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|| '''Molecular Interaction Maps''' || '''Editor(s)''': Allan Kuchinsky||
 		||'''Molecular Interaction Maps''' ||'''Editor(s)''': Allan Kuchinsky ||
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For details on RFCs in general, check out the [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments Wikipedia Entry:  Request for Comments (RFCs)] For details on RFCs in general, check out the [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments Wikipedia Entry: Request for Comments (RFCs)]
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To view/add comments, click on any of 'Comment' links below. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Here is an example to get things started: ["/Comment"].
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To view/add comments, click on any of 'Comment' links below. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Here is an example to get things started: ["/Comment"].

'''Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.''' 		'''Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.'''
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A Molecular Interaction Map (MIM) is a diagram convention that is capable of unambiguous representation of networks containing multi-protein complexes, protein modifications, and enzymes that are substrates of other enzymes. MIMs are described in detail at http://discover.nci.nih.gov/mim/index.jsp and in a seminal article by Kohn et al at http://www.molbiolcell.org/cgi/content/abstract/E05-09-0824v1
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A Molecular Interaction Map (MIM) is a diagram convention that is capable of unambiguous representation of networks containing multi-protein complexes, protein modifications, and enzymes that are substrates of other enzymes. MIMs are described in detail at http://discover.nci.nih.gov/mim/index.jsp
and in a seminal article by Kohn et al at
http://www.molbiolcell.org/cgi/content/abstract/E05-09-0824v1 		An example MIM is below attachment:mim_eg.png
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An example MIM is below inline:mim_eg.png MIMs have been developed at the National Cancer Institute (specifically the Laboratory of Molecular Pharmacology). They are looking into what it would take to develop an Editor to create Molecular Interaction Maps (MIMs) in an editor to yield both a graphical view and a computer-readable format (preferrably Bio''''''Pax). They are interested in seeing if such a MIM editor could be developed for Cytoscape.
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MIMs have been developed at the National Cancer Institute (specifically the
Laboratory of Molecular Pharmacology). They are looking into what
it
would
take to develop an Editor to create Molecular Interaction Maps
(MIMs) in an editor to yield both a graphical view and a
computer-readable format (preferrably Bio''''''Pax).
They are interested in seeing if such a MIM editor could be
developed for
Cytoscape. 		MIM symbols are defined in the figure below:
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MIM symbols are defined in the figure below: attachment:Kohn_SymbDefH3.jpg
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''QUESTION: Is this the most recent definition of map symbols? In particular, are site-specific constructs, such as cleavage, still defined as requirements?''
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inline:Kohn_SymbDefH3.jpg

''QUESTION: Is this the most recent definition of map symbols? In particular, are site-specific constructs, such as cleavage, still defined as requirements?''

This proposal will specify the mapping between MIM constructs and their proposed counterparts in Cytoscape.  A prioritized set of requirements will be presented.  Enhancements needed in the editor, renderer, and/or other Cytoscape components will be identified.
 		This proposal will specify the mapping between MIM constructs and their proposed counterparts in Cytoscape. A prioritized set of requirements will be presented. Enhancements needed in the editor, renderer, and/or other Cytoscape components will be identified.
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From an initial reading of the article by Kohn et al at
http://www.molbiolcell.org/cgi/content/abstract/E05-09-0824v1, an initial description of potential mappings between MIM and Cytoscape constructs was derived.  This is summarized in the figure below. 		From an initial reading of the article by Kohn et al at http://www.molbiolcell.org/cgi/content/abstract/E05-09-0824v1, an initial description of potential mappings between MIM and Cytoscape constructs was derived. This is summarized in the figure below.
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== Requirements ==
== Deferred Items ==
== Open Issues ==
 1. Do they need site-specific connection of edges, e.g. as in proteolytic cleavage? From Mirit's presentation, it appears that metanodes would work just fine.
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 1. How do we represent the "null" node, as in degradation product?
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 1. How do we represent "ditto" nodes, e.g. as in translocation?
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== Requirements ==

== Deferred Items ==

== Open Issues ==
 		 1. Would they need editor support for Manhattan topology, e.g. constraints on edge angles?
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  * ["/Implementation Plan"]
 		 * [:Molecular Interaction Maps/Implementation Plan:/Implementation Plan]
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Molecular Interaction Maps

Editor(s): Allan Kuchinsky

TableOfContents([2])

About this document

This is an official Request for Comment (RFC) for Supporting Molecular Interaction Maps in Cytoscape.

For details on RFCs in general, check out the [http://www.answers.com/main/ntquery?method=4&dsid=2222&dekey=Request+for+Comments&gwp=8&curtab=2222_1&linktext=Request%20for%20Comments Wikipedia Entry: Request for Comments (RFCs)]

Status

* preliminary draft, still brain-dead, take with a grain of NaCl.

How to Comment

To view/add comments, click on any of 'Comment' links below. By adding your ideas to the Wiki directly, we can more easily organize everyone's ideas, and keep clear records. Be sure to include today's date and your name for each comment. Here is an example to get things started: ["/Comment"].

Try to keep your comments as concrete and constructive as possible. For example, if you find a part of the RFC makes no sense, please say so, but don't stop there. Take the extra step and propose alternatives.

Proposal

A Molecular Interaction Map (MIM) is a diagram convention that is capable of unambiguous representation of networks containing multi-protein complexes, protein modifications, and enzymes that are substrates of other enzymes. MIMs are described in detail at http://discover.nci.nih.gov/mim/index.jsp and in a seminal article by Kohn et al at http://www.molbiolcell.org/cgi/content/abstract/E05-09-0824v1

An example MIM is below attachment:mim_eg.png

MIMs have been developed at the National Cancer Institute (specifically the Laboratory of Molecular Pharmacology). They are looking into what it would take to develop an Editor to create Molecular Interaction Maps (MIMs) in an editor to yield both a graphical view and a computer-readable format (preferrably BioPax). They are interested in seeing if such a MIM editor could be developed for Cytoscape.

MIM symbols are defined in the figure below:

attachment:Kohn_SymbDefH3.jpg

QUESTION: Is this the most recent definition of map symbols? In particular, are site-specific constructs, such as cleavage, still defined as requirements?

This proposal will specify the mapping between MIM constructs and their proposed counterparts in Cytoscape. A prioritized set of requirements will be presented. Enhancements needed in the editor, renderer, and/or other Cytoscape components will be identified.

Biological Questions / Use Cases

General Notes

From an initial reading of the article by Kohn et al at http://www.molbiolcell.org/cgi/content/abstract/E05-09-0824v1, an initial description of potential mappings between MIM and Cytoscape constructs was derived. This is summarized in the figure below.

attachment:kohn_mappings.png

Requirements

Deferred Items

Open Issues

  1. Do they need site-specific connection of edges, e.g. as in proteolytic cleavage? From Mirit's presentation, it appears that metanodes would work just fine.
  2. How do we represent the "null" node, as in degradation product?
  3. How do we represent "ditto" nodes, e.g. as in translocation?
  4. Would they need editor support for Manhattan topology, e.g. constraints on edge angles?

Backward Compatibility

Expected growth and plan for growth

References

Implementation Plan

  • [:Molecular Interaction Maps/Implementation Plan:/Implementation Plan]

Comments

PageComment2

Molecular_Interaction_Maps (last edited 2009-02-12 01:03:29 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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