TY - JOUR
T1 - PATIKA
T2 - An integrated visual environment for collaborative construction and analysis of cellular pathways
AU - Demir, E.
AU - Babur, O.
AU - Dogrusoz, U.
AU - Gursoy, A.
AU - Nisanci, G.
AU - Cetin-Atalay, R.
AU - Ozturk, M.
N1 - Funding Information:
The authors wish to thank C.Evren, S.Onay, B.Ozmen, E.Sahin, and E.Senel for their help with the implementation, and Doron Lancet of Weizmann Institute of Science, Rehovot, Israel, for his helpful suggestions. This work was partially supported by a TUBITAK grant to M.Ozturk.
PY - 2002
Y1 - 2002
N2 - Motivation: Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. Results: We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named PATIKA (Pathway Analysis Tool for Integration and Knowledge Acquisition). PATIKA is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that PATIKA will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development.
AB - Motivation: Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. Results: We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named PATIKA (Pathway Analysis Tool for Integration and Knowledge Acquisition). PATIKA is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that PATIKA will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development.
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U2 - 10.1093/bioinformatics/18.7.996
DO - 10.1093/bioinformatics/18.7.996
M3 - Article
C2 - 12117798
AN - SCOPUS:0036326896
SN - 1367-4803
VL - 18
SP - 996
EP - 1003
JO - Bioinformatics
JF - Bioinformatics
IS - 7
ER -