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. Gramene. CMap – User’s View. CMap Schema. CMap Admin. Map Types View. Map Type Create. Map Shapes. I-beam. box. dumbbell. Color & Width. Width from 1-10 pixels Choose from 140 colors.

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Comparative map curation in gramene using cmap

Comparative Map Curation in Gramene Using CMap

Noel Yap,

Ken Y. Clark,

& The Gramene Team








Map shapes
Map Shapes

I-beam

box

dumbbell


Color width
Color & Width

  • Width from 1-10 pixels

  • Choose from 140 colors



Relational maps
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




Feature shapes colors

box

span

line

in-triangle

dumbbell

filled-box

double-arrow

up-arrow

out-triangle

down-arrow

Feature Shapes & Colors












Batch loading via cmap admin pl
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):


Map data file
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


Correspondences
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


Batch loading via cmap admin pl1
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):


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


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

The Gramene Team


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