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Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking.

Soh J, Gordon PM, Taschuk ML, Dong A, Ah-Seng AC, Turinsky AL, Sensen CW - BMC Bioinformatics (2008)

Bottom Line: Bluejay 1.0 also embeds the Seahawk browser for the Moby protocol, enabling users to seamlessly invoke hundreds of Web Services on genomic data of interest without any hard-coding.Bluejay offers a unique set of customizable genome-browsing features, with the goal of allowing biologists to quickly focus on, analyze, compare, and retrieve related information on the parts of the genomic data they are most interested in.We expect these capabilities of Bluejay to benefit the many biologists who want to answer complex questions using the information available from completely sequenced genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Calgary, Faculty of Medicine, Sun Center of Excellence for Visual Genomics, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada. jsoh@ucalgary.ca

ABSTRACT

Background: The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research. Beginning with a browser capable of rendering views of XML-based genomic information and providing scalable vector graphics output, we have now completed version 1.0 of the system with many additional features. Our development efforts were guided by our observation that biologists who use both gene expression profiling and comparative genomics gain functional insights above and beyond those provided by traditional per-gene analyses.

Results: Bluejay 1.0 is a genome viewer integrating genome annotation with: (i) gene expression information; and (ii) comparative analysis with an unlimited number of other genomes in the same view. This allows the biologist to see a gene not just in the context of its genome, but also its regulation and its evolution. Bluejay now has rich provision for personalization by users: (i) numerous display customization features; (ii) the availability of waypoints for marking multiple points of interest on a genome and subsequently utilizing them; and (iii) the ability to take user relevance feedback of annotated genes or textual items to offer personalized recommendations. Bluejay 1.0 also embeds the Seahawk browser for the Moby protocol, enabling users to seamlessly invoke hundreds of Web Services on genomic data of interest without any hard-coding.

Conclusion: Bluejay offers a unique set of customizable genome-browsing features, with the goal of allowing biologists to quickly focus on, analyze, compare, and retrieve related information on the parts of the genomic data they are most interested in. We expect these capabilities of Bluejay to benefit the many biologists who want to answer complex questions using the information available from completely sequenced genomes.

Show MeSH
Hybrid recommender and personalized search. A matched item from the search engine is ranked, based on previously learned user preferences, and then refined by the system's knowledge of its importance. An example: (a) A search for "oxidoreductase"' is performed on the Sulfolobus solfataricus genome; (b) The relevance for each search item is listed in the Relevance column. Items containing "Fe-S" have the highest relevance due to TF-IDF ranking. The user subsequently rates items containing Fe-S low (1) and items containing NADH high (5) using the Feature Rating column (rating action not shown); (c) In a subsequent search for oxidoreductase, the items containing NADH are rated above those containing Fe-S, based on the user profile.
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Figure 4: Hybrid recommender and personalized search. A matched item from the search engine is ranked, based on previously learned user preferences, and then refined by the system's knowledge of its importance. An example: (a) A search for "oxidoreductase"' is performed on the Sulfolobus solfataricus genome; (b) The relevance for each search item is listed in the Relevance column. Items containing "Fe-S" have the highest relevance due to TF-IDF ranking. The user subsequently rates items containing Fe-S low (1) and items containing NADH high (5) using the Feature Rating column (rating action not shown); (c) In a subsequent search for oxidoreductase, the items containing NADH are rated above those containing Fe-S, based on the user profile.

Mentions: The Bluejay system includes a hybrid recommender system composed of a knowledge-based recommender and a content-based recommender [17], as part of its search engine (Figure 4). The knowledge-based component is implemented using the term frequency-inverse document frequency (TF-IDF) text mining algorithm [18] as follows: (i) matched items, annotated genes and other textual items in Bluejay's search results are regarded as "documents"; and (ii) single words found in each document in the search results are taken as "terms". When there is no user profile, the algorithm solely determines the ranking of the search results. Since gene annotations vary widely in length, normalization is applied to the rankings to lessen the influence of document sizes.


Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking.

Soh J, Gordon PM, Taschuk ML, Dong A, Ah-Seng AC, Turinsky AL, Sensen CW - BMC Bioinformatics (2008)

Hybrid recommender and personalized search. A matched item from the search engine is ranked, based on previously learned user preferences, and then refined by the system's knowledge of its importance. An example: (a) A search for "oxidoreductase"' is performed on the Sulfolobus solfataricus genome; (b) The relevance for each search item is listed in the Relevance column. Items containing "Fe-S" have the highest relevance due to TF-IDF ranking. The user subsequently rates items containing Fe-S low (1) and items containing NADH high (5) using the Feature Rating column (rating action not shown); (c) In a subsequent search for oxidoreductase, the items containing NADH are rated above those containing Fe-S, based on the user profile.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2590619&req=5

Figure 4: Hybrid recommender and personalized search. A matched item from the search engine is ranked, based on previously learned user preferences, and then refined by the system's knowledge of its importance. An example: (a) A search for "oxidoreductase"' is performed on the Sulfolobus solfataricus genome; (b) The relevance for each search item is listed in the Relevance column. Items containing "Fe-S" have the highest relevance due to TF-IDF ranking. The user subsequently rates items containing Fe-S low (1) and items containing NADH high (5) using the Feature Rating column (rating action not shown); (c) In a subsequent search for oxidoreductase, the items containing NADH are rated above those containing Fe-S, based on the user profile.
Mentions: The Bluejay system includes a hybrid recommender system composed of a knowledge-based recommender and a content-based recommender [17], as part of its search engine (Figure 4). The knowledge-based component is implemented using the term frequency-inverse document frequency (TF-IDF) text mining algorithm [18] as follows: (i) matched items, annotated genes and other textual items in Bluejay's search results are regarded as "documents"; and (ii) single words found in each document in the search results are taken as "terms". When there is no user profile, the algorithm solely determines the ranking of the search results. Since gene annotations vary widely in length, normalization is applied to the rankings to lessen the influence of document sizes.

Bottom Line: Bluejay 1.0 also embeds the Seahawk browser for the Moby protocol, enabling users to seamlessly invoke hundreds of Web Services on genomic data of interest without any hard-coding.Bluejay offers a unique set of customizable genome-browsing features, with the goal of allowing biologists to quickly focus on, analyze, compare, and retrieve related information on the parts of the genomic data they are most interested in.We expect these capabilities of Bluejay to benefit the many biologists who want to answer complex questions using the information available from completely sequenced genomes.

View Article: PubMed Central - HTML - PubMed

Affiliation: University of Calgary, Faculty of Medicine, Sun Center of Excellence for Visual Genomics, 3330 Hospital Drive NW, Calgary, AB, T2N 4N1, Canada. jsoh@ucalgary.ca

ABSTRACT

Background: The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research. Beginning with a browser capable of rendering views of XML-based genomic information and providing scalable vector graphics output, we have now completed version 1.0 of the system with many additional features. Our development efforts were guided by our observation that biologists who use both gene expression profiling and comparative genomics gain functional insights above and beyond those provided by traditional per-gene analyses.

Results: Bluejay 1.0 is a genome viewer integrating genome annotation with: (i) gene expression information; and (ii) comparative analysis with an unlimited number of other genomes in the same view. This allows the biologist to see a gene not just in the context of its genome, but also its regulation and its evolution. Bluejay now has rich provision for personalization by users: (i) numerous display customization features; (ii) the availability of waypoints for marking multiple points of interest on a genome and subsequently utilizing them; and (iii) the ability to take user relevance feedback of annotated genes or textual items to offer personalized recommendations. Bluejay 1.0 also embeds the Seahawk browser for the Moby protocol, enabling users to seamlessly invoke hundreds of Web Services on genomic data of interest without any hard-coding.

Conclusion: Bluejay offers a unique set of customizable genome-browsing features, with the goal of allowing biologists to quickly focus on, analyze, compare, and retrieve related information on the parts of the genomic data they are most interested in. We expect these capabilities of Bluejay to benefit the many biologists who want to answer complex questions using the information available from completely sequenced genomes.

Show MeSH