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 boxdumbbell 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 box dumbbell 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.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): 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 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.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): 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: 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