PINT: Pathways integration tool

Y. T. Wang; Y. H. Huang; Y. C. Chen; C. L. Hsu; U. C. Yang

doi:10.1093/nar/gkq499

PINT: Pathways integration tool

Y. T. Wang, Y. H. Huang, Y. C. Chen, C. L. Hsu, U. C. Yang^*

^*Corresponding author for this work

Institute of Biomedical Informatics

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

Abstract

New pathway databases generally display pathways by retrieving information from a database dynamically. Some of them even provide their pathways in SBML or other exchangeable formats. Integrating these models is a challenging work, because these models were not built in the same way. Pathways integration Tool (PINT) may integrate the standard SBML files. Since these files may be obtained from different sources, any inconsistency in component names can be revised by using an annotation editor upon uploading a pathway model. This integration function greatly simplifies the building of a complex model from small models. To get new users started, about 190 curated public models of human pathways were collected by PINT. Relevant models can be selected and sent to the workbench by using a user-friendly query interface, which also accepts a gene list derived from high-throughput experiments. The models on the workbench, from either a public or a private source, can be integrated and painted. The painting function is useful for highlighting important genes or even their expression level on a merged pathway diagram, so that the biological significance can be revealed. This tool is freely available at http://csb2.ym.edu.tw/pint/.

Original language	English
Article number	gkq499
Pages (from-to)	W124-W131
Journal	Nucleic acids research
Volume	38
Issue number	SUPPL. 2
DOIs	https://doi.org/10.1093/nar/gkq499
State	Published - 10 Jun 2010

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title = "PINT: Pathways integration tool",

abstract = "New pathway databases generally display pathways by retrieving information from a database dynamically. Some of them even provide their pathways in SBML or other exchangeable formats. Integrating these models is a challenging work, because these models were not built in the same way. Pathways integration Tool (PINT) may integrate the standard SBML files. Since these files may be obtained from different sources, any inconsistency in component names can be revised by using an annotation editor upon uploading a pathway model. This integration function greatly simplifies the building of a complex model from small models. To get new users started, about 190 curated public models of human pathways were collected by PINT. Relevant models can be selected and sent to the workbench by using a user-friendly query interface, which also accepts a gene list derived from high-throughput experiments. The models on the workbench, from either a public or a private source, can be integrated and painted. The painting function is useful for highlighting important genes or even their expression level on a merged pathway diagram, so that the biological significance can be revealed. This tool is freely available at http://csb2.ym.edu.tw/pint/.",

author = "Wang, {Y. T.} and Huang, {Y. H.} and Chen, {Y. C.} and Hsu, {C. L.} and Yang, {U. C.}",

note = "Funding Information: NSC-98-3112-B-010-015 and NSC97-3112-B-010-020 from the National Research Program for Genomic Medicine, National Science Council (Taiwan, Republic of China). Funding for open access charge: the National Research Program for Genomic Medicine, National Science Council (Taiwan, Republic of China).",

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PINT: Pathways integration tool

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