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Graph-based analysis and visualization of experimental results with ONDEX
2006
Bioinformatics
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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
2014
Frontiers in Genetics
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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
2011
Journal of Integrative Bioinformatics
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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
2011
Journal of Integrative Bioinformatics
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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
2011
Computer applications in the biosciences : CABIOS
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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]
2011
Lecture Notes in Computer Science
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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
2011
BMC Bioinformatics
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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
2007
Journal of Integrative Bioinformatics
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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
2008
BioData Mining
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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
2012
BMC Systems Biology
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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
2007
Nucleic Acids Research
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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
2013
2013 IEEE International Conference on Bioinformatics and Biomedicine
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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
2018
F1000Research
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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
2010
Computer applications in the biosciences : CABIOS
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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
2013
PLoS ONE
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, 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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