Comparative map curation in gramene using cmap
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Comparative Map Curation in Gramene Using CMap PowerPoint PPT Presentation


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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

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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


Gramene

Gramene


Cmap user s view

CMap – User’s View


Cmap schema

CMap Schema


Cmap admin

CMap Admin


Map types view

Map Types View


Map type create

Map Type Create


Map shapes

Map Shapes

I-beam

box

dumbbell


Color width

Color & Width

  • Width from 1-10 pixels

  • Choose from 140 colors


Color width1

Color & Width


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 types view

Feature Types View


Feature type create

Feature Type Create


Feature shapes colors

box

span

line

in-triangle

dumbbell

filled-box

double-arrow

up-arrow

out-triangle

down-arrow

Feature Shapes & Colors


Feature lane

Feature Lane


Feature priority

Feature Priority


Correspondences view

Correspondences View


Map sets view

Map Sets View


Create map set

Create Map Set


Species view

Species View


View a map set

View a Map Set


View a map

View a Map


View feature

View Feature


Create correspondence

Create Correspondence


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):


Comparative map curation in gramene using cmap

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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