Capturing Signal Transduction Pathways Using the SBGN standard Haitham Elmarakeby marakebyvtedu What is SBGN wwwsbgnorg Why do we need it Why do we need it Knowledge SBGN ZAP70 in conjunction with SLP76 and ID: 569600
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Beacon Editor: Capturing Signal Transduction Pathways Using the SBGN standard
Haitham Elmarakebymarakeby@vt.eduSlide2
What is SBGN?
www.sbgn.orgSlide3
Why do we need it?Slide4
Why do we need it?
KnowledgeSlide5
SBGN
ZAP70 in conjunction with SLP76 and PLCg_bind and Itk activate PLCg_act
. ZAP70 in conjunction with SLP76 and
PLCg_bind
and
Rlk
activate
PLCg_act
.Slide6
SBGNNo Standard
No consistency between authorsNo consistency between papersSame symbols could mean different things
Standard
Controlled vocabulary with well defined
semantics
Easier
to interpret and compare
diagrams
Easier
to be automated using softwareSlide7
SBGN
Sequential
Non-sequential
ConceptualSlide8
SBGNSlide9Slide10Slide11Slide12Slide13Slide14Slide15
Modified from
Kakumanu et al. (2012)Slide16
Beacon EditorSlide17
Beacon EditorSlide18
Beacon EditorSlide19
Beacon EditorSlide20
Beacon EditorSlide21
Beacon EditorSlide22
Beacon EditorSlide23
Beacon EditorSlide24
Beacon EditorSlide25
DemoSlide26
Beacon EditorSlide27
How to get Beacon Editorhttps://bioinformatics.cs.vt.edu/beacon
Read the User ManualSlide28
How to get Beacon Editor
github.com/marakeby/beaconSlide29
What is next?
Simulation EngineSlide30
Beacon TeamDr. Heath Lenwood, PI (heath@vt.edu
)Dr. Ruth Grene, Co-PI (grene@vt.edu)Dr. Song Li (
songli@vt.edu
)
Haitham
Elmarakeby
(
marakeby@vt.edu
)
NSF grant ABI-1062472Slide31
http://gtdforcios.com/2014/01/18/the-power-of-the-daily-review/finish-line/Slide32
http
://www.languageintelligence.com/blog/post/asking-demographic-questions-international/