KEDRI - Brain-Gene Ontology

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Brain-Gene Ontology

Team
Prof. Nikola Kasabov, Vishal Jain, Paulo C. M. Gottgtroy, Dr. Lubica Benuskova and Frances Joseph

Contact Author
Vishal Jain: vishal.jain@aut.ac.nz

Description
“BGO” system is a teaching and research tool in neuroscience area that includes various concepts, facts, data, graphs, videos, animations, and other information forms, related to brain functions, brain diseases, their genetic basis and the relationship between all of them. Relationships are represented graphically that enables visualisation and creation of new relationships. Behind this system is Computational Neurogenetic Modelling (CNGM), a novel research attempt to simulate brain functions or a brain disease manifestation and ontology maps (linked to diseases) which provides a conceptual framework to store and access factual knowledge.

“BGO” System
The system is incorporated into the Protégé which is a open source ontology building environment developed by the Medical Informatics Department of the Stanford University (http://protege.stanford.edu/index.html).

BGO is based on the two most used biological data sources, named Gene Ontology, and Unified Medical Language System – UMLS, along with knowledge integrated from gene expressions databases. It also incorporates knowledge acquired from biology domain experts and from different literature databases such as PubMed. The user can dive into each item to obtain the description, illustrations, and links to PubMed publications and other relevant web resources.

BGO is represented as a knowledge base which is available to applications that need to use and/or share the knowledge of the domain. BGO utilizes a novel evolving conceptual metadata structure which allows incorporation of new discoveries and adapt its structure. In addition, inclusion of 3D animation, gives both a dynamic narrative introduction and overview to the BGO.

Desired data from the BGO system may be selected and exported in text file or NEUCOM format file to integrate the power of BGO with other novel softwares. To use the BGO in conjunction with other computational intelligence or machine learning tools like “NEUCOM, SIFTWARE, WEKA and CLUSTALW etc. you may have to obtain the licence permission from the respective organization. Please note that at this stage we have made available only the public data from the released version of BGO but if the user is interested in the developed BGO ontology on some other datasets like for example LTP time series microarray dataset, you should be in touch with the corresponding person of this project. In addition, the animations and the demo movie specially made as a tutorial on “how to use the system” are not included in the version currently available through WWW, however they may be provided onto the CD to the potential users.

Acknowledgment
This research work has been supported by the NERF grant AUTX02001 funded by FRST, RELT grant (AUT) and by KEDRI funds. WWW version of BGO is freely available for academic users and is for “non-commercial” use only.

Links
1. Download the BGO System (zipped file containing the Protégé, BGO project and required JAVA version etc.)

2. Readme file (step by step instruction guide on how to install the BGO system on your computer)

3. Reference Papers (list and link to the published papers related to BGO project)

4. Download Protégé

5. Download JAVA




Last updated: 02 Dec 2011 10:07am

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