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

  2. Gramene

  3. CMap – User’s View

  4. CMap Schema

  5. CMap Admin

  6. Map Types View

  7. Map Type Create

  8. Map Shapes I-beam box dumbbell

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

  10. Color & Width

  11. 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

  12. Feature Types View

  13. Feature Type Create

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

  15. Feature Lane

  16. Feature Priority

  17. Correspondences View

  18. Map Sets View

  19. Create Map Set

  20. Species View

  21. View a Map Set

  22. View a Map

  23. View Feature

  24. Create Correspondence

  25. 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):

  26. 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

  27. 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

  28. 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):

  29. 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

  30. 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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