformatics  
An overview of the ONDEX system is presented, concentrating on recently developed features for graph-based analysis and visualization.  ...  ONDEX is a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis.  ...  Rothamsted Research Graph analysis of experimental results with ONDEX  ... 
doi:10.1093/bioinformatics/btl081 pmid:16533819 fatcat:u36k6sbn2nbqzm3rbaw4h34iqm

Interactive exploration of integrated biological datasets using context-sensitive workflows

Fabian Horn, Martin Rittweger, Jan Taubert, Artem Lysenko, Christopher Rawlings, Reinhard Guthke
2014 Frontiers in Genetics  
of the resulting network describe the experimental setting.  ...  The Ondex software framework was extended with customizable context-sensitive menus which allow additional integration and data analysis options for a selected set of candidates during interactive data  ...  To that end, the Ondex system incorporates a JavaScript API (based on Mozilla Rhino v1.7) and a rich selection of binding and analysis functions that can be used both to manipulate the graph and to alter  ... 
doi:10.3389/fgene.2014.00021 pmid:24600467 pmcid:PMC3929842 fatcat:pzzmhnzljvhwtg6qwfgblojb7m

WIBL: Workbench for Integrative Biological Learning

Victor Lesk, Jan Taubert, Chris Rawlings, Stuart Dunbar, Stephen Muggleton
2011 Journal of Integrative Bioinformatics  
The construction of integrated datasets from potentially hundreds of sources with bespoke formats, and their subsequent visualization and analysis, is a recurring challenge in systems biology.  ...  We present WIBL, a visualization and model development environment initially geared towards logic-based modelling of biological systems using integrated datasets.  ...  WIBL allows interaction with the data itself, access to a full model development and execution environment, and analysis of results.  ... 
doi:10.2390/biecoll-jib-2011-156 pmid:21705808 fatcat:miaxrlorjbhqrgms6xalwoigr4

WIBL: Workbench for Integrative Biological Learning

Victor Lesk, Jan Taubert, Chris Rawlings, Stuart Dunbar, Stephen Muggleton
2011 Journal of Integrative Bioinformatics  
SummaryThe construction of integrated datasets from potentially hundreds of sources with bespoke formats, and their subsequent visualization and analysis, is a recurring challenge in systems biology.  ...  We present WIBL, a visualization and model development environment initially geared towards logic-based modelling of biological systems using integrated datasets.  ...  WIBL allows interaction with the data itself, access to a full model development and execution environment, and analysis of results.  ... 
doi:10.1515/jib-2011-156 fatcat:gidd676o6jemflabl3h3xkr524

Customizable views on semantically integrated networks for systems biology

Jochen Weile, Matthew Pocock, Simon J. Cockell, Phillip Lord, James M. Dewar, Eva−Maria Holstein, Darren Wilkinson, David Lydall, Jennifer Hallinan, Anil Wipat
2011 Computer applications in the biosciences : CABIOS  
Results: We have created an integrated dataset for Saccharomyces cerevisiae using the semantic data integration tool Ondex, and have developed a view-based visualization technique that allows for concise  ...  Although well suited to computational manipulation, such integrated datasets are typically too large and complex for easy visualization and interactive exploration.  ...  ACKNOWLEDGEMENTS J.W. and M.P. created the Ondex yeast dataset and all required Ondex workflow modules not already present in the Ondex distribution; J.W. and A.W. designed the view-based visualization  ... 
doi:10.1093/bioinformatics/btr134 pmid:21414991 pmcid:PMC3077072 fatcat:pl3aml5nnvgp3d4rqkgg537qaa

Variation of Background Knowledge in an Industrial Application of ILP [chapter]

Stephen H. Muggleton, Jianzhong Chen, Hiroaki Watanabe, Stuart J. Dunbar, Charles Baxter, Richard Currie, José Domingo Salazar, Jan Taubert, Michael J. E. Sternberg
2011 Lecture Notes in Computer Science  
The background knowledge in these applications is extensive and is derived from public databases in a Prolog format using a new system called Ondex (developers BBSRC Rothamsted).  ...  The results indicate that relatively shallow background knowledge is needed to achieve maximum accuracy.  ...  The first author would also like to thank the Royal Academy of Engineering and Microsoft Research for their support of his research chair.  ... 
doi:10.1007/978-3-642-21295-6_19 fatcat:ywi6vl73ajayrasqspcnjlhlgi

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis

Artem Lysenko, Michael Defoin-Platel, Keywan Hassani-Pak, Jan Taubert, Charlie Hodgman, Christopher J Rawlings, Mansoor Saqi
2011 BMC Bioinformatics  
Results: We have defined the functional coherence of modules with respect to the Gene Ontology (GO) by considering two complementary aspects: (i) the fragmentation of the GO functional categories into  ...  From these we have constructed five relationship networks, four based on single types of data: PPI, co-expression, co-occurrence of protein names in scientific literature abstracts and sequence similarity  ...  KHP and JT were supported by the Ondex BBSRC SABR Grant BB/F006039/1 which also partially supported MS and CJR.  ... 
doi:10.1186/1471-2105-12-203 pmid:21612636 pmcid:PMC3118170 fatcat:2zjsqqyyzbbrrphakbcle7zsqi

The OXL format for the exchange of integrated datasets

Jan Taubert, Klaus Peter Sieren, Matthew Hindle, Berend Hoekman, Rainer Winnenburg, Stephan Philippi, Chris Rawlings, Jacob Köhler
2007 Journal of Integrative Bioinformatics  
AbstractA prerequisite for systems biology is the integration and analysis of heterogeneous experimental data stored in hundreds of life-science databases and millions of scientific publications.  ...  Although OXL was developed with the ONDEX system in mind, it also has the potential to be used in several other biological and non-biological applications described in this paper.Availability: The OXL  ...  The OVTK uses the same "core" and provides additional graph-based visualisation and analysis methods.  ... 
doi:10.1515/jib-2007-62 fatcat:dcu2yd3eunfu5bnrwwta3sdh44

A survey of visualization tools for biological network analysis

Georgios A Pavlopoulos, Anna-Lynn Wegener, Reinhard Schneider
2008 BioData Mining  
There are a wide variety of graph representations available, which most often map the data on 2D graphs to visualize biological interactions.  ...  The analysis and interpretation of relationships between biological molecules, networks and concepts is becoming a major bottleneck in systems biology.  ...  BioPAX is the most expressive language and is based on a rich hierarchy, which as a trade-off can result in a high degree of computational complexity.  ... 
doi:10.1186/1756-0381-1-12 pmid:19040716 pmcid:PMC2636684 fatcat:6qcsxsndmrggvilfw5ssw4zamu

VANTED v2: a framework for systems biology applications

Hendrik Rohn, Astrid Junker, Anja Hartmann, Eva Grafahrend-Belau, Hendrik Treutler, Matthias Klapperstück, Tobias Czauderna, Christian Klukas, Falk Schreiber
2012 BMC Systems Biology  
Networks provide a basis for the integration, analysis and visualization of multi-omics experimental datasets.  ...  These range from network reconstruction, data visualization, integration of various data types, network simulation to data exploration combined with a manifold support of systems biology standards for  ...  Acknowledgements This work has been partly funded by BMBF (grants 0312706A, 3015426A, RUS 10/131) and DAAD (grant 54391720).  ... 
doi:10.1186/1752-0509-6-139 pmid:23140568 pmcid:PMC3610154 fatcat:bnljyn4y3bepbly36smhjwcxjm

PHI-base update: additions to the pathogen host interaction database

R. Winnenburg, M. Urban, A. Beacham, T. K. Baldwin, S. Holland, M. Lindeberg, H. Hansen, C. Rawlings, K. E. Hammond-Kosack, J. Kohler
2007 Nucleic Acids Research  
The number of fields that characterize PHI-base entries has almost doubled.  ...  The pathogen-host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens  ...  ACKNOWLEDGEMENTS The authors would like to thank the FRAC team for allowing inclusion of their data on fungicides and the PAMGO group for compiling a useful ontology on microbe-host interactions.  ... 
doi:10.1093/nar/gkm858 pmid:17942425 pmcid:PMC2238852 fatcat:3icb7nv7zrgvlpanwr3gy7ycee

Integrating semantic transcriptomic data analysis and knowledge extraction from biological literature

Vid Podpecan, Dragana Miljkovic, Marko Petek, Tjasa Stare, Kristina Gruden, Igor Mozetic, Nada Lavrac
2013 2013 IEEE International Conference on Bioinformatics and Biomedicine  
We have integrated a methodology for semantic analysis of transcriptomic data, a system for automated extraction of biological relations from the literature, and a number of supporting components.  ...  The paper presents an approach to the holistic analysis of transcriptomic data which integrates two state-ofthe-art methodologies into a coherent framework.  ...  The text mining feature, however, is rather limited and ONDEX relies on external tools for the analysis of transcriptomic experimental data.  ... 
doi:10.1109/bibm.2013.6732540 dblp:conf/bibm/PodpecanMPSGML13 fatcat:s5e77i2lmzaite53apx5js36oi

KnetMaps: a BioJS component to visualize biological knowledge networks

Ajit Singh, Christopher J. Rawlings, Keywan Hassani-Pak
2018 F1000Research  
KnetMaps loads data in JSON format, visualizes the structure and content of knowledge networks using lightweight JavaScript libraries, and supports interactive touch gestures.  ...  KnetMaps is a BioJS component for the interactive visualization of biological knowledge networks.  ...  Acknowledgements We are grateful to Max Franz for fruitful discussions on cytoscape.js integration, network rendering and other user interaction elements.  ... 
doi:10.12688/f1000research.16605.1 pmid:30755790 pmcid:PMC6347035 fatcat:5psh3tbm5na77dvmewkhecofni

Semantic integration of data on transcriptional regulation

Michael Baitaluk, Julia Ponomarenko
2010 Computer applications in the biosciences : CABIOS  
Results: IntegromeDB, a semantic graph-based 'deep-web'  ...  Motivation: Experimental and predicted data concerning gene transcriptional regulation are distributed among many heterogeneous sources.  ...  Sedova and A. Gupta for valuable discussions and assistance in creation of IntegromeDB and W. Bluhm for critical reading of the manuscript.  ... 
doi:10.1093/bioinformatics/btq231 pmid:20427517 pmcid:PMC2887046 fatcat:7g6zzhyjbzaplhqauhptunr47q

Network-Based Data Integration for Selecting Candidate Virulence Associated Proteins in the Cereal Infecting Fungus Fusarium graminearum

Artem Lysenko, Martin Urban, Laura Bennett, Sophia Tsoka, Elzbieta Janowska-Sejda, Chris J. Rawlings, Kim E. Hammond-Kosack, Mansoor Saqi, Yin-Won Lee
2013 PLoS ONE  
, we found a total of 215 new proteins potentially associated with virulence of which 29 are annotated as hypothetical proteins.  ...  The analysis of already verified virulence genes in phytopathogenic fungi in the context of integrated functional networks can give clues about the underlying mechanisms and pathways directly or indirectly  ...  Methods The Integrated Network Starting with version 3.3 of PHI-base, Fusarium graminearum genes were selected whose contributions to virulence have been tested experimentally and were classified according  ... 
doi:10.1371/journal.pone.0067926 pmid:23861834 pmcid:PMC3701590 fatcat:x24xevyndzavnpflx3epmemufy
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