1. Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team

2. Gramene

3. CMap – User’s View

5. CMap Schema

6. CMap Admin

7. Map Types View

8. Map Type Create

9. Map Shapes boxdumbbell I-beam

10. Color & Width Width from 1-10 pixels Choose from 140 colors

11. Color & Width

12. 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

13. Feature Types View

14. Feature Type Create

15. Feature Shapes & Colors box dumbbell line span up-arrow down-arrow double-arrow filled-box in-triangle out-triangle

16. Feature Lane

17. Feature Priority

18. Correspondences View

19. Map Sets View

20. Create Map Set

21. Species View

22. View a Map Set

23. View a Map

24. View Feature

25. Create Correspondence

26. 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):

27. 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

28. 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

29. 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):

30. CMap Download the source: http://www.gmod.org/cmap 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

31. 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