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What is NetSlim? |
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NetSlim is a public resource of high-confidence signaling pathway maps generated from
NetPath. |
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Why NetSlim? |
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NetPath is a resource of manually curated pathway reactions from the literature developed
by Institute of Bioinformatics in collaboration with Pandey Lab. It currently consists of 10
immune signaling and 10 cancer signaling pathways. The large number of molecules and their interconnectivity present in
NetPath pathways makes the visualization of these pathways
a challenge. In order to overcome this, we have applied certain confidence criteria to reactions
in NetPath to extract the reactions with high-confidence. These reactions were used to generate less complex pathway maps which are hosted in NetSlim. |
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What are the confidence criteria applied to NetPath reactions to generate NetSlim? |
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The confidence criteria applied to NetPath to generate NetSlim is provided in a separate tab in
the home page of NetSlim database. |
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What information can I get from NetSlim? |
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For each pathway in NetSlim, one can view pathway map drawn with the high confidence
reactions using Pathvisio. All the reactions in NetSlim are linked to their respective research
article in PubMed. Each reaction in NetSlim has a brief note which describes the dependence of
reactions on various post-translational modifications and the cells in which the reactions were
reported. In addition, we have provided a brief description of the pathway. |
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Is NetSlim freely available? |
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NetSlim is freely available under an adaptive Creative Commons Attribution 2.5 License which
stipulates that the pathways may be used if adequate credit is given to the authors. |
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What are the different formats available to download? |
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Pathways from NetSlim can be freely downloaded in different file formats such
as .gpml, .GenMAPP, .pdf, .png and .svg. |
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Can I download the literature information associated with each reaction from NetSlim? |
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Since NetSlim is derived from NetPath, all the literature associated with each reaction can be
viewed in NetPath. |
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Why Can't I mouse over each reaction to see the literature information associated with them? |
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Mouse over feature is not enabled right now. We will enable it soon. Currently only .gpml
format supports the visualization of the literature information associated with each reaction.
This format can be downloaded from NetSlim and visualized using PathVisio, which is an
open source tool for displaying and editing biological pathways. It is freely available at (http://
www.pathvisio.org/wiki/PathVisioDownload). |
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What are the future directions for NetSlim? |
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Gene Ontology terms will be provided whenever functional significance of the molecules or
reactions is studied. We will provide NetSlim in System Biology Graphical Notation (SBGN)
format in the future. |
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Can I contribute to NetSlim? |
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Yes. We encourage the scientific community to actively participate in updating this resource.
This can be done by providing your inputs using the feedback feature provided in NetSlim
homepage. |
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