comparative map curation in gramene using cmap noel yap, ken y. clark, & the gramene team

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

box dumbbell I-beam

Color & Width

Width from 1-10 pixels Choose from 140 colors

Color & Width

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 Type Create

Feature Shapes & Colors

boxdumbbell

line span

up-arrow down-arrow double-arrow

filled-box

in-triangle

out-triangle

Feature Lane

Feature Priority

Correspondences View

Map Sets View

Create Map Set

Species View

View a Map Set

View a Map

View Feature

Create Correspondence

Batch loading via cmap_admin.plCurrent data source: Gramene

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--= Main Menu =--

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[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

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

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.plCurrent 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