Comparative Map Curation in Gramene Using CMap

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Comparative Map Curation in Gramene Using CMap

• Noel Yap,
• Ken Y. Clark,
• The Gramene Team

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Gramene
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CMap Users View
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(No Transcript)
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CMap Schema
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CMap Admin
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Map Types View
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Map Type Create
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Map Shapes
I-beam
box
dumbbell
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Color Width

• Width from 1-10 pixels
• Choose from 140 colors

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Color Width
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Relational Maps

• Maps are drawn in relation to other map
• Length in pixels equal to the distance covered by
  all the correspondences on the reference map

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Feature Types View
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Feature Type Create
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Feature Shapes Colors
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Feature Lane
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Feature Priority
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Correspondences View
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Map Sets View
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Create Map Set
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Species View
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View a Map Set
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View a Map
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View Feature
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Create Correspondence
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Batch loading via cmap_admin.pl
Current data source Gramene ----------
-- Main Menu -- ---------- 1
Change current data source 2 Create new map
set 3 Import data for existing map set 4 Make
name-based correspondences 5 Import feature
correspondences 6 Reload correspondence
matrix 7 Export data 8 Delete data 9
Quit What would you like to do? (one choice
only)
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Map Data File

• Tab-delimited text file
• Fields
• map_accession_id
• map_name
• map_start
• map_stop
• feature_accession_id
• feature_name
• feature_aliases
• feature_start
• feature_stop
• feature_type
• feature_dbxref_name
• feature_dbxref_url
• is_landmark
• feature_note

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Correspondences

• Automated correspondences based on feature_name
  and feature_alias
• Correspondence data file
• Tab-delimited text file
• Fields
• feature_name1
• feature_accession_id1
• feature_name2
• feature_accession_id2
• evidence
• is_enabled

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Batch loading via cmap_admin.pl
Current data source Gramene ----------
-- Main Menu -- ---------- 1
Change current data source 2 Create new map
set 3 Import data for existing map set 4 Make
name-based correspondences 5 Import feature
correspondences 6 Reload correspondence
matrix 7 Export data 8 Delete data 9
Quit What would you like to do? (one choice
only)
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CMap

• Download the source http//www.gmod.org/cmap
• Future developments
• Multiple feature aliases
• Generic attribute system for all objects and
  object types
• Generic DBXREF (hyperlink) system
• Zoom/unzoom
• More user-configurable options

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The Gramene Team

• Cornell University
• Susan McCouch
• Ed Buckler
• Pankaj Jaiswal
• Junjian Ni
• Noel Yap

• Cold Spring Harbor Labs
• Lincoln Stein
• Doreen Ware
• Ken Clark
• Steve Schmidt
• Kiran Ratnapu
• Wei Zhao
• Liya Ren