Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.
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Transcript of Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.
![Page 1: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/1.jpg)
Comparative Map Curation in Gramene Using CMap
Noel Yap,Ken Y. Clark,& The Gramene Team
![Page 2: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/2.jpg)
Gramene
![Page 3: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/3.jpg)
CMap – User’s View
![Page 4: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/4.jpg)
![Page 5: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/5.jpg)
CMap Schema
![Page 6: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/6.jpg)
CMap Admin
![Page 7: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/7.jpg)
Map Types View
![Page 8: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/8.jpg)
Map Type Create
![Page 9: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/9.jpg)
Map Shapes
box dumbbell I-beam
![Page 10: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/10.jpg)
Color & Width
Width from 1-10 pixels Choose from 140 colors
![Page 11: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/11.jpg)
Color & Width
![Page 12: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/12.jpg)
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
![Page 13: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/13.jpg)
Feature Types View
![Page 14: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/14.jpg)
Feature Type Create
![Page 15: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/15.jpg)
Feature Shapes & Colors
boxdumbbell
line span
up-arrow down-arrow double-arrow
filled-box
in-triangle
out-triangle
![Page 16: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/16.jpg)
Feature Lane
![Page 17: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/17.jpg)
Feature Priority
![Page 18: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/18.jpg)
Correspondences View
![Page 19: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/19.jpg)
Map Sets View
![Page 20: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/20.jpg)
Create Map Set
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Species View
![Page 22: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/22.jpg)
View a Map Set
![Page 23: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/23.jpg)
View a Map
![Page 24: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/24.jpg)
View Feature
![Page 25: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/25.jpg)
Create Correspondence
![Page 26: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/26.jpg)
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):
![Page 27: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/27.jpg)
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
![Page 28: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/28.jpg)
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
![Page 29: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/29.jpg)
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):
![Page 30: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/30.jpg)
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
![Page 31: Comparative Map Curation in Gramene Using CMap Noel Yap, Ken Y. Clark, & The Gramene Team.](https://reader036.fdocuments.in/reader036/viewer/2022081514/5a4d1afd7f8b9ab059984b2d/html5/thumbnails/31.jpg)
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