comparative map curation in gramene using cmap noel yap, ken y. clark, & the gramene team
DESCRIPTION
CMap – User’s ViewTRANSCRIPT
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
-=-=-=-=-=-=-=-=-=-=
--= 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
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