Pathways database system: an integrated system for biological pathways

Krishnamurthy, L.; Nadeau, Joseph H.; Özsoyoǧlu, Gültekin; Özsoyoğlu, Z. Meral; Schaeffer, Greg; Taşan, Murat; Xu, Wanhong

doi:10.1093/bioinformatics/btg113

Cited by 81 publications

(58 citation statements)

References 2 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Dr Z. Meral Ozsoyoglu of Case Western Reserve University discussed recent advances in computational tools for storing, indexing, querying, visualizing and analysing biological (genetic regulatory, signalling and metabolic) pathways (Krishnamurthy et al 2003). She focused on a newly integrated set of database software tools, called PathCase (Ozsoyoglu et al 2006).…”

Section: Integration Of Strategies To Understand Complexitymentioning

confidence: 99%

Integration of structural and functional genomics

2006

View full text Add to dashboard Cite

SummaryThis paper introduces a special issue of Animal Genetics, which is devoted to the recent symposium held at Iowa State University entitled ÔIntegration of Structural and Functional GenomicsÕ. We describe issues and needs that confront the animal genomics community, and describe how this symposium was structured to address these issues by improving communication and collaboration across species and disciplines. The session topics and oral presentations are briefly described for all invited speakers.

show abstract

Section: Integration Of Strategies To Understand Complexitymentioning

confidence: 99%

Integration of structural and functional genomics

2006

View full text Add to dashboard Cite

show abstract

“…Biological entities, such as proteins and molecules, consist of sequences of elements, in the same way that the navigational patterns consist of sequences of categories of the portal hierarchy [7,9,5]. However, in this field, user requirements are different and, thus, mining tasks needed are different, too (e.g.…”

Section: Related Workmentioning

confidence: 99%

“…However, in this field, user requirements are different and, thus, mining tasks needed are different, too (e.g. one can ask for the cofactors of a reaction) [7]. Also, there are many approaches that exploit Web logs of proxy servers to observe users behavior in Internet sites [4,8,10,11,17].…”

Section: Related Workmentioning

confidence: 99%

See 1 more Smart Citation

NaviMoz: Mining Navigational Patterns in Portal Catalogs

Christodoulou¹,

Dalamagas²,

Sellis³

2006

Current Trends in Database Technology – EDBT 2006

View full text Add to dashboard Cite

Abstract. Portal Catalogs is a popular means of searching for information on the Web. They provide querying and browsing capabilities on data organized in a hierarchy, on a category/subcategory basis. This paper presents mining techniques on user navigational patterns in the hierarchies of portal catalogs. Specifically, we study and implement navigation retrieval methods and clustering tasks based on navigational patterns. The above mining tasks are quite useful for portal administrators, since they can be used to observe users' behavior, extract personal preferences and re-organize the structure of the portal to satisfy better user needs and navigational habits. These mining tasks have been implemented in the NaviMoz, a prototype system for mining navigational patterns in portal catalogs.

show abstract

“…Biochemical pathways interaction data, in general, lead to biological or cellular networks (Krishnamurthy et al, 2003). They are often abstracted using graph modeling.…”

Section: Introductionmentioning

confidence: 99%

Knowledge Discovery in Biochemical Pathways Using Minepathways

Gaol¹

2010

Journal of Computer Science

View full text Add to dashboard Cite

Problem statement:The advancement of the biochemical research gives profound effect to the collection of biochemical data. Approach: In the recent years, data and networks in biochemical pathways are abundant that allow to do process mining in order to obtain useful information. By using graph theory as a tool to model these interactions, it can be formally find the solution. Results: The core of the problem of mining patterns is a subgraph isomorphism which until now has been in the NPclass problems. Early identification showed that in the context biochemical pathways has unique node labeling that result simplifying pattern mining problem radically. Conclusion: Process will be more efficient because the end result that is needed is maximum pattern that could reduce redundant patterns. The algorithm that used is a modification of the maximum item set patterns that are empirically most efficiently at this time.

show abstract

Pathways database system: an integrated system for biological pathways

Abstract: Available on request from the authors.

Cited by 81 publications

References 2 publications

Integration of structural and functional genomics

Integration of structural and functional genomics

NaviMoz: Mining Navigational Patterns in Portal Catalogs

Knowledge Discovery in Biochemical Pathways Using Minepathways

Contact Info

Product

Resources

About