Molecular_Interaction_Maps/MimEditorUseCaseComments

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About this document

This page describes some general background and common characterisitcs for the use cases prepared as part of the Molecular_Interaction_Maps RFC.

Origins

These use cases were originally authored by:

• DavidKane

• MiritAladjem

• KurtKohn

The initial BioPAX mappings were developed by:

• JoshuaPothen

The initial draft of the MIM to Cytoscape concept mapping was completed by:

• AllanKuchinsky (He also wrote the intial draft of Molecular_Interaction_Mapswiki page)

We also received additional concept mapping guidance from the Attendees of the 2006 Cytoscape User Meeting and Hackathon (CytoscapeRetreat2006/UserMeetingNotes and HackathonNotes)

Key to the MIM notation: http://discover.nci.nih.gov/mim/mapDesc.html

Reference article on notation: http://www.molbiolcell.org/cgi/content/abstract/E05-09-0824v1

Definitions

• Species: A protein, modified protein, or protein complex.

Evidence

The basic Kohn notation does not include a direct mechanism for attaching evidence to a particular reaction. In some of the mims, we have added a text element A1, which can be subsequently linked or keyed to annotation information. These text keys are placed close to the features that annotate. More directly associating evidence to the map elements appears frequently throughout the use cases.

Comments

b12-arbiter-b - 2006-11-20 20:16:15

Species could include other molecules, such as DNA, RNA, lipids, etc. -- K. Kohn