Transcript Function-process links - Gene Ontology Consortium

Function-process links
Conclusions of the electron
transport working group.
biosynthetic
UDP-glucose
process
metabolic
process
galactose
carbohydrate
metabolic
catabolic
response
process
process
to desiccation
glucose
metabolic
process
Process
hp
hp
hp
hp
hp
hp
UTP:glucose-1-phosphate uridylyltransferase activity
α-D-glucose 1-phosphate + UTP ->
UDP-D-glucose + diphosphate
Function
colanic
acid
biosynthetic
process
hp
Lysine biosynthesis pathways
Process
lysine
biosynthesis
is_a
is_a
is_a
is_a
is_a
is_a
lysine
biosynthesis
7?
is_a
lysine
biosynthesis
1
Function
lysine
lysine
biosynthesis
biosynthesis
3
5
lysine
lysine
lysine
biosynthesis
biosynthesis
biosynthesis
4
2
6
Process
Lysine Biosynthesis
= has_part
Function
Shared function?
Non-shared function
new GO term
existing GO term
Process
Lysine Biosynthesis
Process B
= has_part
Function
Shared function?
Non-shared function
new GO term
existing GO term
Process
Lysine Biosynthesis
Process B
Process C
= has_part
Function
Shared function?
Non-shared function
new GO term
existing GO term
Process
Lysine Biosynthesis
Process B
Function
Relationship explosion
(or Editorial office explosion)
Process C
Where do pathways start and
end?
process 2
A
B
C
process 1
process 3
D
Use cases
• Can we slim from function up to process?
• Can we infer annotations to process from those to function?
has_part
Process
polyamine
biosynthesis
urea cycle
has_function
Function
arginosuccinate
synthase activity
has_function but
only as part_of
urea cycle
has_function
but only as
part_of
polyamine
biosynthesis
Gene
products
Gene product x
Gene product y
has_part
Process
polyamine
biosynthesis
urea cycle
has_function
Function
?
Gene
products
Gene product x
Gene product y
has_part
Process
polyamine
biosynthesis
urea cycle
has_function
Function
No
has_part
cannot be
used for
slimming.
Gene
products
Gene product x
Gene product y
Can we infer annotations to process from those to function?
• No. There is too much variation in process details,
and too many functions are shared.
So what can we do?
Process
phosphorylation
part_of
Function
kinase activity
We can make relationships between single step processes
and their respective functions.
Process
glucose transport
part_of
Function
glucose transporter activity
We can make any obvious relationship where part_of holds,
and this will allow useful slimming.
We can mine the other links from pathway databases
and make non-curated sometimes_part_of links.
sometimes_part_of
What does this buy us?
Very full coverage of function-process links.
No manual link curation.
What work does it involve?
We maintain the mapping files e.g. reactome2go.
We write the mining scripts.
Acknowledgements
Michelle Gwinn-Giglio
Debbie Siegele
Ingrid Keseler
Harold Drabkin
Jennifer Deegan
Chris Mungall
Peifen Zhang
Part_of
Car
part_of?
http://www.treehugger.com/
e-zip-2008-trailz-hybrid-electric-bike.jpg
wheel
Part_of
Car
part_of?
car wheel
http://www.classicnation.com/pictures/images/
car_shows/goodguys_columbus/
goodguys-columbus-car-show-047.jpg
has_part
wheel
has_part
car
http://www.aa1car.com/library/wheel_missing.jpg
Process:
Travel from New York to California
(by car)
Process: Travel from New York to California via Minnesota
(Google maps)
Process: Travel from New York to California via Oklahoma
Process: Travel from New York to California via Iowa
Travel from
New York to California
is_a
is_a
is_a
Travel from
New York to California via
Iowa
Travel from
New York to California via
Minnesota
Travel from
New York to California via
Oklahoma
Travel from
New York to California
Process
is_a
Travel from
New York to California
via Minnesota
sometimes
_has_part
is_a
is_a
Travel from
New York to California
via Iowa
sometimes
_has_part
Travel from
Wisconsin to Minnesota
Travel from
Iowa to Nebraska
Function
Travel from
New York to California
via Oklahoma
sometimes
_has_part
Travel from
Missouri to Oklahoma
Do the sub-process share any
functions?
Function: get in the car.
http://www.ozbadge.com/sitebuildercontent/sitebuilderpictures/wapol1911ford.jpg
Travel from
New York to California
Process
is_a
Travel from
New York to California
via Minnesota
is_a
is_a
Travel from
New York to California
via Iowa
has_part
has_part
Get in car
Function
Travel from
New York to California
via Oklahoma
has_part
Travel from
New York to California
Process
is_a
Travel from
New York to California
via Minnesota
is_a
is_a
Travel from
New York to California
via Iowa
Any part_of children?
Function
Travel from
New York to California
via Oklahoma
Photosynthetic electron transport chain
http://genomics.energy.gov/gallery/gtl/originals/422.jpg
http://thumbs.dreamstime.com/
thumb_55/1145821933432C7c.jpg
Green
plants
+
Algae
+
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/84150f.jpg
Other photosynthetic
bacteria
Anoxygenic
Cyanobacteria
Oxygenic
http://genomicsgtl.energy.gov/benefits/hfromh2o.shtml
process
terms
photosynthetic electron transport chain (psth)
is_a
is_a
anoxygenic psth
oxygenic psth
part_of
has
part
has
part
H2S -> NADPH
+S
H2O -> O2
+ NADPH
Function
terms
part_of
lightharvesting
Option 1
process
terms
photosynthetic electron transport chain (psth)
part_of
H2O -> O2
+ NADPH
Function
terms
part_of
lightharvesting
part_of
H2S -> NADPH
+S
Option 2
- No annotations for function
- no photosynthetic functions
But…
arginine
biosynthetic
process
urea
cycle
hp
hp
polyamine
biosynthesis
hp
Process
arginosuccinate synthase activity
Catalysis of the reaction: ATP + L-citrulline + L-aspartate = AMP
+diphosphate + (N(omega)-L-arginino)succinate
Function
Urea cycle and
metabolism of
amino groups
Process
Arginine
and proline
metabolism
hp
hp
Glutamate
metabolism
Nitrogen
metabolism
hp
hp
carbamoyl-phosphate synthase activity
Catalysis of a reaction that results in
the formation of carbamoyl phosphate.
Function