Transcript Proposal to integrate Reactome usage in Pathway updates.

Nu GO
Pathway content improvement.
How to store an expert’s brain
and use it to understand omics.
Chris Evelo
NuGO WP7
BiGCaT Bioinformatics
the European Nutrigenomics Organisation
Nu GO
Mapping
Annotation/
coupling
the European Nutrigenomics Organisation
Nu GO
Scientist know GenMapp
Advantages:
• Easy to use,
• Reasonable visualisation
• Some pathway statistics
• Interesting content
Disadvantages:
• Small academic initiative, uncertain lifespan
• No info on reactions, metabolites, location
• No change (e.g. time course) visualisation
the European Nutrigenomics Organisation
Nu GO
Proposed workflow
Combine and forward
existing maps
to limited group of experts
Text mining
from key genes/metabolites
Forward improved maps
to limited group of experts
Think of best way to store
pathway information
Develop storage format
plus tools
Collect back page info
Forward new draft to a
larger group of experts
within NuGO
Develop/adapt entry tools
plus converters
Test resulting maps
Make maps available
the European Nutrigenomics Organisation
Nu GO
GenMapp/BioPAX
Current GenMapp
Not a very elegant solution...
BioPAX
And
a
lot
of
format
specific
work…
BioPAX plus editor
Layout
data
But it does store extra
information
about interactions, reactions
metabolites, localizations etc
in BioPAX format. New GenMapp
Expert data
the European Nutrigenomics Organisation
Nu GO
Proposed at EBI
Using Reactome
Current GenMapp
could allow us to:
• store everything
• use high quality entry tools
Expert data
• ad an extra round of curation
And…
(referees)
use in Reactome
• develop Reactome – BioPAX
itself
BioPAX
converters together
Reactome
• convince BioPAX about BioPax
“plus” plus
??
Layout data
• to work with GenMapp on a more
general problem
New GenMapp
the European Nutrigenomics Organisation
Adaptation EBI
Nu GO
Current GenMapp
Expert data
BioPAX
Reactome
BioPax plus
??
Layout data
New GenMapp
the European Nutrigenomics Organisation
Adaptation MDP/GenMapp
Rachel van Haaften
Nu GO(BiGCaT/NuGO) and
Marjan van Erk Rachel van Haaften
(TNO/NuGO) will test
This
step hasand
not
(BiGCaT/NuGO)
GMML (GenMapp
Markup
this and give user been
taken
Marjan
van care
Erk off
Language)
is a superset
of
Current
GenMapp
feedback
as of yet…
(TNO/NuGO)
will
BioPAX 1. BioPAX
could
visitviews.
EBI early 2005
contain graphical
toBiGCaT
learn doing
this
Expert
data 2 = BioPAX2).
(GMML
students
BioPAX
will create
GenMapp
Philippe
Rocca and
But, how doe we make
2 – GMML
Imre Vastrik
BioPAX Plus/GMML 2
that happen?
NUGO/EBI
converters
with help
(EBI/Reactome)
will
from Lynn
Ferrante
define
a way to get
(GenMapp.org)
Reactome views andGMML
Reactome
export them to
GenMapp2
EBI
MDP4/GenMapp
GenMapp 2
the European Nutrigenomics Organisation