Gramene Using CMap

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15 Νοε 2013 (πριν από 3 χρόνια και 11 μήνες)

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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

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


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[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


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=
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=
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=
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=


--
= 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